http://2014.igem.org/wiki/index.php?title=Special:Contributions/J.plum&feed=atom&limit=50&target=J.plum&year=&month=2014.igem.org - User contributions [en]2024-03-29T06:32:53ZFrom 2014.igem.orgMediaWiki 1.16.5http://2014.igem.org/Team:Aachen/Notebook/IndexTeam:Aachen/Notebook/Index2014-10-17T20:23:08Z<p>J.plum: /* List of abbreviations */</p>
<hr />
<div>{{Team:Aachen/Header}}<br />
<br />
= List of abbreviations =<br />
<center><br />
List of commonly used abbreviations:<br />
{| class="wikitable sortable"<br />
! align="center" |'''Abbreviation'''<br />
!! align="center" |'''Full term'''<br />
|-<br />
| ATP || Adenosinetriphosphate<br />
|-<br />
| BFP || Blue fluorescent protein<br />
|-<br />
| BSA || Bovine serum albumin<br />
|-<br />
| CAM|| Chloramphenicol<br />
|-<br />
| CFP|| Cyan fluorescent protein<br />
|-<br />
| CFU|| Colony forming units<br />
|-<br />
| CDS || Coding sequence<br />
|-<br />
| dNTP || Desoxynucleotidtriphosphate<br />
|-<br />
| EDTA || Ethylenediaminetetraacetic acid<br />
|-<br />
| DSMZ || German collection of microorganisms and cell cultures <br />
|-<br />
| DIY || Do it yourself<br />
|-<br />
| eYFP || Enhanced yellow flourescenct protein<br />
|-<br />
| F || Fluorescence <br />
|-<br />
| FRET || Förster resonance energy transfer<br />
|-<br />
| Gal-3 || Galactin-3 <br />
|-<br />
| GFP || Green fluorescent protein <br />
|-<br />
| GUI || Graphical user interface <br />
|-<br />
| His || Histidin<br />
|-<br />
| HM || Hartman Medium<br />
|-<br />
| HSL || Homoserine lactone<br />
|-<br />
| HSV || hue-saturation-value<br />
|-<br />
| HF || High frequency<br />
|-<br />
| IPTG || Isopropyl β-D-1-thiogalactopyranoside <br />
|-<br />
| LPS || Lipopolysaccharide <br />
|-<br />
| MRSA || Multi resistant ''Staphylococcus aureus'' <br />
|-<br />
| NIAID || National Institute of Allergy and Infectious Diseases<br />
|-<br />
| NTA || Nitrilotriacetic acid<br />
|-<br />
| OD || Optical density <br />
|-<br />
| 3-oxo-C{{sub|12}} HSL || 3-Oxo-dodecanoyl homoserine lactone<br />
|-<br />
| PBS || Phosphate buffered saline<br />
|-<br />
| PCR || Polymerase chain reaction<br />
|-<br />
| RBS || Ribosome binding site <br />
|-<br />
| REACh || Resonance Energy-Accepting Chromoprotein<br />
|-<br />
| RFP || Red fluorescent protein <br />
|-<br />
| SDS-PAGE || Sodium dodecyl sulfate polyacrylamide gel electrophoresis<br />
|-<br />
| SRM || Statistical region merging <br />
|-<br />
| TEV || Tobacco etch virus <br />
|-<br />
| WHO || World health organisation<br />
|-<br />
|}<br />
</center><br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/LabEquipmentTeam:Aachen/Notebook/LabEquipment2014-10-17T20:20:31Z<p>J.plum: /* Lab Equipment */</p>
<hr />
<div>{{Team:Aachen/Header}}<br />
<br />
= Lab Equipment =<br />
<br />
<center><br />
Equipment used in our project:<br />
{| class="wikitable sortable"<br />
! align="center" |'''Equipment'''<br />
!! align="center" |'''Company'''<br />
|-<br />
| Avanti 30 Centrifuge || Beckman<br />
|-<br />
| Äkta Prime Plus || GE Healthcare<br />
|-<br />
| Biofuge "pico" Heraues || Thermo Scientific<br />
|-<br />
| Cleanbench || Scanlaf<br />
|-<br />
| Clark Electrode || Hamilton<br />
|-<br />
| GenePulser XCell || BioRad <br />
|-<br />
| Fermenter 1L || Sartorius<br />
|-<br />
| Fermenter control unit Biostat A-Plus || Sartorius<br />
|-<br />
| Freezer || Thermo Scientific <br />
|-<br />
| Geldoc || Herolab<br />
|-<br />
| Geldoc XR+ || Biorad<br />
|-<br />
| Heatplate || Yellow line <br />
|-<br />
| Megafuge 16R Heraeus || Thermo Scientific <br />
|-<br />
| Incubator || VWR<br />
|-<br />
| Mastercycler gradient || Eppendorf<br />
|-<br />
| Micro Centrifuge || Roth<br />
|-<br />
| Microscope ICG-50|| Leica<br />
|-<br />
| Microscope AF6000 LX Videomicroscope || Leica<br />
|-<br />
| Microscope Software LAS AF 3.2.09652 || Leica<br />
|-<br />
| Microscope Orthoplan || Leica<br />
|-<br />
| NanoVue Plus || GE Healthcare<br />
|-<br />
| Pico 17 Centrifuge || Thermo Scientific<br />
|-<br />
| PowerPac 200 + 300 || BioRad<br />
|-<br />
| pH Electrode || Mettler Toledo <br />
|-<br />
| pH/ORP Meter || Hanna Instruments<br />
|-<br />
| Programmable Thermal Controller || MJ Research<br />
|-<br />
| Pipet boy || Sartorius <br />
|-<br />
| Stirrer || Unkermotoren germany<br />
|-<br />
| Shaker || New Brunswick<br />
|-<br />
| Spectrophotometer 1200 || Fisher Bioblock Scientific<br />
|-<br />
| Platereader Synergy MX || BioTek<br />
|-<br />
| Platereader Software GenX || BioTek<br />
|-<br />
| Thermomixer Compact || Eppendorf<br />
|-<br />
| Thermocylcler Primus 25|| MWG Biotech<br />
|-<br />
| Waterbath || Lauda<br />
|-<br />
| Waterbath Frigomix 1000 || Sartorius<br />
|-<br />
| Varifuge 3.0R || Heraues <br />
|-<br />
| Vortexer || Fisher Scientific<br />
|-<br />
<br />
<br />
|}<br />
<br />
<br />
Kits:<br />
{| class="wikitable sortable"<br />
! align="center" |'''Kit'''<br />
!! align="center" |'''Company'''<br />
|-<br />
| GoTaq Green Mastermix || Promega <br />
|-<br />
| Gibson assembly cloning kit || NEB <br />
|-<br />
| illustra Plasmid Prep Mini Spin Kit || GE Healthcare <br />
|-<br />
| PCR DNA and Gel Band Purification Kit || GE Healthcare <br />
|-<br />
| iGEM Biobrick Assembly Kit || NEB <br />
|-<br />
| Transformation efficiency kit || iGEM Headquarters<br />
|-<br />
| KAPA2G Fast ReadyMix || Kapa Biosystems<br />
|-<br />
|}<br />
</center><br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T20:05:57Z<p>J.plum: /* The OD/F Device - A Project Spin-Off */</p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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= ''Cellock Holmes'' - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;margin-left:20px;"><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called ''Cellocks'', that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''''WatsOn'''''] , our measurement device. ''WatsOn'' is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;margin-left:20px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we present our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device]. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF technical details] as well as [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy construction manuals] are published on our wiki. We demonstrate immediate application of the OD/F Device in '''schools, community labs''' and in the '''bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Interlab_StudyTeam:Aachen/Interlab Study2014-10-17T19:37:27Z<p>J.plum: </p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
= Interlab Study =<br />
<br />
As our team is competing in the Measurement track for this year's competition, we were also required to participate in the [https://2014.igem.org/Tracks/Measurement/Interlab_study iGEM 2014 Measurement Interlab Study]. This study aims to '''collect data from iGEM teams all over the world''' on the fluorescence of '''three genetic devices expressing GFP'''. The devices differ in their plasmid copy properties and the strength of the promotor. <br />
<br />
We introduced the three constructs into ''E. coli'' cells and measured '''fluorescence as well as optical density''' of the liquid cultures over a period of 18 hours, using '''a spectrophotometer and a plate reader''', respectively. The obtained results confirmed our hypothesis that the fluorescence of the BioBrick in the high copy plasmid pSB1C3, J23101.E0240, would exhibit a stronger signal than the constructs I20260, which is the low to mid copy plasmid pSB3K3, and J23115.E0240, which has a weaker promotor than J23101.E0240. During the experiment, we could observe a typical growth curve for ''E.coli'' including lag, exponential, stationary and death phase. We could show that the fluorescence we measured is rather a function of each cell than the whole culture, since all cultures had comparable optical densities.<br />
<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid" style="width:1040px"><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Interlab_Study#isexperimentaldesign" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"><div class="menukachel">Experimental Design</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/10/Aachen_14-10-13_Yellow_Flask_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"><br />
</div><br />
</a><br />
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<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Interlab_Study#isexpectedresults" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"><div class="menukachel">Expected Results</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/7/78/Aachen_14-10-13_Green_Flask_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Interlab_Study#ismaterials" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"><div class="menukachel">Materials & Methods</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/3/30/Aachen_14-10-13_Empty_Falcon_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Interlab_Study#isresults" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"><div class="menukachel">Results</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-13_Graph_Panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Interlab_Study#isdiscussion" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"><div class="menukachel">Discussion</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/3/3b/Aachen_14-10-13_Graph_with_Error_Bars_Panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
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</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Yellow_Flask_iNB.png|right|150px]]<br />
<br />
==Experimental Design==<br />
<span class="anchor" id="isexperimentaldesign"></span><br />
<br />
For the Interlab Study, we tested GFP-containing BioBricks for fluorescence and optical density. Subject of the study were the BioBricks I20260, J23101.E0240 and J23115.E0240. The latter consists of a [http://parts.igem.org/Part:pSB3K3 pSB3K3] backbone with an insert, a combination of the promoter [http://parts.igem.org/Part:BBa_J23101 J23101], the RBS [http://parts.igem.org/Part:BBa_B0032 B0032], the GFP coding sequence [http://parts.igem.org/Part:BBa_E0040 E0040] and the terminator [http://parts.igem.org/Part:BBa_B0015 B0015]. J23101.E0240 has the same insert as I20260, but has [http://parts.igem.org/Part:pSB1C3 pSB1C3] as a backbone. J23115.E0240 only differs from J23101.E0240 in the use of another promotor, namely [http://parts.igem.org/Part:BBa_J23115 J23115]. As a '''negative control''', we used just B0015 in pSB1C3.<br />
<br />
{{Team:Aachen/Figure|Flasks.png|align=center|width=400px}}<br />
<br />
{{Team:Aachen/Figure|Aachen_14-10-11_BioBricks_for_Interlab_iNB.png|align=center|title=Genetic devices tested|subtitle=Composition of I20260, J23101.E0240 (left) and J23115.E040 (right)|width=500px}}<br />
<br />
Over a time span of 18 hours the optical density and fluorescence of cultures containing these BioBricks were measured every 2 hours using the spectrophotometer and plate reader, respectively. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Green_Flask_iNB.png|right|150px]]<br />
<br />
==Expected Results==<br />
<span class="anchor" id="isexpectedresults"></span><br />
<br />
Fluorescence was expected to develop in cultures containing I20260, J23101.E0240 and J23115.E0240, as all include the GFP coding sequence. However, the signal was expected to be stronger in J23101.E0240 than in I20260 since pS1C3 is a high copy plasmid while pSB3K3 is a low to mid copy plasmid. Because of this, a higher fluorescence was expected of J23101.E0240 compared to I20260 even though they share the same insert. J23115.E0240, too, was supposed to produce a fluorescent signal, but J23115 (the mutated version K823012 was used) is a lot weaker promotor than J23101. Therefore, a lot lower - if any - fluorescence is expected with this BioBrick.<br />
<br />
{{Team:Aachen/Figure|Aachen_14-10-16_Plasmid_Promotor_Strength_iNB.png|title=Diagram illustrating the different plasmid and promotor properties|subtitle=Plasmid pSB1C3 has a higher copy number than pSB3K3, and J23101 is a stronger promotor than J23115.|width=800px}}<br />
<br />
B0015 was used as our '''negative control''' as the insert only contains a terminator and no expression cassette for GFPmut3b, and so no fluorescence was expected.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Empty_Falcon_iNB.png|right|150px]]<br />
<br />
==Materials and Methods==<br />
<span class="anchor" id="ismaterials"></span><br />
<br />
===Constructs and strains===<br />
All constructs used were transformed into [https://www.neb.com/products/c3019-neb-10-beta-competent-e-coli-high-efficiency NEB 10β] cells. The constructs I20260 as well as B0015 were taken directly from the iGEM 2014 distribution plates. The constructs J23101.E0240 as well as J23115.E0240 were made using the [http://parts.igem.org/Help:Assembly/3A_Assembly 3A Assembly]. Therefore, the subparts J23101, J23115 as well as E0240 were transformed directly from the 2014 distribution plates into [https://www.neb.com/products/c3019-neb-10-beta-competent-e-coli-high-efficiency NEB 10β] cells. Afterwards the plasmids were recovered using the [https://us.vwr-cmd.com/bin/public/demidoccdownload/50001659/7057R_ge_healthcare_illustra_nucleic_acid_sample_preparation.pdf illustra plasmidPrep Mini Spin Kit]. The purified plasmids J23101 and J23115 were cut with the restriction enzymes EcoRI and SpeI, while E0240 was cut with XbaI and PstI. The restricted plasmids were then ligated together using the T4 DNA Ligase. Afterwards, the ligation product was introduced into the pSB1C3 linearized backbone provided by iGEM headquarters with the 2014 distribution which we had also cut with EcoRI and PstI. All restrictions and ligations were performed using enzymes and buffers of the [http://shop2.neb-online.de/4DCGI/ezshop?action=Direktanzeige&Artikelnummer=NEBIGEM1%40&WorldNr=01&ButtonName=website&skontaktid=1055557&skontaktkey=RrbLvNPZxLRIFbyyyGOZambWfZKxFK NEB iGEM Kit]. The final product was once again transformed into [https://www.neb.com/products/c3019-neb-10-beta-competent-e-coli-high-efficiency NEB 10β] cells.<br />
<br />
The correct identity of the resulting constructs were confirmed by sequencing. The sequencing data (consensus sequences) can be found [https://2014.igem.org/File:Sequencing_Interlab_Study_iGEM_Aachen_2014.zip here].<br />
<br />
Note: We used the mutated version of J23115 as sent out by the iGEM headquarters. The mutation makes J23115 effectively the same promoter as K823012. We will still refer to the promoter as J23115 though, to keep it more easily recognizable with the other Interlab Study results.<br />
<br />
===Inoculation and Cultivation===<br />
The cultivation of our bacteria was performed in 500&nbsp;ml shake flasks filled with 50&nbsp;ml [https://2014.igem.org/Team:Aachen/Notebook/Protocols#LB_medium LB medium]. The cultures were kept at 37°C and 300&nbsp;rpm shaking frequency. Appropiate antibiotics were added to each media (kanamycin for I20260, chloramphenicol for B0015, J23101.E0240 and J23115.E0240). Both antibiotics were added from a 1000X stock stored at -20°C for a final concentration of 35&nbsp;µg/ml chloramphenicol and 50&nbsp;µg/ml kanamycin, respectively.<br />
<br />
The precultures were inoculated from the same cryo stocks. They were cultivated for 16 hours and then sampled for OD measurement with a spectrophotometer. Then 2&nbsp;ml of each preculture were centrifuged (5 minutes, 6000&nbsp;g) and then washed twice with PBS buffer. Afterwards, all cultures were inoculated to have the same starting OD. Inoculations were carried out under sterile conditions at the clean bench.<br />
<br />
===Sampling===<br />
To draw samples, the shake flasks were taken out of the 37°C room and brought onto a nearby bench. 3&nbsp;ml of sample were taken out next to a Bunsen burner flame and pipetted into three 2&nbsp;ml cuvettes. As soon as all samples were taken the flasks were taken back onto the shaker in the 37°C room. The whole process of taking samples for all 12 flasks (3 biological replicates for each construct) took 5 minutes and samples were taken every 2 hours.<br />
<br />
After 4 hours, we had to dilute the samples with LB medium in a ratio of 1:4, and from the 6th to 18th hour we had to dilute in a ratio of 1:9.<br />
<br />
After the measurement of OD in the spectrometer, 100&nbsp;µl of each sample were taken out and put on a 96-well plate (Thermo microfluor 1, flat-bottom, black) to measure fluorescence. <br />
<br />
Each measurement occured in a technical triplicate, resulting in 36 different samples being processed in every sampling step.<br />
<br />
===Measurement of OD using a spectrophotometer===<br />
For OD measurement, the [http://www.unicosci.com/spectro/1200detail.htm Unico Spectrophotometer 1201 of Fisher Bioblock Scientific] was used. The measurement was taken at 600&nbsp;nm and we used pure LB medium (from the same batch as the medium used for cultivation) as our blank. We only measured OD up to an absorbance of 0.8. At a higher OD, we diluted the sample with LB medium (again from the same batch as our cultivation medium). Dilution was done by first filling the cuvettes with the LB medium, and then adding our cultivation sample. Subsequently, each cuvette was vortexed thoroughly. The solution was allowed to settle before measurement.<br />
<br />
===Measurement of fluorescence using a microplate reader===<br />
Measurement of fluorescence was performed using the ''' [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek]''' with the Gen5 software, using the following parameters:<br />
{| class="wikitable"<br />
|-<br />
! Parameter !! value<br />
|-<br />
| Software version || 2.1.2014<br />
|-<br />
| Reader Type || Synergy Mx<br />
|-<br />
| Read || GFP 100<br />
|-<br />
| Measurement || fluorescence endpoint<br />
|-<br />
| Measurement range || full plate<br />
|- <br />
| Filter || filter set 1<br />
|- <br />
| Excitation || 496&nbsp;±&nbsp;9.0&nbsp;nm<br />
|- <br />
| Emission || 516&nbsp;±&nbsp;9.0&nbsp;nm<br />
|-<br />
| Gain || 100<br />
|-<br />
| Read Speed || normal<br />
|- <br />
| Delay || 100 msec<br />
|-<br />
| Measurement s/data point || 10<br />
|-<br />
| Read height || 8&nbsp;mm<br />
|}<br />
<br />
As for the OD measurement, we used LB medium as our blank. Since samples for fluorescence measurement were acquired from the cuvettes for the OD measurement, sample processed in plate reader had the same dilutions.<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
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[[File:Aachen_14-10-13_Graph_Panel_iNB.png|right|150px]]<br />
<br />
==Results==<br />
<span class="anchor" id="isresults"></span><br />
<br />
After observing the optical density (OD) and fluorescence for 18 hours while taking samples every 2 hours, the following results were obtained:<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-13 InterlabGraph1 iFG.PNG|align=center|title=Interlab Study Results|subtitle=Our measurements of fluorescence and optical density of the three genetic devices and a negative control.|width=700px}}<br />
<br />
This shows that all cultures had ODs in the same range throughout the experiment. After the exponential growth phase the stationary phase started shortly after 4 hours of cultivation time. The OD did not change from thereon until a cultivation time of 16 hours after which it started to decline. <br />
<br />
The development of fluorescence followed largely the pattern of the OD, but differed a lot in between the different cultures. J23101.E0240 exhibited fluorescence three times stronger than I20260, and about 10 times stronger than B0015 and J23115.E0240. The latter two did not differ in terms of fluorescent signal.<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
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[[File:Aachen_14-10-13_Graph_with_Error_Bars_Panel_iNB.png|right|150px]]<br />
<br />
==Discussion==<br />
<span class="anchor" id="isdiscussion"></span><br />
<br />
The OD is an indirect measurement of the biomass in the shake flask. Through the correlation of both measurements the results show that the difference in biomass of the cultures is not significantly enough to affect the fluorescence data. Therefore, the fluorescence data can be interpreted as a direct result of the fluorescence per cell instead of an overall fluorescence per culture. <br />
<br />
The fluorescence data shows a '''strong difference between the I20260 and J23110.E240'''. Even though both inserts are the same, there is a difference in fluorescence, as expected, because of the different plasmid backbones. The high copy plasmid pSB1C3 shows a '''3 times stronger fluorescence signal''' per cell than the low to mid copy plasmid pSB3K3. This can be directly related to the number of plasmids in the cells coding for GFP.<br />
<br />
Both J23115.E0240 and B0015 show no significant fluorescence. The increase at 4 hours is explained by the '''increase of OD resulting in noise'''. B0015 behaves therefore as expected. J23115.E0240 in its original, non-mutated state was supposed to show a slight but weaker fluorescence than J23101.E0240. However, the mutations introduced made the '''promoter non-functional''', which lead to no expression of GFP and therefore no observation of fluorescence.<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Software/MeasurartyTeam:Aachen/Notebook/Software/Measurarty2014-10-17T19:34:39Z<p>J.plum: </p>
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<br />
= ''Measurarty'' =<br />
<br />
''Measurarty'' is the evil player in the game of ''Cellock Holmes'' and ''WatsOn''.<br />
''Measurarty'' is the pathogen detection logic behind our project.<br />
Using our ''Measurarty'' algorithm, we want to automatically detect pathogens from the chip photos delivered by WatsOn, without human interaction.<br />
Besides reducing the risk of human errors, this makes our device usable by almost everyone.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
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<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#intro" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Intro</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/1b/Aachen_Measurarty_Intro_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#SRM" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">SRM!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/2d/Aachen_Puzzels_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#segment" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Segment!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/e1/Aachen_SEgment_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#classification" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Classify!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/f/f9/Aachen_Classify_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#measurartyachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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[[File:Aachen_Measurarty_Intro_button.png|right|150px]]<br />
<br />
== ''Measurarty'' - An Introduction ==<br />
<span class="anchor" id="intro"></span><br />
<br />
Our [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware device control software] is able to take images of incubated chips inside WatsOn. Yet, that does not bring the user closer to the answer of the question:<br />
<br />
<center>'''What's on the chip?'''</center><br />
<br />
In fact, answering this question seems trivial for a human: Just check whether a colony grown has grown on the chip and you're done. This task is even easier with our chip system, because these show fluorescence wherever a pathogen has been detected.<br />
<br />
But is this an easy task for a computer? Actually not. The task of automatic detection is tried by several disciplines in computer science, from pattern recognition over machine learning to by medical imaging chairs.<br />
<br />
Here, we would like to present a pipeline for this task that makes use of '''easy segmentation and classification algorithms'''.<br />
First, ''Measurarty'' segments the target image using '''Statistical Region Merging (SRM)''' in order to find regions of similar properties. After this step, we can segment the picture using '''histogram thresholding''' in [http://en.wikipedia.org/wiki/HSL_and_HSV HSV color space] to find candidate regions for pathogens.<br />
Finally, a classification algorithm can detect the pathogen on our chips.<br />
<br />
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[[File:Aachen_Puzzels_button.png|right|150px]]<br />
<br />
== Statistical Region Merging (SRM) ==<br />
<span class="anchor" id="SRM"></span><br />
<br />
Before briefly introducing Statistical Region Merging (SRM), we would like to explain why we need this step, and why this algorithm is an ideal choice.<br />
<br />
Compared to other clustering algorithms, SRM is quite leight weight, yet delivers ''deterministic'' results and is not dependent on a certain seed (like ''k''-means, for example).<br />
<br />
On the other hand, it can create as many refinements as one wants and is thus flexible enough for the our purposes. Finally there's already been knowledge about this algorithm in the group.<br />
<br />
Statistical Region Merging (SRM) (Nook and Nielson, 2004) is a clustering technique also used directly for image segmentation.<br />
A region $R$ is a set of pixels and the cardinality $\lvert R \rvert$ determines how many pixels are in one region.<br />
Starting with a sorted set of connected regions (w. r. t. some distance function $f$), two regions $R$ and $R'$ are merged if the qualification criteria $\vert \overline{R'}-\overline{R} \vert \leq \sqrt{b^2(R)+b^2(R')}$ with $b(R) = g \cdot \sqrt{\frac{\ln \frac{\mathcal{R}_{\lvert R \rvert}}{\delta}}{2Q\lvert R \rvert}}$ is fulfilled.<br />
Therefore, $\mathcal{R}_{\lvert R \rvert}$ is the set of regions with $\lvert R \rvert$ pixels.<br />
Typically $Q$ is chosen as $Q \in \lbrack 256, 1\rbrack$ and $\delta = \frac{1}{\lvert I \rvert^2}$.<br />
<br />
The $Q$ parameter mainly influences the merging process. For an example, see the figure ''SRM Regions'' below. The lower the chosen value for $Q$, more coarse the regions become. Using a union-find structure, the segmentation does not need to be recalculated for each $Q$ level. For the step from $q$ to $\frac{q}{2}$, just the qualification criteria needs to be applied to the regions from the $q$ result. A MATLAB implementation is also available (Boltz, 2009).<br />
<br />
{{Team:Aachen/FigureDual|Aachen_srm_regions_3.PNG|Aachen_srm_regions_2.PNG|title1=SRM regions in random colors|title2=SRM regions (average color)|subtitle1=Different regions from an SRM run starting at $Q=256$ (top left) and going to $Q=1$ (bottom right). Each region is assigned a random color.|subtitle2=Different regions from an SRM run starting at $Q=256$ (top left) and going to $Q=1$ (bottom right). Each region is assigned the average color of that region.|width=425px}} <br />
<br />
=== SRM Clustering ===<br />
<br />
In our project, we used Statistical Region Merging for clustering. In contrast to other algorithms, such as ''k-means'', this approach is highly deterministic.<br />
For our purposes we only have one SRM run for $Q=256$.<br />
<br />
In MATLAB, we use the previously mentioned code from MATLAB Fileexchange (Boltz, 2009).<br />
For our Qt-based GUI we implemented the SRM method ourselves.<br />
<br />
The SRM clustering reduces the amount of different colors in the image and hence eases the recognition of parts belonging together.<br />
<br />
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<div class="codediv"><br />
<pre><code class="matlab"><br />
Qlevel = 256;<br />
[maps,images]=singlesrm(double(image),Qlevel);<br />
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[[File:Aachen_SEgment_button.png|right|150px]]<br />
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== Segmentation ==<br />
<span class="anchor" id="segment"></span><br />
<br />
In the segmentation stage all background regions are removed. This task is quite crucial. If one removes too few, the final stage of finding pathogens might get irritated.<br />
On the other hand, if one removes too many regions, positive hits might get removed early before detection. This surely must be avoided.<br />
<br />
We opted for a simple thresholding step because it showed that while being easy, it is an effective weapon against the uniform background. In fact, the good image quality we wanted to reach with our device allows now less sophisticated methods.<br />
Also the less computational intensive the steps are, the better they might even run directly on the Raspberry Pi in our device!<br />
<br />
The HSV thresholding is performed on each component seperately. For more information on the HSV color space we refer to [http://en.wikipedia.org/wiki/HSL_and_HSV Wikipedia]. The first component is the hue which we select to be inbetween $0.462$ and $0.520$ to select any blue-greenish color. We will not see bright green due to the filter selection in our device.<br />
The saturation value must be high, between $0.99$ and $1.0$.<br />
Moreover, the value component of the HSV image has to lie between $0.25$ and $0.32$, which assumes a relatively dark color.<br />
<br />
Indeed, these values are not problem specific, but specific for each setup and therefore have to be determined empirically.<br />
<br />
The remainder of this stage creates a mask of pixels that fulfill the conditions.<br />
<br />
* image of masked bit<br />
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<pre><code class="matlab"><br />
% Auto-generated by colorThresholder app on 15-Oct-2014<br />
%-------------------------------------------------------<br />
function [maskedRGBImage] = createMask(srmimg)<br />
RGB = srmimg;<br />
<br />
% Convert RGB image to chosen color space<br />
I = rgb2hsv(RGB);<br />
<br />
% Define thresholds for channel 1 based on histogram settings<br />
channel1Min = 0.462;<br />
channel1Max = 0.520;<br />
<br />
% Define thresholds for channel 2 based on histogram settings<br />
channel2Min = 0.99;<br />
channel2Max = 1.000;<br />
<br />
% Define thresholds for channel 3 based on histogram settings<br />
channel3Min = 0.25;<br />
channel3Max = 0.32;<br />
<br />
% Create mask based on chosen histogram thresholds<br />
BW = (I(:,:,1) >= channel1Min ) & (I(:,:,1) <= channel1Max) & ...<br />
(I(:,:,2) >= channel2Min ) & (I(:,:,2) <= channel2Max) & ...<br />
(I(:,:,3) >= channel3Min ) & (I(:,:,3) <= channel3Max);<br />
<br />
% Initialize output masked image based on input image.<br />
maskedRGBImage = RGB;<br />
<br />
% Set background pixels where BW is false to zero.<br />
maskedRGBImage(repmat(~BW,[1 1 3])) = 0;<br />
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end<br />
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[[File:Aachen_Classify_button.png|right|150px]]<br />
<br />
== Classification ==<br />
<span class="anchor" id="classification"></span><br />
<br />
=== Smoothness Index ===<br />
<br />
For position prediction in virtual environments, jitter or noise in the output signal is not wanted though often present.<br />
Since discovering smooth areas is a similar problem to jitter detection, a simple method for determining jitter can be used to measure non-jitter, smoothness (Joppich, Rausch and Kuhlen, 2013).<br />
It is assumed that jitter-free areas of a position signal do not differ in velocity.<br />
<br />
Smooth areas do not differ in intensity, and therefore only low changes in velocity (intensity change) can be recorded.<br />
For the reduction of noise, this operation is performed on the smoothed input image.<br />
Then the smoothness $s$ of a pixel $p$ in its k-neighbourhood $\mathcal{N}_k$ can be determined as:<br />
\begin{equation}<br />
s(p) = \sum\limits_{p' \in \mathcal{N}_k} \nabla(p') / \arg\max\limits_{p} s(p)<br />
\end{equation}<br />
<br />
Using thresholding, $TS_l \leq s(p) \leq TS_u \wedge TI_l \leq I \leq TI_u$, different areas, such as background or pathogen, can be selected.<br />
<br />
For the empirical choice of thresholds, it can be argued that these are tailored to the specific case.<br />
While this surely is true to a certain extent, the here presented method has been successfully tested on images from a completely different domain, and no changes to the thresholds have been made to make it work.<br />
A proper theoretical evaluation is emphasized, however, is probably not the aim of the iGEM competition.<br />
<br />
Finally, selecting for the red region, this delivers the location of possible pathogens.<br />
Since the size of the agar chips is variable but fixed a quantitative analysis can be performed by counting pixels for instance.<br />
<br />
=== Empirical Evaluation ===<br />
<br />
Using our MATLAB code we found the lower threshold for the smoothness index to be $TS_l = 0.85$ and the upper threshold $TS_u = \infty$.<br />
Similarly, for $TI_l = 235$ and $TI_u = \infty$.<br />
<br />
Using these settings, we can find a response already in images taken after 42&nbsp;minutes.<br />
<br />
Ideally, one would rate the quality of the image segmentation using some ground truth, such as manual delineations. This still has to be done for our method.<br />
However, from visual observations, our method is showing promising results.<br />
<br />
* image of smoothness index<br />
<br />
=== Automatic Classification ===<br />
<br />
<br />
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<pre><code class="matlab"><br />
function [mask, seg] = automaticseeds(im)<br />
<br />
imc = im;<br />
<br />
%% to grayscale and filtering<br />
Z = double(rgb2gray(im));<br />
Z = 255 * Z / max(max(Z));<br />
<br />
filtertype = 'disk';<br />
Z = filter2(fspecial(filtertype), Z);<br />
Z = filter2(fspecial(filtertype), filter2(fspecial(filtertype), Z));<br />
Z = 255 * Z / max(max(Z)); <br />
<br />
%% calculating similarity score/smoothness index<br />
k=4;<br />
sSI = similarity(Z,k);<br />
sSI = sSI / max(max(sSI)); <br />
<br />
%% classify<br />
pathogene = ((sSI > 0.85) == 1) & ((Z > 235) == 1); <br />
<br />
mask = ones( size(imc) );<br />
seg = zeros( size(imc) );<br />
<br />
<br />
%% output<br />
for i=1:size(im,1)<br />
for j=1:size(im,2)<br />
<br />
if (pathogene(i,j) == 1)<br />
seg(i,j,1:3) = [255 0 0];<br />
mask(i, j, 1:3) = [0 0 0];<br />
end<br />
end<br />
end<br />
end<br />
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[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="measurartyachievements"></span><br />
<br />
''Measurarty'' is the image analysis logic behind our project.<br />
It is comprised of simple constructs put together into a pipeline, that is clearly laid out, easily maintainable and - if needed - easily adaptable.<br />
For example, changing from green to red fluorescence, only means to change the ''createMask'' function to select another target area.<br />
<br />
Overall the results look convincing. We have not yet performed a comparison to a manual delineation, however, by eye the results look promising and have a low error.<br />
<br />
Talking about computational complexity, the MATLAB code of course performs better than our own C++ implementation, which must be regarded as a proof-of-principle.<br />
<br />
Space-wise, the code depends heavily on the image size $O( x \cdot y)$ (width $x$, height $y$, which also limits the number of edges in SRM between regions, as each pixel is one region to start with. However, it cannot take less memory, as the image is stored in an uncompressed format.<br />
<br />
On the computational side, the thresholding, image conversion and gradient steps are linear in the number of pixels, and are thus in $O(x \cdot y)$.<br />
Unfortunately, the summation of the gradient for the smoothness index adds a heavy factor to it (k-neighbourhood for smoothness index).<br />
Due to the merging step in our C++-SRM algorithm implementation, our code has to do $O(x^2 \cdot y^2)$ comparisons, which then finally results in a runtime complexity of $O( x^2 \cdot y^2)$.<br />
<br />
*include image here<br />
<br />
From the above figure it can also be seen that the detected amount of pathogenic-area correlates with time after induction.<br />
The lag-phase can be explained first by the lag-phase of the cells, which first need to generate a response to the pathogen, and on the other hand, by too low fluorescence which is not detectable.<br />
The pixel count also meets the expectation when looking at the sample files by eye.<br />
<br />
It can be concluded that the ''Measurarty'' pipeline defines a robustly working chip-analysis algorithm which can detect pathogens from images supplied by ''WatsOn''.<br />
Therefore, this algorithm closes the gap between our biology, detection hardware and the user who wants easy-to-interpret results.<br />
<br />
For future prospects, it would be interesting to do a proper performance analysis on our code, to find hotspots and optimize the code. Many ''for''-loops leave plenty of room for vectorization and loop-unrolling. Parallelization, specifically with respect to embedded hardware such as the Raspberry Pi or Odroid U3, is limited to the extend that the overhead created would probably eliminate the improvements.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
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== Source Code ==<br />
<span class="anchor" id="source"></span><br />
<br />
''Measuarty'' is the image analysis logic behind our project. It has been prototyped and developed in [http://www.mathworks.de/academia/student-competitions/igem/ MATLAB], and only later been ported into our WatsOn GUI.<br />
<br />
We are happy to provide you with a zip-ped download of our MATLAB code here, as well as on the iGEM softwarerepository on [https://github.com/orgs/igemsoftware/teams/aachen2014 github].<br />
<br />
* MATLAB code<br />
* link [https://github.com/orgs/igemsoftware/teams/aachen2014 github]<br />
<br />
For the C++ conversion please see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware our WatsOn Software] section.<br />
<br />
=== Using the MATLAB Code ===<br />
<br />
In general, please follow the included ''README.MD'' file. Our package comes with a set of test files from one of our experiments.<br />
After installing the Statistical Region Merging code (see readme), you can simply run ''igem_srm_demo.m''. Select your current folder, and MATLAB will automatically segment and classify the included jpg-images.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== References ==<br />
<span class="anchor" id="measurartyrefs"></span><br />
<br />
* Boltz, S. (2009, October 20). Image segmentation using statistical region merging - File Exchange - MATLAB Central. Image segmentation using statistical region merging. Retrieved December 12, 2013, from http://www.mathworks.com/matlabcentral/fileexchange/25619-image-segmentation-using-statistical-region-merging<br />
<br />
* Joppich, M., Rausch, D., & Kuhlen, T. (2013). Adaptive human motion prediction using multiple model approaches.. Virtuelle und erweiterte Realität (p. 169–180). 10. Workshop der GI-Fachgruppe VR/AR: Shaker.<br />
<br />
* Nock, R., & Nielsen, F. (2004). Statistical region merging. IEEE Transactions on Pattern Analysis and Machine Intelligence, 26(11), 1452-1458.<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Project/Measurement_DeviceTeam:Aachen/Project/Measurement Device2014-10-17T19:32:25Z<p>J.plum: /* Measurarty */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
{{Team:Aachen/FigureFloatRight|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=270px}}<br />
<html><br></html><br />
The ''WatsOn'' device aims to answer the central question "What's on the chip?". The device is designed to incubate the sensing cells and capture images. <html><br></html>The interactive ''WatsOn'' software enables the end user not only to take images and time lapse shootings, but also analyzes the images and visualizes the presence/absence of a pathogen.<br />
<br />
The construction manual and the technical details are published in our [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy wiki].<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Modus Operandi</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/thumb/c/c7/Aachen_WatsOn_easy.png/600px-Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonhardware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Hardware</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonsoftware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Software</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonmeasurarty" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measurarty</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/21/Aachen_14-10-16_Measurarty_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== Modus Operandi ==<br />
<span class="anchor" id="watsonapplication"></span><br />
<br />
{{Team:Aachen/Figure|How_two_use_watsOn_flowsheet_V7_ipo.png|title=How to use ''WatsOn''|subtitle=This scheme illustrates handling WatsOn when testing the 2D biosensor chip for a fluorescent signal.|width=1000px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Hardware_button_iNB.png|right|150px]]<br />
<br />
== Hardware ==<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Elektronikkomponenten1.jpg|title=Hardware components|subtitle=From top left to bottom right: Arduino, Peltier element, Raspberry Pi, relay, cables, MOSFET, temperature display, camera, LEDs and resistors.|width=520px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen in the first section was build from laser cutted acrylic glass.<br />
<br />
The electronic circuit is a combination of the components displayed in the image above. We combined the Raspberry Pi - a small single-board computer running a Linux operating system - and an Arduino board which is a programmable microcontroller. The Arduino operates the excitation LEDs and a Peltier heater for incubation. For taking images of the sensor chips we used the Raspberry Pi camera module which is directly connected to the board.<br />
<br />
''WatsOn'' is designed such that it can be easily copied. Our work heavily emphasizes the Open Source concept. Therefore a detailed description of all components and the wiring can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware Engineering section of our Notebook].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<!-- [[File:Aachen_14-10-16_Software_button_iNB.png|right|150px]] --><br />
<br />
== Software ==<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
{{Team:Aachen/FigureDual|Aachen_WatsOn_igem_GUI_originalImage.png|Aachen_WatsOn_igem_GUI_analyzedImage.png|title1=image taken with the camera |title2=analyzed image |subtitle1= |subtitle2= |width=500px}}<br />
<br />
The ''WatsOn'' software is responsible for presenting a user interface on the display of the device and to take images with the LED wavelength selected by the user. Therefore, it is separated into three single components: the graphical user interface (GUI) with a backend script running on the Raspberry Pi and the code on the Arduino board.<html><br/></html><br />
The GUI (left image) provides the user with the option to take a single image or a time lapse shooting and specify parameters for the camera and the wavelength of the LEDs. The wavelength used in our device are 480nm for GFP and 450nm for iLOV. Furthermore, the images are analysed for the presence or absence of P. aeruginosa by analysing the image and providing the user with a visual feedback (right image). All taken images can be saved to disk manually for single images and automatically for time lapse shootings.<html><br/></html><br />
Further details on the software including the backend which gives the possibility of using the GUI remotely on a different device (e.g. notebook) in the same local network can be found here [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Measurarty_button_iNB.png|right|150px]]<br />
<br />
== ''Measurarty'' ==<br />
<span class="anchor" id="watsonmeasurarty"></span><br />
<center><br />
{{Team:Aachen/Figure|Aachen_srm_regions_3.PNG|title=SRM component of our image analysis component ''Measurarty''|subtitle=SRM is one of the core components of our image analysis approach. This image shows the different regions created.|width=500px}}<br />
</center><br />
<br />
''Measurarty'' is the '''image analysis software''' of our device and is designed to allow an automatic segmentation and classification of our '''agar chip pictures'''.<br />
Therefore, it accepts an image from ''WatsOn'' as an input and produces an output image with pathogenic regions marked in red.<br />
<br />
This component mainly focuses on recognizing pathogens early, such that pure thresholding is not necessary.<br />
We therefore designed a pipeline and established a smoothness index to make statements about the pathogenity of a chip as early as possible, but also with as much certainty as possible.<br />
<br />
A sample output of the segmentation is presented below, showing that the pipeline works as intended.<br />
<br />
{{Team:Aachen/FigureDual|Aachen_K131026_Pseudomonas_aeruginosa_detection.gif|Aachen_Pseudomonas_aeruginosa_Measurarty_slower.gif|title1=Detection of ''Pseudomonas aeruginosa'' with K131026|title2=Optimized detection of ''Pseudomonas aeruginosa'' using ''Measurarty''|subtitle1=Direct detection of ''Pseudomonas aeruginosa'' on sensor chips. Sensor cells used were K131026.|subtitle2=''Measurarty'' is able to reliably identify the fluorescence response of the sensor cells which is produced in a response to ''Pseudomonas aeruginosa''.|width=480px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="watsonachievements"></span><br />
<br />
We developed ''WatsOn'' to meet the following requirements: i.e. the device<br />
*incubates the sensing cells and the sampling chip <br />
*illuminates the chip with the right excitation wavelength for our fluorescence proteins<br />
*takes pictures and time lapse shootings of the chips<br />
*uses cheap filter slides to block the light emitted from the LEDs<br />
*analyzes the fluorescence signal<br />
*gives feedback to the user about the presence or absence of P. aeruginosa through a GUI (graphical user interface)<br />
*prevents escape of potentially sampled pathogens and our genetically engineered cells<br />
*is portable and fast in analyzing the images<br />
<br />
With our final device we achieved all of the above mentioned goal. ''WatsOn'' is housed in a closed casing and is able to take images and time lapse shooting using LEDs with required wavelengths, analyze the image and visualize the result.<br />
<br />
All technical details including laser cutting plans, the list of needed components, source codes for the different software and a building instruction are open-source and available on our wiki[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/ODFTeam:Aachen/Notebook/Engineering/ODF2014-10-17T19:30:08Z<p>J.plum: /* Technical Components */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
{{Team:Aachen/Stylesheet}}<br />
= OD/F Device =<br />
<br />
On this page we present the technical details of our OD/F device. You can skip to specific chapters by clicking on the panels below:<br />
<center><br />
<html><ul class="team-grid" style="width:1064px;"><br />
<!-- Overview --><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#dev" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br><br />
<b>General Considerations</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#od" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>OD Device</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/04/Aachen_Cuvette_button_v1_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#f" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>F Device</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
Building the OD/F device has been an interesting task. On the one hand, this device has been developed mainly by the IT division of our team. On the other hand, we got assistance from biologists suffering from color-blindness, yet eager to help selecting the best color filters for the LEDs.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
= General Considerations =<br />
<span class="anchor" id="dev"></span><br />
<br />
=== Measuring Principle ===<br />
<br />
The measuring principle for both optical density (OD) and fluorescence measurement is depicted below.<br />
For OD measurement we shine through the sample with an LED and a fixed width. A filter blocks any other light but 600&nbsp;nm. This way, the sensor mainly senses the 600&nbsp;nm light which is needed for OD600 measurement.<br />
<br />
For fluorescence measurement a similar approach is chosen. The filter again is used to block the exciting light from being sensed. That way only the emitted light from the fluorescence protein is measured.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
The details about selecting filters, code and a construction manual follows.<br />
<br />
=== Cuvette Holder ===<br />
The essential part of this device is the '''cuvette holder which has also been the most tricky thing to design'''. In short, we had to overcome a dilemma created by the need for an optimal height for the sensor:<br />
* A too low sensor position bears problems with sedimentation as well as light diffraction from the bottom of the cuvette.<br />
* The sensor has to be as close as possible to the bottom so that enough light shines through for the fluorescence measurement.<br />
<br />
As a compromise, we place the sensor at a height of 0.75&nbsp;cm, which, as it turned out later, is very close to one of the standard heights (0.2&nbsp;cm, 0.8&nbsp;cm, 1.2&nbsp;cm) of OD meters. It is important to note that despite the official minimal fill height of 1.2&nbsp;mL of the 1.5&nbsp;mL cuvettes we used, our device also works with filling volumens of just 1&nbsp;mL which in fact comes closer to reality in the lab.<br />
<br />
The final cuvette holder design is rendered from a [https://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=raw stl-file] shown below:<br />
<br />
<html><br />
<center> <br />
<iframe src="https://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=render<br />
" width=500px height=500px frameBorder="0"></iframe><br />
</center><br />
</html><br />
<br />
=== Light Filters ===<br />
Once the cuvette holder was finished, '''finding good filters was a tough challenge'''. A main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters unfortunately could not be considered. Instead, filters used for illumination of theaters seemed to be an ideal solution.<br />
<br />
Especially for the fluorescence measurements of GFP finding the right filter has been a big problem. [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501&nbsp;nm and a peak emission at 511&nbsp;nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485&nbsp;nm reduce false positive results below 500&nbsp;nm. However, no adequate filter for these settings could be found.<br />
Eventually, using the dark greenish [http://leefilters.com/lighting/colour-details.html#736 Twickenham Green] filter only little amounts of light shorter than 500&nbsp;nm gets through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20% only, for the target emission wavelength of 511&nbsp;nm.<br />
<br />
For the OD measurement, too, we had similar problems. Indeed, due to our goal of inexpensive parts, we only filter light below 600&nbsp;nm. Further filters would lower the base transmittance and result in a loss of resolution which is not tolerable.<br />
Finally the red filter [http://leefilters.com/lighting/colour-details.html#019 Fire] permits over 70&nbspr; of the light to the sensor and is thus suited for our purposes.<br />
<br />
The following LED and filter combination has been chosen by us:<br />
<br />
{| class="wikitable"<br />
! Mode<br />
! Fluorescence Protein<br />
! Filter<br />
! Peak Excitation<br />
! Peak Emission<br />
|-<br />
| Fluorescence<br />
| GFPmut3b<br />
| Twickenham Green<br />
| 501nm<br />
| 511nm<br />
|-<br />
| Optical Density<br />
| --<br />
| Fire<br />
| 600nm<br />
| 600nm<br />
|}<br />
<br />
<html><br />
<sup><span class="anchor" id="fn1"></span>1. Quite a good random number generator from a computer-scientific perspective!<a href="#ref1" title="">↩</a></sup><br />
</html><br />
<br />
== Linearity ==<br />
<span class="anchor" id="lin"></span><br />
As for any scientifc device it is crucial to question the results one gets from the device. To ensure that our device actually works, we performed a set of measurements which are presented below.<br />
<br />
It is crucial that the selected hardware is mapping reality into the digital world of our $\mu$-Controller.<br />
In order to sense reality our setup uses a light to frequency sensor, [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf TSL235R-LF].<br />
The light to frequency sensor resembles the most to a photo transistor and thus is less sensible to temperature than a light dependant resistor.<br />
Additionally counting a frequency using interrupts seems to be easier and more accurate than using the analog to digital converter.<br />
<br />
Using a dilution series of purified [https://2011.igem.org/Team:Glasgow/LOV2 iLOV] we could determine the characteristic curve for the light sensor. Finally we can conclude that the sensor is linear as expected and shown in the [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf datasheet].<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Linearity iFG.PNG|title=Linearity of TSL235R-LF sensor|subtitle=Dilution series of GFP expressing E. coli showing linearity between fluorescence count and dilution.|width=700px}}<br />
</center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
[[File:Aachen_Cuvette_button_v1_ipo.png|right|150px]]<br />
<br />
= OD Device =<br />
<span class="anchor" id="od"></span><br />
<br />
We are measuring optical density using the presented cuvette holder.<br />
Particularly for optical density measurement the amount of light shining through the sample is crucial.<br />
If there is too few light, there will be not enough light registered at the sensor, and the resolution of the measurement shrinks. This should be prevented.<br />
The chosen light to frequency sensor is reported to be very sensitive on the amount of light shining on it.<br />
There are reports of the sensor breaking when put into [https://www.sparkfun.com/products/9768 sunlight on a nice day], and not being sensitive at both high light or low light [http://kesslerarduino.wordpress.com/author/kevinmkessler/page/2/ conditions].<br />
<br />
Commercial systems usually use a laser beam to shine through the sample. For reasons of available components, we omitted this in our plans. Finding a suitable orange laser is not easy.<br />
Instead we chose an LED, which unfortunately scatters light, both in the spectrum as well as in all directions.<br />
Using a filter we reduce the effect of scattering.<br />
Finally the [http://leefilters.com/lighting/colour-details.html#019 Fire 019] filters solves our problems, but is far away from ideal.<br />
<br />
== Evaluation ==<br />
=== From Transmittance to True Optical Density ===<br />
At very low levels, uncorrected photometric determinations of cell densities show a decreasing proportionaility to actual cell density.<br />
<br />
This can also be observed using our OD measurement device.<br />
<br />
In general, photometric determination of bacterial concentrations depends primarily on light scattering, rather than light absorption. Therefore. often not absorption is measured, but transmittance. For this, the relationship between optical density (OD) and transmitted light $\frac{I_0}{I}$ exists as:<br />
<br />
$$ OD = \frac{I_0}{I} = \kappa \cdot c$$<br />
<br />
However, this equation is linear only in a certain range.<br />
While one can tackle this non-linearity by using dilutions of the culture, correcting the error systematically is another way to overcome this limitation.<br />
<br />
For our OD device we needed to correlate the transmittance measured by our sensor to an optical density anyway.<br />
Our team members from the deterministic sciences emphasized on the correction method, which was conducted according to Lawrence and Maier [1]:<br />
<br />
* The relative density ($RD$) of each sample in a dilution series is calculated using $\frac{min(dilution)}{dilution}$.<br />
* The uncorrected optical density is derived from the transmission T [%]: $OD = 2 - \log T$<br />
* Finally, the unit optical density is calculated as $\frac{OD}{TD}$.<br />
* The average of the stable unit optical densities is used to calculate the true optical density $ OD_{unit} \cdot RD $.<br />
This way, the correlation between transmission and true optical density can be computed.<br />
The derived function allows the conversion from transmission to optical density on our device and therefore calibrates our device.<br />
<br />
Lawrence and Maier could show that correcting transmittance this way, the corrected optical density shows a linear relationship between true optical density and dry weight in cell suspensions.<br />
<br />
In our experiments, we find in accordance to [1] that the correction majorly depends on the technical equipment used, especially the LED, sensor and cuvettes.<br />
While this at first sight looks disappointing, it is also expected:<br />
Transmittance is the fraction of light not absorbed by some medium relative to the cell-free and clear medium.<br />
However, the transmittance is not only dependent on the amount of cells in the way of the light's beam, but also how much light shines through the cuvette in which fashion, and in which fraction is received by the sensor in which angles.<br />
<br />
Using the above formula we performed this experiment for Pseudomonas putida and Saccharomyces cerevisiae.<br />
<br />
=== Experiments ===<br />
<br />
We performed several experiments during the development of the OD/F device.<br />
Finally we can relate the measured transmittance to the true Optical Density, and further, we can relate that true OD to the one of the photospectrometer in our lab.<br />
By doing to we can calibrate our device to meaningful values.<br />
<br />
We have done this according to the previous section for Pseudomonas putida and Saccharomyces cerevisiae.<br />
<br />
The final function for calculating the OD from the transmission calculated by our device can be calculated as<br />
<br />
$$ OD = f(T) \circ g(device) $$<br />
<br />
where $f$ transforms transforms transmittance to true optical density for our device, and $g$ transforms true optical density of our device into the true optical density of the photospectrometer. This way our device is calibrated according to the photospectrometer.<br />
<br />
==== ''Pseudomonas putida'' ====<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida iFG.PNG|title=True Optical Density to Transmittance plot for P. putida|subtitle=|width=700px}}<br />
</center><br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida OD iFG.PNG|title=Corrolating the true optical density of the OD/F device to true optical density of the photospectrometer|subtitle=|width=700px}}<br />
</center><br />
<br />
==== ''Saccharomyces cerevisiae'' ====<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer iFG.PNG|title=True Optical Density to Transmittance plot for S. cerivisiae|subtitle=|width=700px}}<br />
</center><br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer OD iFG.PNG|title=Corrolating the true optical density of the OD/F device to true optical density of the photospectrometer|subtitle=|width=700px}}<br />
</center><br />
<br />
From these plots it can first be seen that our device delivers robust and reproducible results for both procaryotes and eucaryotes.<br />
Also the function from transmittance to true od can be expressed as a lower polynomial function, making its calculation easily possible on a low-end device like a microcontroller.<br />
<br />
Most encouraging is that the function for relating the true OD of our device to the photospectrometer is, as seen by the regression coefficient, close together for both ''P. putida'' and ''S. cerivisae''. In fact, 3.416 and 3.461 are such close together, that the minor deviation could be just measuring inaccuracy.<br />
Therefore we fix the regression coefficient for converting true OD of our device to true OD of the photospectrometer to 3.432 .<br />
<br />
It is interesting to note, that also the function $f$ for the conversion of transmittance to true optical density fit nicely together, as can be seen in the following figure.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_ODallstrains1.png|title=Transmission of different cell types at OD-values from 0.001-1|subtitle=The transmittance data of NIH&nbsp;3T3 cells align with the transmittance of ''P.&nbsp;putida'' and ''S.&nbsp;cerevisiae'' strains, even though the measured optical densities are lower by 1-2 orders of magnitude.|width=800px}}<br />
</center><br />
<br />
By this evaluation we have shown that our self-build optical density measurement device can compete with commercial systems, and moreover, is easy to calibrate by just calculating the true optical density.<br />
Therefore we present a device which measures accurately and is made of easily available parts at a low cost.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_17-10-14_Glowing_cuvette-ipo.png|right|150px]]<br />
<br />
= F device =<br />
<span class="anchor" id="f"></span><br />
<br />
Similarly to the OD measurement, the fluorescence is measured using the same cuvette holder. In fact, if one does not build a combined device, the only thing one is supposed to change is the cuvette holder. <br />
However, as for optical density measurement, a filter needs to be placed between led, sample and the light sensor.<br />
Selecting the filter has been troublesome.<br />
Either the tried filters had a good transmittance but did not screen for the correct wavelength, or they screened for the correct wavelength but showed bad transmittance.<br />
Finally we chose the [ Twickenham green] filter with bad transmittance, and raised the sampling interval from 1&nbsp;s to 4&nbsp;s to allow a distinct signal.<br />
This is by far not optimal, but delivers stable and reliable results.<br />
<br />
For fluorescence measurement we luckily are not that much relying on the optical density of the cell culture to measure (if the sample contains cells at all).<br />
We compared the values of our device against the [https://2014.igem.org/Team:Aachen/Notebook/LabEquipment platereader].<br />
<br />
== Evaluation ==<br />
Figure 1 shows the absolute measurements for both the platereader and our OD/F device. The abrupt jump at 50% concentration can be explained by a second dilution step and is prevalent in both devices.<br />
It can be seen that the platereader show a much higher difference between the GFP and non-GFP cell culture at a higher standard deviation.<br />
Another interesting metric is the difference between the GFP and non-GFP, which can be seen as the normalized fluorescence measure.<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachn 15-10-14 F platereader ODF iFG.PNG|title=Fluorescence Measurement comparison OD/F device and Platereader|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F device shows no significant.|width=700px}}<br />
</center><br />
<br />
If one compares the results there, as in Figure 2, interesting observations can be made.<br />
First, both platereader and OD/F device show very similar results.<br />
The regression curves differ only in a linear factor.<br />
Most interestingly the general fit of the OD/F device to a linear function seems to be better than the platereader.<br />
Overall the linearity which has been observed earlier (in testing the general setup) could be verified.<br />
Therefore our do-it-yourself OD/F device can be used to determine fluorescence.<br />
At higher concentrations our OD/F device struggles regarding accuracy. However, this is also true for the platereader, but at a lower rate.<br />
<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 F platereader ODF2 iFG.PNG|title=Fluorescence Measurement comparison OD/F device and Platereader|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F device shows no significant. A non-GFP expressing E. coli dilution has been used to normalize the GFP dilution series. A linear correlation can be seen.|width=700px}}<br />
</center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How to Build Your Own Device =<br />
<span class="anchor" id="diy"></span><br />
== Technical Components ==<br />
<br />
While the casing and the cuvette holder are custom made, most of the parts are pre-made and only need to be bought. The previous section lists all needed parts. To get all these parts for creating your own OD/F device is easy by using the internet. A lot of companies all over the world are specialized in selling electronically equipment not only in the internet but also in local shops. However '''potential customers have a market access''' connected to the parts of building. <br />
<br />
Please find our custom parts for download below. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F device a test :) ! <span class="anchor" id="ref2"></span><br />
<br />
* cuvette holder [https://2014.igem.org/Template:Team:Aachen/cuvette.stl?action=raw STL file]<br />
* casing single device [ SVG file]<br />
* casing combined device [ SVG file]<br />
* Arduino Code for single device [https://2014.igem.org/Template:Team:Aachen/arduino_single.ino?action=raw Sketchbook (.ino)]<br />
* Arduino Code for combined device [https://2014.igem.org/Template:Team:Aachen/arduino_combined.ino?action=raw Sketchbook (.ino)]<br />
<br />
You will need a special [http://www.exp-tech.de/images/product_images/description%20images/YWRobot/1602/LiquidCrystal_I2C1602V2.rar library] for the display, which can not be uploaded for legal reasons.<br />
<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.94||1.19||0.94||1.19<br />
|-<br />
! -!!Total OD!!-!!-!! 46.01 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! -!!Total F!!-!!-!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! -!!Total OD/F!!-!!-!! 53.44 !! 67.89 <br />
|-<br />
|}<br />
</center><br />
<br />
For more detailed economical information about the OD/F project visit our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
== Breadboards ==<br />
<br />
=== Optical Density ===<br />
<br />
{{Team:Aachen/Figure|Aachen ODdevice Steckplatine.png|align=center|title=Breadboard of our OD device|subtitle=To build your own OD device, connect the parts as shown in this diagram.|width=900px}}<br />
<br />
If you want to build our OD device, make sure to use the following secret ingredients:<br />
* Filter: [http://www.leefilters.com/lighting/colour-details.html#019 Fire 019]<br />
* LED: [http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== 600 nm] Dialight 550-2505F<br />
<br />
=== Fluorescence ===<br />
<br />
{{Team:Aachen/Figure|Aachen_Fdevice_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}}<br />
If you want to build the OD device, make sure to use the following secret ingredients:<br />
* Filter: [http://www.leefilters.com/lighting/colour-details.html#736 Twickenham Green 736]<br />
* LED: [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html 480 nm] NSPBR70BSS LED<br />
<br />
=== Combined Device ===<br />
Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing.<br />
All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino.<br />
Right at the bottom we present you the differences in wiring things up.<br />
Building the combined device is straight forward and very similar to the single device. You will need a slightly larger connector, a different lid for your case, and maybe more cables. The changed fritzing-layout is presented below.<br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_combined_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}}<br />
<br />
== Construction Steps ==<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_ODF_9.JPG|300px]] || First we want to assemble the casing. Once you have all the cut parts, you can start to assemble them. For cutting, we really recommend using a laser cutter.<br />
|-<br />
| [[File:Aachen_ODF_8.JPG|300px]] || Attach the cuvette-holder holders such that the cuvette holder is placed directly under the opening hole.<br />
|-<br />
| [[File:Aachen_ODF_4.JPG|300px]] || Next build the lid of the device. At this stage you can already mount the button. We recommend to glue any parts.<br />
|-<br />
| [[File:Aachen_ODF_3.JPG|300px]] || Your lid finally should look like this.<br />
|-<br />
| [[File:Aachen_ODF_11.JPG|150px]][[File:Aachen_ODF_10.JPG|150px]] || Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole! Please attach a piece of filter foil (approx. $7 \times 7 mm^2$) from the inside in front of the light to frequency converter. Forceps is highly recommended.<br />
|-<br />
| [[File:Aachen_ODF_12.JPG|300px]] || Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue!<br />
|-<br />
| [[File:Aachen_ODF_14.JPG|300px]] || As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins, 9pins for combined) and connect them as we did.<br />
|-<br />
| [[File:Aachen_ODF_1.JPG|300px]] || Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard.<br />
|-<br />
| [[File:Aachen_ODF_2.JPG|300px]] || Then connect the button to 5V on the one side, and to GND via a resistor on the other side. Connect this side also to port __ on your Arduino. This will sense the blank. Next connect the display to the Arduino and our connector. See the Fritzing diagram at the bottom for a detailed information.<br />
|-<br />
| [[File:Aachen_ODF_13.JPG|300px]] || Now put everything into the case and ...<br />
|-<br />
| [[File:Aachen_ODF_6.JPG|300px]] || ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing.<br />
|-<br />
| [[File:Aachen_ODF_7.JPG|300px]] || Congratulations! You have finished constructing your own OD/F device!<br />
|-<br />
| [[File:Aachen_zwei_Kuevetten.jpg|300px]] || ... or even the combined device!<br />
|}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== References ==<br />
Lawrence, J. V., & Maier, S. (1977). Correction for the inherent error in optical density readings. Applied and Environmental Microbiology, 33(2), 482–484. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=170707&tool=pmcentrez&rendertype=abstract.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/ODFTeam:Aachen/Notebook/Engineering/ODF2014-10-17T19:27:38Z<p>J.plum: </p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
{{Team:Aachen/Stylesheet}}<br />
= OD/F Device =<br />
<br />
On this page we present the technical details of our OD/F device. You can skip to specific chapters by clicking on the panels below:<br />
<center><br />
<html><ul class="team-grid" style="width:1064px;"><br />
<!-- Overview --><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#dev" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br><br />
<b>General Considerations</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#od" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>OD Device</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/04/Aachen_Cuvette_button_v1_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#f" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>F Device</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
Building the OD/F device has been an interesting task. On the one hand, this device has been developed mainly by the IT division of our team. On the other hand, we got assistance from biologists suffering from color-blindness, yet eager to help selecting the best color filters for the LEDs.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
= General Considerations =<br />
<span class="anchor" id="dev"></span><br />
<br />
=== Measuring Principle ===<br />
<br />
The measuring principle for both optical density (OD) and fluorescence measurement is depicted below.<br />
For OD measurement we shine through the sample with an LED and a fixed width. A filter blocks any other light but 600&nbsp;nm. This way, the sensor mainly senses the 600&nbsp;nm light which is needed for OD600 measurement.<br />
<br />
For fluorescence measurement a similar approach is chosen. The filter again is used to block the exciting light from being sensed. That way only the emitted light from the fluorescence protein is measured.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
The details about selecting filters, code and a construction manual follows.<br />
<br />
=== Cuvette Holder ===<br />
The essential part of this device is the '''cuvette holder which has also been the most tricky thing to design'''. In short, we had to overcome a dilemma created by the need for an optimal height for the sensor:<br />
* A too low sensor position bears problems with sedimentation as well as light diffraction from the bottom of the cuvette.<br />
* The sensor has to be as close as possible to the bottom so that enough light shines through for the fluorescence measurement.<br />
<br />
As a compromise, we place the sensor at a height of 0.75&nbsp;cm, which, as it turned out later, is very close to one of the standard heights (0.2&nbsp;cm, 0.8&nbsp;cm, 1.2&nbsp;cm) of OD meters. It is important to note that despite the official minimal fill height of 1.2&nbsp;mL of the 1.5&nbsp;mL cuvettes we used, our device also works with filling volumens of just 1&nbsp;mL which in fact comes closer to reality in the lab.<br />
<br />
The final cuvette holder design is rendered from a [https://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=raw stl-file] shown below:<br />
<br />
<html><br />
<center> <br />
<iframe src="https://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=render<br />
" width=500px height=500px frameBorder="0"></iframe><br />
</center><br />
</html><br />
<br />
=== Light Filters ===<br />
Once the cuvette holder was finished, '''finding good filters was a tough challenge'''. A main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters unfortunately could not be considered. Instead, filters used for illumination of theaters seemed to be an ideal solution.<br />
<br />
Especially for the fluorescence measurements of GFP finding the right filter has been a big problem. [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501&nbsp;nm and a peak emission at 511&nbsp;nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485&nbsp;nm reduce false positive results below 500&nbsp;nm. However, no adequate filter for these settings could be found.<br />
Eventually, using the dark greenish [http://leefilters.com/lighting/colour-details.html#736 Twickenham Green] filter only little amounts of light shorter than 500&nbsp;nm gets through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20% only, for the target emission wavelength of 511&nbsp;nm.<br />
<br />
For the OD measurement, too, we had similar problems. Indeed, due to our goal of inexpensive parts, we only filter light below 600&nbsp;nm. Further filters would lower the base transmittance and result in a loss of resolution which is not tolerable.<br />
Finally the red filter [http://leefilters.com/lighting/colour-details.html#019 Fire] permits over 70&nbspr; of the light to the sensor and is thus suited for our purposes.<br />
<br />
The following LED and filter combination has been chosen by us:<br />
<br />
{| class="wikitable"<br />
! Mode<br />
! Fluorescence Protein<br />
! Filter<br />
! Peak Excitation<br />
! Peak Emission<br />
|-<br />
| Fluorescence<br />
| GFPmut3b<br />
| Twickenham Green<br />
| 501nm<br />
| 511nm<br />
|-<br />
| Optical Density<br />
| --<br />
| Fire<br />
| 600nm<br />
| 600nm<br />
|}<br />
<br />
<html><br />
<sup><span class="anchor" id="fn1"></span>1. Quite a good random number generator from a computer-scientific perspective!<a href="#ref1" title="">↩</a></sup><br />
</html><br />
<br />
== Linearity ==<br />
<span class="anchor" id="lin"></span><br />
As for any scientifc device it is crucial to question the results one gets from the device. To ensure that our device actually works, we performed a set of measurements which are presented below.<br />
<br />
It is crucial that the selected hardware is mapping reality into the digital world of our $\mu$-Controller.<br />
In order to sense reality our setup uses a light to frequency sensor, [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf TSL235R-LF].<br />
The light to frequency sensor resembles the most to a photo transistor and thus is less sensible to temperature than a light dependant resistor.<br />
Additionally counting a frequency using interrupts seems to be easier and more accurate than using the analog to digital converter.<br />
<br />
Using a dilution series of purified [https://2011.igem.org/Team:Glasgow/LOV2 iLOV] we could determine the characteristic curve for the light sensor. Finally we can conclude that the sensor is linear as expected and shown in the [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf datasheet].<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Linearity iFG.PNG|title=Linearity of TSL235R-LF sensor|subtitle=Dilution series of GFP expressing E. coli showing linearity between fluorescence count and dilution.|width=700px}}<br />
</center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
[[File:Aachen_Cuvette_button_v1_ipo.png|right|150px]]<br />
<br />
= OD Device =<br />
<span class="anchor" id="od"></span><br />
<br />
We are measuring optical density using the presented cuvette holder.<br />
Particularly for optical density measurement the amount of light shining through the sample is crucial.<br />
If there is too few light, there will be not enough light registered at the sensor, and the resolution of the measurement shrinks. This should be prevented.<br />
The chosen light to frequency sensor is reported to be very sensitive on the amount of light shining on it.<br />
There are reports of the sensor breaking when put into [https://www.sparkfun.com/products/9768 sunlight on a nice day], and not being sensitive at both high light or low light [http://kesslerarduino.wordpress.com/author/kevinmkessler/page/2/ conditions].<br />
<br />
Commercial systems usually use a laser beam to shine through the sample. For reasons of available components, we omitted this in our plans. Finding a suitable orange laser is not easy.<br />
Instead we chose an LED, which unfortunately scatters light, both in the spectrum as well as in all directions.<br />
Using a filter we reduce the effect of scattering.<br />
Finally the [http://leefilters.com/lighting/colour-details.html#019 Fire 019] filters solves our problems, but is far away from ideal.<br />
<br />
== Evaluation ==<br />
=== From Transmittance to True Optical Density ===<br />
At very low levels, uncorrected photometric determinations of cell densities show a decreasing proportionaility to actual cell density.<br />
<br />
This can also be observed using our OD measurement device.<br />
<br />
In general, photometric determination of bacterial concentrations depends primarily on light scattering, rather than light absorption. Therefore. often not absorption is measured, but transmittance. For this, the relationship between optical density (OD) and transmitted light $\frac{I_0}{I}$ exists as:<br />
<br />
$$ OD = \frac{I_0}{I} = \kappa \cdot c$$<br />
<br />
However, this equation is linear only in a certain range.<br />
While one can tackle this non-linearity by using dilutions of the culture, correcting the error systematically is another way to overcome this limitation.<br />
<br />
For our OD device we needed to correlate the transmittance measured by our sensor to an optical density anyway.<br />
Our team members from the deterministic sciences emphasized on the correction method, which was conducted according to Lawrence and Maier [1]:<br />
<br />
* The relative density ($RD$) of each sample in a dilution series is calculated using $\frac{min(dilution)}{dilution}$.<br />
* The uncorrected optical density is derived from the transmission T [%]: $OD = 2 - \log T$<br />
* Finally, the unit optical density is calculated as $\frac{OD}{TD}$.<br />
* The average of the stable unit optical densities is used to calculate the true optical density $ OD_{unit} \cdot RD $.<br />
This way, the correlation between transmission and true optical density can be computed.<br />
The derived function allows the conversion from transmission to optical density on our device and therefore calibrates our device.<br />
<br />
Lawrence and Maier could show that correcting transmittance this way, the corrected optical density shows a linear relationship between true optical density and dry weight in cell suspensions.<br />
<br />
In our experiments, we find in accordance to [1] that the correction majorly depends on the technical equipment used, especially the LED, sensor and cuvettes.<br />
While this at first sight looks disappointing, it is also expected:<br />
Transmittance is the fraction of light not absorbed by some medium relative to the cell-free and clear medium.<br />
However, the transmittance is not only dependent on the amount of cells in the way of the light's beam, but also how much light shines through the cuvette in which fashion, and in which fraction is received by the sensor in which angles.<br />
<br />
Using the above formula we performed this experiment for Pseudomonas putida and Saccharomyces cerevisiae.<br />
<br />
=== Experiments ===<br />
<br />
We performed several experiments during the development of the OD/F device.<br />
Finally we can relate the measured transmittance to the true Optical Density, and further, we can relate that true OD to the one of the photospectrometer in our lab.<br />
By doing to we can calibrate our device to meaningful values.<br />
<br />
We have done this according to the previous section for Pseudomonas putida and Saccharomyces cerevisiae.<br />
<br />
The final function for calculating the OD from the transmission calculated by our device can be calculated as<br />
<br />
$$ OD = f(T) \circ g(device) $$<br />
<br />
where $f$ transforms transforms transmittance to true optical density for our device, and $g$ transforms true optical density of our device into the true optical density of the photospectrometer. This way our device is calibrated according to the photospectrometer.<br />
<br />
==== ''Pseudomonas putida'' ====<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida iFG.PNG|title=True Optical Density to Transmittance plot for P. putida|subtitle=|width=700px}}<br />
</center><br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida OD iFG.PNG|title=Corrolating the true optical density of the OD/F device to true optical density of the photospectrometer|subtitle=|width=700px}}<br />
</center><br />
<br />
==== ''Saccharomyces cerevisiae'' ====<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer iFG.PNG|title=True Optical Density to Transmittance plot for S. cerivisiae|subtitle=|width=700px}}<br />
</center><br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer OD iFG.PNG|title=Corrolating the true optical density of the OD/F device to true optical density of the photospectrometer|subtitle=|width=700px}}<br />
</center><br />
<br />
From these plots it can first be seen that our device delivers robust and reproducible results for both procaryotes and eucaryotes.<br />
Also the function from transmittance to true od can be expressed as a lower polynomial function, making its calculation easily possible on a low-end device like a microcontroller.<br />
<br />
Most encouraging is that the function for relating the true OD of our device to the photospectrometer is, as seen by the regression coefficient, close together for both ''P. putida'' and ''S. cerivisae''. In fact, 3.416 and 3.461 are such close together, that the minor deviation could be just measuring inaccuracy.<br />
Therefore we fix the regression coefficient for converting true OD of our device to true OD of the photospectrometer to 3.432 .<br />
<br />
It is interesting to note, that also the function $f$ for the conversion of transmittance to true optical density fit nicely together, as can be seen in the following figure.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_ODallstrains1.png|title=Transmission of different cell types at OD-values from 0.001-1|subtitle=The transmittance data of NIH&nbsp;3T3 cells align with the transmittance of ''P.&nbsp;putida'' and ''S.&nbsp;cerevisiae'' strains, even though the measured optical densities are lower by 1-2 orders of magnitude.|width=800px}}<br />
</center><br />
<br />
By this evaluation we have shown that our self-build optical density measurement device can compete with commercial systems, and moreover, is easy to calibrate by just calculating the true optical density.<br />
Therefore we present a device which measures accurately and is made of easily available parts at a low cost.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_17-10-14_Glowing_cuvette-ipo.png|right|150px]]<br />
<br />
= F device =<br />
<span class="anchor" id="f"></span><br />
<br />
Similarly to the OD measurement, the fluorescence is measured using the same cuvette holder. In fact, if one does not build a combined device, the only thing one is supposed to change is the cuvette holder. <br />
However, as for optical density measurement, a filter needs to be placed between led, sample and the light sensor.<br />
Selecting the filter has been troublesome.<br />
Either the tried filters had a good transmittance but did not screen for the correct wavelength, or they screened for the correct wavelength but showed bad transmittance.<br />
Finally we chose the [ Twickenham green] filter with bad transmittance, and raised the sampling interval from 1&nbsp;s to 4&nbsp;s to allow a distinct signal.<br />
This is by far not optimal, but delivers stable and reliable results.<br />
<br />
For fluorescence measurement we luckily are not that much relying on the optical density of the cell culture to measure (if the sample contains cells at all).<br />
We compared the values of our device against the [https://2014.igem.org/Team:Aachen/Notebook/LabEquipment platereader].<br />
<br />
== Evaluation ==<br />
Figure 1 shows the absolute measurements for both the platereader and our OD/F device. The abrupt jump at 50% concentration can be explained by a second dilution step and is prevalent in both devices.<br />
It can be seen that the platereader show a much higher difference between the GFP and non-GFP cell culture at a higher standard deviation.<br />
Another interesting metric is the difference between the GFP and non-GFP, which can be seen as the normalized fluorescence measure.<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachn 15-10-14 F platereader ODF iFG.PNG|title=Fluorescence Measurement comparison OD/F device and Platereader|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F device shows no significant.|width=700px}}<br />
</center><br />
<br />
If one compares the results there, as in Figure 2, interesting observations can be made.<br />
First, both platereader and OD/F device show very similar results.<br />
The regression curves differ only in a linear factor.<br />
Most interestingly the general fit of the OD/F device to a linear function seems to be better than the platereader.<br />
Overall the linearity which has been observed earlier (in testing the general setup) could be verified.<br />
Therefore our do-it-yourself OD/F device can be used to determine fluorescence.<br />
At higher concentrations our OD/F device struggles regarding accuracy. However, this is also true for the platereader, but at a lower rate.<br />
<br />
<br />
<center><br />
{{Team:Aachen/Figure|align=center|Aachen 15-10-14 F platereader ODF2 iFG.PNG|title=Fluorescence Measurement comparison OD/F device and Platereader|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F device shows no significant. A non-GFP expressing E. coli dilution has been used to normalize the GFP dilution series. A linear correlation can be seen.|width=700px}}<br />
</center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How to Build Your Own Device =<br />
<span class="anchor" id="diy"></span><br />
== Technical Components ==<br />
<br />
While the casing and the cuvette holder are custom made, most of the parts are pre-made and only need to be bought. The previous section lists all needed parts. To get all these parts for creating your own OD/F device is easy by using the internet. A lot of companies all over the world are specialized in selling electronically equipment not only in the internet but also in local shops. However '''potential customers have a market access''' connected to the parts of building. <br />
<br />
Please find our custom parts for download below. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F device a test :) ! <span class="anchor" id="ref2"></span><br />
<br />
* cuvette holder [https://2014.igem.org/Template:Team:Aachen/cuvette.stl?action=raw STL file]<br />
* casing single device [ SVG file]<br />
* casing combined device [ SVG file]<br />
* Arduino Code for single device [https://2014.igem.org/Template:Team:Aachen/arduino_single.ino?action=raw Sketchbook (.ino)]<br />
* Arduino Code for combined device [https://2014.igem.org/Template:Team:Aachen/arduino_combined.ino?action=raw Sketchbook (.ino)]<br />
<br />
You will need a special [http://www.exp-tech.de/images/product_images/description%20images/YWRobot/1602/LiquidCrystal_I2C1602V2.rar library] for the display, which can not be uploaded for legal reasons.<br />
<br />
<br />
'''Table 2''': Needed number of pieces, components and prices for creating your own OD or F device<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs € !! Costs $ !! Final € !! Final $ <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]|| - € || $11.65 || 9.17 € || $11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]|| - € || $3.14 || 2.47 € || $3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]|| - € || $3.28 || 2.58 € || $3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]|| - € || $1.99 || 1.57 € || $1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]|| - € || $3.69 || 2.90 € || $3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]|| - € || $2.00 || 1.57 € || $2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]|| - € || $0.11 || 0.09 € || $2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]|| - € || $2.51 || 1.98 € || $2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]|| - € || $2.80 || 2.20 € || $2.80 <br />
|-<br />
| 1||cuvette holder (3D print service of your choice)|| 6.44 € || $8.18 || 6.44 € || $8.18 <br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)|| 7.98 € || $10.14 || 7.98 € || $10.14 <br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]|| - € || $2.88 || 2.27 € || $2.88 <br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]|| - € || $2.72 || 2.14 € || $2.72 <br />
|-<br />
| || || || || || <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]|| 0.99 € || $1.11 || 0.87 € || $1.11 <br />
|-<br />
! Total OD !!!!!!!! 45.94 € !! $58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480nm]|| 0.99 € || $1.26 || 0.99 € || $1.26 <br />
|-<br />
! Total F !!!!!!!! 46.06 € !! $58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]|| 0.99 € || $1.11 || 0.87 € || $1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480nm]|| 0.99 € || $1.26 || 0.99 € || $1.26 <br />
|-<br />
! Total OD/F !!!!!!!! 47.05 € !! $59.78 <br />
|-<br />
|}<br />
<br />
For more detailed economical information about the OD/F project visit our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
== Breadboards ==<br />
<br />
=== Optical Density ===<br />
<br />
{{Team:Aachen/Figure|Aachen ODdevice Steckplatine.png|align=center|title=Breadboard of our OD device|subtitle=To build your own OD device, connect the parts as shown in this diagram.|width=900px}}<br />
<br />
If you want to build our OD device, make sure to use the following secret ingredients:<br />
* Filter: [http://www.leefilters.com/lighting/colour-details.html#019 Fire 019]<br />
* LED: [http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== 600 nm] Dialight 550-2505F<br />
<br />
=== Fluorescence ===<br />
<br />
{{Team:Aachen/Figure|Aachen_Fdevice_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}}<br />
If you want to build the OD device, make sure to use the following secret ingredients:<br />
* Filter: [http://www.leefilters.com/lighting/colour-details.html#736 Twickenham Green 736]<br />
* LED: [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html 480 nm] NSPBR70BSS LED<br />
<br />
=== Combined Device ===<br />
Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing.<br />
All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino.<br />
Right at the bottom we present you the differences in wiring things up.<br />
Building the combined device is straight forward and very similar to the single device. You will need a slightly larger connector, a different lid for your case, and maybe more cables. The changed fritzing-layout is presented below.<br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_combined_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}}<br />
<br />
== Construction Steps ==<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_ODF_9.JPG|300px]] || First we want to assemble the casing. Once you have all the cut parts, you can start to assemble them. For cutting, we really recommend using a laser cutter.<br />
|-<br />
| [[File:Aachen_ODF_8.JPG|300px]] || Attach the cuvette-holder holders such that the cuvette holder is placed directly under the opening hole.<br />
|-<br />
| [[File:Aachen_ODF_4.JPG|300px]] || Next build the lid of the device. At this stage you can already mount the button. We recommend to glue any parts.<br />
|-<br />
| [[File:Aachen_ODF_3.JPG|300px]] || Your lid finally should look like this.<br />
|-<br />
| [[File:Aachen_ODF_11.JPG|150px]][[File:Aachen_ODF_10.JPG|150px]] || Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole! Please attach a piece of filter foil (approx. $7 \times 7 mm^2$) from the inside in front of the light to frequency converter. Forceps is highly recommended.<br />
|-<br />
| [[File:Aachen_ODF_12.JPG|300px]] || Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue!<br />
|-<br />
| [[File:Aachen_ODF_14.JPG|300px]] || As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins, 9pins for combined) and connect them as we did.<br />
|-<br />
| [[File:Aachen_ODF_1.JPG|300px]] || Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard.<br />
|-<br />
| [[File:Aachen_ODF_2.JPG|300px]] || Then connect the button to 5V on the one side, and to GND via a resistor on the other side. Connect this side also to port __ on your Arduino. This will sense the blank. Next connect the display to the Arduino and our connector. See the Fritzing diagram at the bottom for a detailed information.<br />
|-<br />
| [[File:Aachen_ODF_13.JPG|300px]] || Now put everything into the case and ...<br />
|-<br />
| [[File:Aachen_ODF_6.JPG|300px]] || ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing.<br />
|-<br />
| [[File:Aachen_ODF_7.JPG|300px]] || Congratulations! You have finished constructing your own OD/F device!<br />
|-<br />
| [[File:Aachen_zwei_Kuevetten.jpg|300px]] || ... or even the combined device!<br />
|}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== References ==<br />
Lawrence, J. V., & Maier, S. (1977). Correction for the inherent error in optical density readings. Applied and Environmental Microbiology, 33(2), 482–484. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=170707&tool=pmcentrez&rendertype=abstract.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T19:26:10Z<p>J.plum: </p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
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<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. The placed it into a aluminium casing for security reasons. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T19:24:45Z<p>J.plum: /* Technical Components */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. The placed it into a aluminium casing for security reasons. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T19:23:17Z<p>J.plum: /* Technical Components */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information on ''WatsOn'' and on the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. The placed it into a aluminium casing for security reasons. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T19:22:34Z<p>J.plum: /* DIY: How To Build Your Own WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information on ''WatsOn'' and on the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''WatsOn''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. The placed it into a aluminium casing for security reasons. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T19:20:34Z<p>J.plum: /* WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.94||1.19||0.94||1.19<br />
|-<br />
! -!!Total OD!!-!!-!! 46.01 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! -!!Total F!!-!!-!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! -!!Total OD/F!!-!!-!! 53.44 !! 67.89 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T19:19:48Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.94||1.19||0.94||1.19<br />
|-<br />
! -!!Total OD!!-!!-!! 46.01 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! -!!Total F!!-!!-!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! -!!Total OD/F!!-!!-!! 53.44 !! 67.89 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T19:17:23Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.94||1.19||0.94||1.19<br />
|-<br />
! Total OD !!!!!!!! 46.01 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 53.44 !! 67.89 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T19:11:15Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.94||1.19||0.94||1.19<br />
|-<br />
! Total OD !!!!!!!! 46.01 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T18:55:35Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||1.08||1.19||1.08||1.19<br />
|-<br />
! Total OD !!!!!!!! 46.15 !! 58.45 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.19||0.87||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T18:52:09Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.19||0.87||1.19<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.19||0.87||1.19 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-17T18:29:43Z<p>J.plum: </p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh 1===<br />
<br />
This part is an RFC &#91;25&#93; dark quencher that is based upon K1319000 (the RFC [25] version of E0030/EYFP).<br />
Two mutations were introduced that eliminated fluorescence:<br />
<br />
*L90I<br />
*Y145W<br />
<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realised and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh 1 in proximity to each other which allows GFP and REACh 1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh 1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows for a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh 1 cancelling the FRET interaction and providing a GFP fluorescence response. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh 2===<br />
<br />
This part is an RFC &#91;25&#93; dark quencher that is based upon K1319000 (the RFC [25] version of E0030/EYFP).<br />
Three mutations were introduced that eliminated fluorescence:<br />
<br />
*L90I<br />
*Y145W<br />
*H148R<br />
<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realised and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh 2 in proximity to each other which allows GFP and REACh 2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh 2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows for a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh 2 cancelling the FRET interaction and providing a GFP fluorescence response. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
The trunkated galectin-3 is a 26&nbsp;kDa protein that binds certain LPS patterns.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was codon-optimized for expression in ''E. coli''. The part contains the S219V anti-self cleavage mutation. <br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces the [http://parts.igem.org/Part:BBa_K1319004 TEV protease] when induced with IPTG in a DE3 strain or if combined with a T7 RNA-Polymerase generator.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses K1319000 behind a J23101 constitutive promotor.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses K1319001 behind a J23101 constitutive promotor.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses K1319002 behind a J23101 constitutive promotor.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a E0040.K1319001 fusion protein (GFP-REACh1) behind a J23101 promotor. The linker between the two proteins contains a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] [http://parts.igem.org/Part:BBa_K1319016 cleavage site].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a E0040.K1319002 fusion protein (GFP-REACh1) behind a J23101 promotor. The linker between the two proteins contains a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] [http://parts.igem.org/Part:BBa_K1319016 cleavage site].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a E0040.K1319000 fusion protein (GFP-EYFP) behind a J23101 promotor.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-His (B0032.E1010.K1319003.K1319016.B0015).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Project/Measurement_DeviceTeam:Aachen/Project/Measurement Device2014-10-17T18:26:22Z<p>J.plum: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
{{Team:Aachen/FigureFloatRight|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=270px}}<br />
<html><br></html><br />
The ''WatsOn'' device aims to answer the central question "What's on the chip?". The device is designed to incubate the sensing cells and capture images. <html><br></html>The interactive ''WatsOn'' software enables the end user not only to take images and time lapse shootings, but also analyzes the images and visualizes the presence/absence of a pathogen.<br />
<br />
The construction manual and the technical details are published in our [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy wiki].<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Modus Operandi</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/thumb/c/c7/Aachen_WatsOn_easy.png/600px-Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonhardware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Hardware</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonsoftware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Software</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonmeasurarty" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measurarty</div></div><br />
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<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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== Modus Operandi ==<br />
<span class="anchor" id="watsonapplication"></span><br />
<br />
{{Team:Aachen/Figure|How_two_use_watsOn_flowsheet_V7_ipo.png|title=How to use ''WatsOn''|subtitle=This scheme illustrates handling WatsOn when testing the 2D biosensor chip for a fluorescent signal.|width=1000px}}<br />
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[[File:Aachen_14-10-16_Hardware_button_iNB.png|right|150px]]<br />
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== Hardware ==<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Elektronikkomponenten1.jpg|title=Hardware components|subtitle=From top left to bottom right: Arduino, Peltier element, Raspberry Pi, relay, cables, MOSFET, temperature display, camera, LEDs and resistors.|width=520px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen in the first section was build from laser cutted acrylic glass.<br />
<br />
The electronic circuit is a combination of the components displayed in the image above. We combined the Raspberry Pi - a small single-board computer running a Linux operating system - and an Arduino board which is a programmable microcontroller. The Arduino operates the excitation LEDs and a Peltier heater for incubation. For taking images of the sensor chips we used the Raspberry Pi camera module which is directly connected to the board.<br />
<br />
''WatsOn'' is designed such that it can be easily copied. Our work heavily emphasizes the Open Source concept. Therefore a detailed description of all components and the wiring can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware Engineering section of our Notebook].<br />
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<!-- [[File:Aachen_14-10-16_Software_button_iNB.png|right|150px]] --><br />
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== Software ==<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
{{Team:Aachen/FigureDual|Aachen_WatsOn_igem_GUI_originalImage.png|Aachen_WatsOn_igem_GUI_analyzedImage.png|title1=image taken with the camera |title2=analyzed image |subtitle1= |subtitle2= |width=500px}}<br />
<br />
The ''WatsOn'' software is responsible for presenting a user interface on the display of the device and to take images with the LED wavelength selected by the user. Therefore, it is separated into three single components: the graphical user interface (GUI) with a backend script running on the Raspberry Pi and the code on the Arduino board.<html><br/></html><br />
The GUI (left image) provides the user with the option to take a single image or a time lapse shooting and specify parameters for the camera and the wavelength of the LEDs. The wavelength used in our device are 480nm for GFP and 450nm for iLOV. Furthermore, the images are analysed for the presence or absence of P. aeruginosa by analysing the image and providing the user with a visual feedback (right image). All taken images can be saved to disk manually for single images and automatically for time lapse shootings.<html><br/></html><br />
Further details on the software including the backend which gives the possibility of using the GUI remotely on a different device (e.g. notebook) in the same local network can be found here [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware].<br />
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[[File:Aachen_14-10-16_Measurarty_button_iNB.png|right|150px]]<br />
<br />
== ''Measurarty'' ==<br />
<span class="anchor" id="watsonmeasurarty"></span><br />
<center><br />
{{Team:Aachen/Figure|Aachen_srm_regions_3.PNG|title=SRM component of our image analysis component ''Measurarty''|subtitle=SRM is one of the core components of our image analysis approach. This image shows the different regions created.|width=500px}}<br />
</center><br />
<br />
''Measurarty'' is the '''image analysis software''' of our device and is designed to allow an automatic segmentation and classification of our '''agar chip pictures'''.<br />
Therefore, it accepts an image from ''WatsOn'' as an input and produces an output image with pathogenic regions marked in red.<br />
<br />
This component mainly focuses on recognizing pathogens early, such that pure thresholding is not necessary.<br />
We therefore designed a pipeline and established a smoothness index to make statements about the pathogenity of a chip as early as possible, but also with as much certainty as possible.<br />
<br />
A sample output of the segmentation is presented below, showing that the pipeline works as intended.<br />
<br />
{{Team:Aachen/FigureDual|Aachen_K131026_Pseudomonas_aeruginosa_detection.gif|Aachen_Pseudomonas_aeruginosa_Measurarty_slower.gif|title1=Detection of ''Pseudomonas aeruginosa'' with K131026|title2=Optimized detection of ''Pseudomonas aeruginosa"" using ''Measurarty''|subtitle1=Direct detection of ''Pseudomonas aeruginosa'' on sensor chips. Sensor cells used were K131026.|subtitle2=''Measurarty'' is able to reliably identify the fluorescence response of the sensor cells which is produced in a response to ''Pseudomonas aeruginosa''.|width=480px}}<br />
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{{Team:Aachen/BlockSeparator}}<br />
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[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="watsonachievements"></span><br />
<br />
We developed ''WatsOn'' to meet the following requirements: i.e. the device<br />
*incubates the sensing cells and the sampling chip <br />
*illuminates the chip with the right excitation wavelength for our fluorescence proteins<br />
*takes pictures and time lapse shootings of the chips<br />
*uses cheap filter slides to block the light emitted from the LEDs<br />
*analyzes the fluorescence signal<br />
*gives feedback to the user about the presence or absence of P. aeruginosa through a GUI (graphical user interface)<br />
*prevents escape of potentially sampled pathogens and our genetically engineered cells<br />
*is portable and fast in analyzing the images<br />
<br />
With our final device we achieved all of the above mentioned goal. ''WatsOn'' is housed in a closed casing and is able to take images and time lapse shooting using LEDs with required wavelengths, analyze the image and visualize the result.<br />
<br />
All technical details including laser cutting plans, the list of needed components, source codes for the different software and a building instruction are open-source and available on our wiki[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn].<br />
<br />
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{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T18:13:14Z<p>J.plum: /* Economical View */</p>
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[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do It Yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/OD/F_deviceTeam:Aachen/OD/F device2014-10-17T18:11:35Z<p>J.plum: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= OD/F Device =<br />
<br />
Measuring '''Optical Density''' (OD) or absorbance is one of the key and indispensable element in the field of microbiology. One question that has to be answered often is '''how many cells are in a suspension'''? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.<br />
<br />
Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive science research at a low cost.<br />
<br />
Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to '''simultaneously measure both fluorescence and OD'''. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfmeasuringprinciple" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measuring Principle</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfoutlook" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/67/Aachen_14-10-16_Outlook_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
== Measuring Principle ==<br />
<span class="anchor" id="odfmeasuringprinciple"></span><br />
<br />
Measuring Principle<br />
The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurement, the sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD{{sub|600}} measurement.<br />
<br />
For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.<br />
<br />
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F Device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=Our OD/F Device|subtitle= |width=650px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen 17-10-14 Glowing cuvette-ipo.png|right|150px]]<br />
<br />
== ''Modus operandi'' of OD/F Device==<br />
<span class="anchor" id="odfapplication"></span><br />
<br />
The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=|subtitle=|width=1000px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="odfachievements"></span><br />
<br />
When building the OD/F Device, '''our goal''' was to develop a system that<br />
<br />
* is straightforward to use<br />
* is at least as accurate as commercially available systems but at the same time costs significantly less<br />
* produces stable, reproducible results<br />
* weights little and is easy to carry around<br />
* uses widely available parts and is easy to build<br />
* can measured both optical density and fluorescence<br />
<br />
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-quality filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?<br />
<br />
[graphs showing the awesomeness of our OD/F Device]<br />
<br />
The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter.<br />
<br />
Have we been re-invented the wheel? No!<br />
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing. <br />
<br />
Regarding fluorescence, we are also not re-inventing the wheel. The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device and some proven commercial system to, for example, assess linearity of the measurement.<br />
<br />
We made a commercial assessment of the OD/F Device that results in a total cost of 60 $. The unit is built from light plexiglass for the casing and the compact design and weighs less than 200 g and can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] on our wiki.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
<br />
== Outlook ==<br />
<span class="anchor" id="odfoutlook"></span><br />
<br />
We have achieved a lot of our goals.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/OD/F_deviceTeam:Aachen/OD/F device2014-10-17T18:11:03Z<p>J.plum: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= OD/F Device =<br />
<br />
Measuring '''Optical Density''' (OD) or absorbance is one of the key and indispensable element in the field of microbiology. One question that has to be answered often is '''how many cells are in a suspension'''? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.<br />
<br />
Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive science research at a low cost.<br />
<br />
Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to '''simultaneously measure both fluorescence and OD'''. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfmeasuringprinciple" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measuring Principle</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfoutlook" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/67/Aachen_14-10-16_Outlook_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
== Measuring Principle ==<br />
<span class="anchor" id="odfmeasuringprinciple"></span><br />
<br />
Measuring Principle<br />
The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurement, the sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD{{sub|600}} measurement.<br />
<br />
For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.<br />
<br />
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F Device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=Our OD/F Device|subtitle= |width=650px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen 17-10-14 Glowing cuvette-ipo.png|right|150px]]<br />
<br />
== ''Modus operandi'' of OD/F Device==<br />
<span class="anchor" id="odfapplication"></span><br />
<br />
The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=|subtitle=|width=1000px}}<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="odfachievements"></span><br />
<br />
When building the OD/F Device, '''our goal''' was to develop a system that<br />
<br />
* is straightforward to use<br />
* is at least as accurate as commercially available systems but at the same time costs significantly less<br />
* produces stable, reproducible results<br />
* weights little and is easy to carry around<br />
* uses widely available parts and is easy to build<br />
* can measured both optical density and fluorescence<br />
<br />
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-quality filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?<br />
<br />
[graphs showing the awesomeness of our OD/F Device]<br />
<br />
The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter.<br />
<br />
Have we been re-invented the wheel? No!<br />
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing. <br />
<br />
Regarding fluorescence, we are also not re-inventing the wheel. The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device and some proven commercial system to, for example, assess linearity of the measurement.<br />
<br />
We made a commercial assessment of the OD/F Device that results in a total cost of 60 $. The unit is built from light plexiglass for the casing and the compact design and weighs less than 200 g and can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] on our wiki.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
<br />
== Outlook ==<br />
<span class="anchor" id="odfoutlook"></span><br />
<br />
We have achieved a lot of our goals.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/OD/F_deviceTeam:Aachen/OD/F device2014-10-17T18:10:03Z<p>J.plum: /* Achievements */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= OD/F Device =<br />
<br />
Measuring '''Optical Density''' (OD) or absorbance is one of the key and indispensable element in the field of microbiology. One question that has to be answered often is '''how many cells are in a suspension'''? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.<br />
<br />
Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive science research at a low cost.<br />
<br />
Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to '''simultaneously measure both fluorescence and OD'''. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfmeasuringprinciple" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measuring Principle</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfoutlook" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/67/Aachen_14-10-16_Outlook_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
== Measuring Principle ==<br />
<span class="anchor" id="odfmeasuringprinciple"></span><br />
<br />
Measuring Principle<br />
The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurement, the sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD{{sub|600}} measurement.<br />
<br />
For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.<br />
<br />
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F Device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=Our OD/F Device|subtitle= |width=650px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen 17-10-14 Glowing cuvette-ipo.png|right|150px]]<br />
<br />
== ''Modus operandi'' of OD/F Device==<br />
<span class="anchor" id="odfapplication"></span><br />
<br />
The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=|subtitle=|width=1000px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="odfachievements"></span><br />
<br />
When building the OD/F Device, '''our goal''' was to develop a system that<br />
<br />
* is straightforward to use<br />
* is at least as accurate as commercially available systems but at the same time costs significantly less<br />
* produces stable, reproducible results<br />
* weights little and is easy to carry around<br />
* uses widely available parts and is easy to build<br />
* can measured both optical density and fluorescence<br />
<br />
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-quality filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?<br />
<br />
[graphs showing the awesomeness of our OD/F Device]<br />
<br />
The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter.<br />
<br />
Have we been re-invented the wheel? No!<br />
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing. <br />
<br />
Regarding fluorescence, we are also not re-inventing the wheel. The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device and some proven commercial system to, for example, assess linearity of the measurement.<br />
<br />
We made a commercial assessment of the OD/F Device that results in a total cost of 60 $. The unit is built from light plexiglass for the casing and the compact design and weighs less than 200 g and can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] on our wiki.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
<br />
== Outlook ==<br />
<span class="anchor" id="odfoutlook"></span><br />
<br />
We have achieved a lot of our goals.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/OD/F_deviceTeam:Aachen/OD/F device2014-10-17T18:09:39Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= OD/F Device =<br />
<br />
Measuring '''Optical Density''' (OD) or absorbance is one of the key and indispensable element in the field of microbiology. One question that has to be answered often is '''how many cells are in a suspension'''? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.<br />
<br />
Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive science research at a low cost.<br />
<br />
Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to '''simultaneously measure both fluorescence and OD'''. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfmeasuringprinciple" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measuring Principle</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfoutlook" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/67/Aachen_14-10-16_Outlook_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]<br />
<br />
== Measuring Principle ==<br />
<span class="anchor" id="odfmeasuringprinciple"></span><br />
<br />
Measuring Principle<br />
The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurement, the sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD{{sub|600}} measurement.<br />
<br />
For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.<br />
<br />
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F Device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}<br />
</center><br />
<br />
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=Our OD/F Device|subtitle= |width=650px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen 17-10-14 Glowing cuvette-ipo.png|right|150px]]<br />
<br />
== ''Modus operandi'' of OD/F Device==<br />
<span class="anchor" id="odfapplication"></span><br />
<br />
The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=|subtitle=|width=1000px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="odfachievements"></span><br />
<br />
When building the OD/F Device, '''our goal''' was to develop a system that<br />
<br />
* is straightforward to use<br />
* is at least as accurate as commercially available systems but at the same time costs significantly less<br />
* produces stable, reproducible results<br />
* weights little and is easy to carry around<br />
* uses widely available parts and is easy to build<br />
* can measured both optical density and fluorescence<br />
<br />
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-quality filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?<br />
<br />
[graphs showing the awesomeness of our OD/F device]<br />
<br />
The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter.<br />
<br />
Have we been re-invented the wheel? No!<br />
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing. <br />
<br />
Regarding fluorescence, we are also not re-inventing the wheel. The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device and some proven commercial system to, for example, assess linearity of the measurement.<br />
<br />
We made a commercial assessment of the OD/F Device that results in a total cost of 60 $. The unit is built from light plexiglass for the casing and the compact design and weighs less than 200 g and can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] on our wiki.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
<br />
== Outlook ==<br />
<span class="anchor" id="odfoutlook"></span><br />
<br />
We have achieved a lot of our goals.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T17:58:27Z<p>J.plum: /* Cellock Holmes - A Case of Identity */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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= ''Cellock Holmes'' - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;margin-left:20px;"><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called ''Cellocks'', that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''''WatsOn'''''] , our measurement device. ''WatsOn'' is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;margin-left:20px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we provide the OD/F Device. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all technical details as well as construction manuals are published on our wiki. We demonstrate immediate application of the OD/F Device '''in schools, community labs and in the bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPracticesTeam:Aachen/PolicyPractices2014-10-17T17:54:36Z<p>J.plum: /* Economical View */</p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= Policy & Practices =<br />
<br />
During the past summer, we not only refined the technical and biological sides of ''Cellock Holmes'' but also considered other aspects of our iGEM project such as '''social acceptance''', '''biosafety''' and '''economical relevance'''. Will society accept the technology we develop? How can we convince skeptics that synthetic biology is safe? Does our product have economical relevance and how can we best market what we built? What is the target group that might benefit from our devices, and can we make our developments available to not only the privileged population but to everybody in the world? At the meetup of the German iGEM teams in Munich earlier this summer, we also prepared a suggestion on how to handle '''intellectual proporty rights on BioBricks'''.<br />
<br />
These are only a few of the questions we discussed within our team. To read more about the different aspects of our Policy & Practices work, please click on a panel below: <br />
<br />
<center><br />
<html><ul class="team-grid" style="width:1040px"><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppsocialacceptance" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Social Acceptance</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_14-10-13_Love_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbiosafety" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Biosafety</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/11/Aachen_14-10-13_Pathogen_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppeconomics" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Economical View</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/bd/Aachen_14-10-13_Money_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbbaip" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Intellectual Property on BioBricks</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9b/Aachen_14-10-14_IP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppblog" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Blog</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b8/Aachen_14-10-13_Blogger_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Love_Cell_iNB.png|right|150px]]<br />
<br />
== Spreading the Idea of Synthetic Biology ==<br />
<span class="anchor" id="ppsocialacceptance"></span><br />
<br />
How can we convince people that the technology we develop is safe to use and that the problems we tackle with our project concern everybody? Unfortunately, a lot people around the world are scared of genetically modified organisms and any application related to them. Though we believe that '''natural skepticism''' towards new and unproved technologies is not just good but especially desirable, the current fear some people encounter gene technology with is a bit disproportionate and might be counterproductive to technological and scientific advance in related fields.<br />
<br />
However, as reported, for example, in an [http://www.rundschau-online.de/magazin/gentechnik--risiko-oder-chance-,15184902,15929266.html article] published in a major local newspaper's magazine, Kölner Stadtanzeiger, the social acceptance of biotechnological products could be higher if people felt informed better and understood the underlying science. Following up on this, we thought about how we can inform people '''factually but in a comprehensible way''' about gene technology and synthetic biology. Before we talk about fancy devices in synthetic biology, how can we '''get down to the underlying issue''' of social rejection of gene technology in general? <br />
<br />
At the same time, '''young students''' interested in science and engineering are the most valuable future source of innovation. One day, they might be the researchers who develop the solutions to the most pressing issues of our world. For that reason, informing this group of people is of utmost importance and was therefore prioritized in our Policy & Practices work.<br />
<br />
Combining these two thoughts, we visited '''two schools''', the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] in Aachen and the [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] in Hilden, where we talked to students about synthetic biology and the iGEM competition, but also explained the scientific background and social aspects of our project. A delegation of our team also visited the [https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire MakerFaire] in Hannover, a family-friendly '''exhibition for tinkerers''' of all kinds, to spread the idea of synthetic biology and to discuss our project with the public. When we organized the [https://2014.igem.org/Team:Aachen/Meetup Aachen iGEM Meetup 2014], we also made sure to include a '''public part''' where all teams who participated in our meetup had the opportunity to present their project to a general audience.<br />
<br />
To read more about our different public projects, please click on the respective logo below.<br />
<br />
<html><ul class="team-grid" style="width:1064px;"><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b> Kaiser-Karls-Gymnasium</b><br />
<br/><br/><br />
Teaching Module "Synthetic Biology" for High Schools<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/f/f7/Aachen_14-10-10_Logo_Kaiser-Karls-Gymnasium.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> NEAnderLab </b><br />
<br/><br/><br />
In Cooperation with the Gymnasium an Neandertal<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/d/d8/Aachen_14-10-10_Logo_NEAnderLab.jpg); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> MakerFaire </b><br />
<br/><br/><br />
Visit of a DIY Exhibition<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/53/Aachen_14-10-10_Logo_MakerFaire.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Meetup" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> Aachen iGEM Meetup 2014 </b><br />
<br/><br/><br />
Including Public Presentations<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5b/Aachen_14-10-10_Meetup_Logo_white_background_iVA.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
</ul></html><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
== Biosafety ==<br />
<span class="anchor" id="ppbiosafety"></span><br />
<br />
Our iGEM team is committed to reflect all aspects of the entire project, including biosafety. From the beginning on, the team thoroughly discussed safety issues that could potentially arise with the implementation of ''Cellock Holmes''. The results of these discussions fundamentally influenced the design of [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''Watson''] and the choice of potential application fields. Read more about our safety considerations on our [https://2014.igem.org/Team:Aachen/Safety Safety] page.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Money_Cell_iNB.png|right|150px]]<br />
<br />
== Economical View ==<br />
<span class="anchor" id="ppeconomics"></span><br />
<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific advance'''<br />
<br />
For both our [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] and our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device], we are following an economical strategy focused on the open source principle. Low cost and the use of easily available parts have '''heavily influenced the design choices''' made when developing our devices. You can find more information on our page [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View].<br />
<br />
{{Team:Aachen/Figure|Aachen Social Vision.png|width=800px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-14_IP_iNB.png|right|150px]]<br />
<br />
== Intellectual Property on BioBricks ==<br />
<span class="anchor" id="ppbbaip"></span><br />
<br />
During the meetup of the German iGEM teams from 23rd to 25th May also workshops took place in which amongst others we discussed the topic of bioethics. Moral questions were addressed, regarding the value of life and human influence on it, as well as questions dealing with the possible socioeconomic effects of synthetic biology.<br />
<br />
Especially the topic of an '''open source vs. patent''' controlled field accounted for a large part of the discussion. During the discussion one student brought up the point that the legal status of parts in registry remains unclear, and that there are parts where only upon a closer look it becomes clear that the rights are company–owned. Because the issue of '''uncertain legal status of parts''' in the registry persists, the German iGEM teams '''wrote a proposal''' on how to deal with intellectual property rights in the Registry of Standard Biological Parts.<br />
<br />
For for information on intellectual property on BioBricks, read the [https://2014.igem.org/Team:Aachen/PolicyPractices/BioBrickIntellectualProperty full proposal] the German iGEM teams composed.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Blogger_Cell_iNB.png|right|150px]]<br />
<br />
== Blog ==<br />
<span class="anchor" id="ppblog"></span><br />
<br />
On our [https://2014.igem.org/Team:Aachen/Blog Blog] we post entries about recent news concerning our team's work and activities. We also write about general news from the field of synthetic biology, biotechnology and medicine. <br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T17:51:50Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low-budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the '''principle of open source''' including both open hardware and open software, information where to get the necessary components, quantities, step-by-step technical construction manuals and circuit diagrams are '''published online for free'''. Potential customers can follow our provided instructions and acquire information from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering Engineering page]. Therefore, our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to '''spread the idea of open hardware''', too. In accordance with the motto "Do it yourself!" (DIY) we offer low-budget versions through reducing costs at as many points as possible, except for the basic costs for material. Customers with a little technical dexterity, motivation to try something new and who are keen to experiment can follow our step-by-step construction manual to create their own custom-made devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Social Vision.png|title=Social vision as economical strategy for creating access to low-budget technical equipment.|width=800px}}<br />
</center><br />
To make our product more user-friendly, we '''considered offering device kits'''. When offering kits customers do not have to order a lot of separate device parts from different suppliers. However, this introduces the disadvantage of a '''loss of flexibility'''. Yet it is very important to have the '''opportunity to modify''' the devices, for example, by choosing alternative parts or including add-ons, because research requiring novel techniques advances quickly in the natural sciences. With our concept, improvements and adjustments are thus immediately realizable.<br />
<br />
Lastly, we want to mention that our vision is limited because it is incompatible with capitalism which rules the global market. Generally, companies are profit oriented and follow a different economical strategy than our iGEM team. As '''non-profit concept''', our idea is therefore limited to a group of customers with lower budgets. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor] has been designed according to our social vision. So far, we have not found comparable devices on the market. Here, we definitely take a pioneer role. Following our DIY concept, you can create your own ''WatsOn'' for '''just $310''' using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn construction manual]. All components for putting a ''WatsOn'' together are easily available all over the world using the following links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices in combination with the DIY concept opens a grand new customer market and lets our device '''compete with commercially available products'''. Especially in developing counties our ''WatsOn'' could help improve health infrastructure since high cost are eliminated as an obstacle. The low material costs and the high technical flexibility turn ''WatsOn'' into an adequate device for developing countries, community labs and the biohacking scene. Particularly for developing countries, such a low-budget device poses a '''good alternative to regular devices''' for detecting pathogens and other bacteria. With our device, we create access to modern technology and working methods for everybody.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
For ''WatsOn'', we offer both the construction manual and the image processing software ''Measurarty''. Since we do not offer everything in one kit, it is possible for the user to modify the device and software according to personal needs such as '''adjusting the range od detectable microorganisms'''. By engineering the ''Cellocks'' detection of other pathogens is theoretically possible. However, please always mind the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens. Moverover, it is possible to detect not just the fluorescence of GFP and iLOV. Just by changing the filters and/or LEDs, the device can be modified such that the fluorescence '''other regularly used reporter proteins like YFP, CFP or RFP can be detected'''. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device, we '''offer a low-cost solution for community labs, biohackers and high schools'''. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and disadvantes of our OD/F Device compared to commercially available devices|subtitle=We compared the devices in portability, affordability, reliability, user-friendliness, capabilities, precision and accuracy.|width=400px}}<br />
</center><br />
<br />
For an economic analysis, we deal with F Device and the OD Device separately. The reason for this is the bad comparability to commercial devices. Latter do not combine the measurument of fluorescence and OD while being in the same product class of small, portable devices. With our OD/F Device, we offer a '''solution to combine both measurement methods in one mobile device'''. With the instructions provided by us it possible to either build an OD Device or an F Device or an OD/F Device. We are offering a high degree of flexibility by enabling the user to modify our device according to own ideas and wishes. <br />
<br />
Both portability and low cost are two out of several factors that we heavily place importance on. Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, cost $1.250 or more, and can measure optical density only. On top of that, they are heavy, hardly portable and therefore not easy to handle. However, they are able to work with a broader range of wavelengths and show higher accuracy and precision. For measuring fluorescence, devices such as [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate readers] are available. Yet comparing a commercial device with our F Device is really difficult because we could not find one that is both portable and able to measure at 480&nbsp;nm.<br />
<br />
To compare our device to another commercially availalbe system we chose the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures the OD at 600&nbsp;nm, too, but costs almost $920. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy $60] as shown in the chart on the left. The '''cost savings''' here are round about '''$850''', money that could definetly be invested into other research projects or equipment instead. Nonetheless, one weakness of our device is the low reliability compared to commercial devices. This is due to use of low cost materials. Prices are given in both Euro and US-Dollar for better accountability and easy conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191o Male Headers]||2.14||2.72||2.14||2.72<br />
|- style="border-top: 2px solid #808080;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|- style="border-top: 2px solid #808080;;"<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
To build your own OD/F Device, all you have to do is order the required parts listed above, invest some time and have a little technical dexterity. This DIY aspect could also have a positive learning effect, for example, for students in schools, universities and other educational institutions. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperations with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab], one of our target groups '''already gathered first experience''' using our OD/F Device. This proves that our device is suitable for school everday life. When working with the schools, we got a lot of positive feedback from the instructors as well as the students.<br />
<br />
In summary, in our OD/F Device, we see a piece of equipment to measure OD and fluorescence, two quantities regularly used in biology, that is open source and perfectly fit for low-budget instutions such as schools, universities, community labs and the biohacking scene.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/File:Aachen_Social_Vision.pngFile:Aachen Social Vision.png2014-10-17T17:50:46Z<p>J.plum: </p>
<hr />
<div></div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Protocols/detectionTeam:Aachen/Notebook/Protocols/detection2014-10-17T17:44:40Z<p>J.plum: /* Measurement of Fluorescence */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/detection" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">2D Detection of<br/>IPTG & HSL</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/22/Aachen_14-10-14_button_chip_manufacturing_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Culture_medium_and_conditions" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Culture Media</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/10/Aachen_14-10-13_Yellow_Flask_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Molecular_biological_methods" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Molecular biological methods</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/7/75/Aachen_14-10-14_Eppi_with_green_cells_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Analytical_methods" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Analytical methods</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/4/4d/Aachen_14-10-14_Lense_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
= 2D Detection of IPTG and HSL =<br />
<br />
The method of the chip production was developed by this year's iGEM Team Aachen with [https://2014.igem.org/User:Aschechtel Anna] as driving force and person in charge. A lot of parameters were tested and the final protocol for the production of the sensor chips the way there were used for detection in the project is published below.<br />
<br />
== Chip Production ==<br />
<br />
'''Cell Preparation'''<br />
<br />
# over night culture of sensor cells (50&nbsp;ml in a 250&nbsp;ml flask with) max. 16&nbsp;h<br />
# centrifuge all 50&nbsp;ml by 3000&nbsp;g for 10&nbsp;min at RT (21°C).<br />
# discard the supernatant<br />
# re-suspend the pellet in 1&nbsp;mL tempered (~21°C) LB-medium.<br />
<br />
<br />
'''Agar Preparation'''<br />
<br />
# autoclave 50&nbsp;ml medium with 1.5%(w/v) agarose (has to be multiplied with the number of chips prepared).<br />
# cool it down to 45°C in a water bath.<br />
<br />
<br />
'''Chip Preparation'''<br />
<br />
# mix the cooled medium with the cells by inverting gently.<br />
# pour it in the chip mold, avoiding bubble formation (!).<br />
# wait for approximately 20 min until the agar has solidified.<br />
# cut out the chips with a scalpel.<br />
# put two chips into a labeled petri dish and store additional 4 chips in labeled petri dishs in the refrigerator.<br />
# incubate two chips for 1&nbsp;h at 37°C prior to induction.<br />
<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen 14-10-09 flowsheet chip manufacturingV8 ipo.png|title=Sensor-chip manufacturing|subtitle=Scheme illustrating the work flow during chip production. For the production steps see above.|width=1000px}}<br />
</center><br />
<br />
== Measurement of Fluorescence ==<br />
<br />
For measurement of a fluorescence response in our sensor chips we used three different methods.<br />
<br />
'''First''', the '''Gel Doc™ XR+''' (BIO-RAD) was used, exciting with UV light for an exposure time of 1&nbsp;s.<br />
<br />
'''Second''', we used our own device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''''WatsOn'''''] with blue light for excitation (450 or 480&nbsp;nm) and special filters infront of the camera for selecting the appropriate emission spectrum. You can read even more about building your own WatsOn [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn here].<br />
<br />
'''Third''', we used the '''Synergy Mx microplate reader''' (BioTek), putting the sensor chips into the lid of a common clear well plate. GFP was measured with an excitation of 496&nbsp;±&nbsp;9&nbsp;nm and an emission of 516&nbsp;±&nbsp;9&nbsp;nm and iLOV with an excitation of 450&nbsp;±&nbsp;9&nbsp;nm and emission of 495&nbsp;±&nbsp;9&nbsp;nm.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/detection" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">2D Detection of<br/>IPTG & HSL</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/22/Aachen_14-10-14_button_chip_manufacturing_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Culture_medium_and_conditions" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Culture Media</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/10/Aachen_14-10-13_Yellow_Flask_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Molecular_biological_methods" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Molecular biological methods</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/7/75/Aachen_14-10-14_Eppi_with_green_cells_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:106px;margin-left: 12px;margin-right: 12px;" ><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols/Analytical_methods" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height:100px; width: 100px;" ><div class="menukachel" style="top: 10%; font-size: 14px;">Analytical methods</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/4/4d/Aachen_14-10-14_Lense_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height:100px; width: 100px;"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Software/MeasurartyTeam:Aachen/Notebook/Software/Measurarty2014-10-17T17:24:59Z<p>J.plum: /* Achievements */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
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<html><br />
<link rel="stylesheet" href="https://2014.igem.org/Team:Aachen/Scripts/highlight.pack.default.css?action=raw&ctype=text/css"><br />
<script src="https://2014.igem.org/Team:Aachen/Scripts/highlight.pack.js?action=raw&ctype=text/javascript"></script><br />
<script>hljs.initHighlightingOnLoad();</script><br />
</html><br />
<br />
= ''Measurarty'' =<br />
<br />
''Measurarty'' is the evil player in the game of ''Cellock Holmes'' and ''WatsOn''.<br />
Measurarty is the pathogen detection logic behind our project.<br />
Using our ''Measurarty'' algorithm, we want to automatically detect pathogens from the chip photos delivered by WatsOn, without human interaction.<br />
Besides reducing the risk of human errors, this makes our device usable by almost everyone.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#intro" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Intro</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/1b/Aachen_Measurarty_Intro_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#SRM" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">SRM!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/2d/Aachen_Puzzels_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#segment" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Segment!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/e1/Aachen_SEgment_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#classification" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Classify!</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/f/f9/Aachen_Classify_button.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 8px;margin-right: 8px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty#measurartyachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
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<br />
</ul><br />
</center><br />
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<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_Measurarty_Intro_button.png|right|150px]]<br />
<br />
== ''Measurarty'' - An Introduction ==<br />
<span class="anchor" id="intro"></span><br />
<br />
Our [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware device control software] is able to take images of incubated chips inside WatsOn. Yet, that does not bring the user closer to the answer of the question:<br />
<br />
<center>'''What's on the chip?'''</center><br />
<br />
In fact, answering this question seems trivial for a human: Just check whether a colony grown has grown on the chip and you're done. This task is even easier with our chip system, because these show fluorescence wherever a pathogen has been detected.<br />
<br />
But is this an easy task for a computer? Actually not. The task of automatic detection is tried by several disciplines in computer science, from pattern recognition over machine learning to by medical imaging chairs.<br />
<br />
Here, we would like to present a pipeline for this task that makes use of '''easy segmentation and classification algorithms'''.<br />
First, ''Measurarty'' segments the target image using '''Statistical Region Merging (SRM)''' in order to find regions of similar properties. After this step, we can segment the picture using '''histogram thresholding''' in [http://en.wikipedia.org/wiki/HSL_and_HSV HSV color space] to find candidate regions for pathogens.<br />
Finally, a classification algorithm can detect the pathogen on our chips.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_Puzzels_button.png|right|150px]]<br />
<br />
== Statistical Region Merging (SRM) ==<br />
<span class="anchor" id="SRM"></span><br />
<br />
Before briefly introducing Statistical Region Merging (SRM), we would like to explain why we need this step, and why this algorithm is an ideal choice.<br />
<br />
Compared to other clustering algorithms, SRM is quite leight weight, yet delivers ''deterministic'' results and is not dependent on a certain seed (like ''k''-means, for example).<br />
<br />
On the other hand, it can create as many refinements as one wants and is thus flexible enough for the our purposes. Finally there's already been knowledge about this algorithm in the group.<br />
<br />
Statistical Region Merging (SRM) (Nook and Nielson, 2004) is a clustering technique also used directly for image segmentation.<br />
A region $R$ is a set of pixels and the cardinality $\lvert R \rvert$ determines how many pixels are in one region.<br />
Starting with a sorted set of connected regions (w. r. t. some distance function $f$), two regions $R$ and $R'$ are merged if the qualification criteria $\vert \overline{R'}-\overline{R} \vert \leq \sqrt{b^2(R)+b^2(R')}$ with $b(R) = g \cdot \sqrt{\frac{\ln \frac{\mathcal{R}_{\lvert R \rvert}}{\delta}}{2Q\lvert R \rvert}}$ is fulfilled.<br />
Therefore, $\mathcal{R}_{\lvert R \rvert}$ is the set of regions with $\lvert R \rvert$ pixels.<br />
Typically $Q$ is chosen as $Q \in \lbrack 256, 1\rbrack$ and $\delta = \frac{1}{\lvert I \rvert^2}$.<br />
<br />
The $Q$ parameter mainly influences the merging process. For an example, see the figure ''SRM Regions'' below. The lower the chosen value for $Q$, more coarse the regions become. Using a union-find structure, the segmentation does not need to be recalculated for each $Q$ level. For the step from $q$ to $\frac{q}{2}$, just the qualification criteria needs to be applied to the regions from the $q$ result. A MATLAB implementation is also available (Boltz, 2009).<br />
<br />
{{Team:Aachen/FigureDual|Aachen_srm_regions_3.PNG|Aachen_srm_regions_2.PNG|title1=SRM regions in random colors|title2=SRM regions (average color)|subtitle1=Different regions from an SRM run starting at $Q=256$ (top left) and going to $Q=1$ (bottom right). Each region is assigned a random color.|subtitle2=Different regions from an SRM run starting at $Q=256$ (top left) and going to $Q=1$ (bottom right). Each region is assigned the average color of that region.|width=425px}} <br />
<br />
=== SRM Clustering ===<br />
<br />
In our project, we used Statistical Region Merging for clustering. In contrast to other algorithms, such as ''k-means'', this approach is highly deterministic.<br />
For our purposes we only have one SRM run for $Q=256$.<br />
<br />
In MATLAB, we use the previously mentioned code from MATLAB Fileexchange (Boltz, 2009).<br />
For our Qt-based GUI we implemented the SRM method ourselves.<br />
<br />
The SRM clustering reduces the amount of different colors in the image and hence eases the recognition of parts belonging together.<br />
<br />
<html><br />
<div class="codediv"><br />
<pre><code class="matlab"><br />
Qlevel = 256;<br />
[maps,images]=singlesrm(double(image),Qlevel);<br />
</code></pre><br />
</div><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_SEgment_button.png|right|150px]]<br />
<br />
== Segmentation ==<br />
<span class="anchor" id="segment"></span><br />
<br />
In the segmentation stage all background regions are removed. This task is quite crucial. If one removes too few, the final stage of finding pathogens might get irritated.<br />
On the other hand, if one removes too many regions, positive hits might get removed early before detection. This surely must be avoided.<br />
<br />
We opted for a simple thresholding step because it showed that while being easy, it is an effective weapon against the uniform background. In fact, the good image quality we wanted to reach with our device allows now less sophisticated methods.<br />
Also the less computational intensive the steps are, the better they might even run directly on the Raspberry Pi in our device!<br />
<br />
The HSV thresholding is performed on each component seperately. For more information on the HSV color space we refer to [http://en.wikipedia.org/wiki/HSL_and_HSV Wikipedia]. The first component is the hue which we select to be inbetween $0.462$ and $0.520$ to select any blue-greenish color. We will not see bright green due to the filter selection in our device.<br />
The saturation value must be high, between $0.99$ and $1.0$.<br />
Moreover, the value component of the HSV image has to lie between $0.25$ and $0.32$, which assumes a relatively dark color.<br />
<br />
Indeed, these values are not problem specific, but specific for each setup and therefore have to be determined empirically.<br />
<br />
The remainder of this stage creates a mask of pixels that fulfill the conditions.<br />
<br />
* image of masked bit<br />
<br />
<html><br />
<div class="codediv"><br />
<pre><code class="matlab"><br />
% Auto-generated by colorThresholder app on 15-Oct-2014<br />
%-------------------------------------------------------<br />
function [maskedRGBImage] = createMask(srmimg)<br />
RGB = srmimg;<br />
<br />
% Convert RGB image to chosen color space<br />
I = rgb2hsv(RGB);<br />
<br />
% Define thresholds for channel 1 based on histogram settings<br />
channel1Min = 0.462;<br />
channel1Max = 0.520;<br />
<br />
% Define thresholds for channel 2 based on histogram settings<br />
channel2Min = 0.99;<br />
channel2Max = 1.000;<br />
<br />
% Define thresholds for channel 3 based on histogram settings<br />
channel3Min = 0.25;<br />
channel3Max = 0.32;<br />
<br />
% Create mask based on chosen histogram thresholds<br />
BW = (I(:,:,1) >= channel1Min ) & (I(:,:,1) <= channel1Max) & ...<br />
(I(:,:,2) >= channel2Min ) & (I(:,:,2) <= channel2Max) & ...<br />
(I(:,:,3) >= channel3Min ) & (I(:,:,3) <= channel3Max);<br />
<br />
% Initialize output masked image based on input image.<br />
maskedRGBImage = RGB;<br />
<br />
% Set background pixels where BW is false to zero.<br />
maskedRGBImage(repmat(~BW,[1 1 3])) = 0;<br />
<br />
end<br />
</code></pre><br />
</div><br />
</html><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_Classify_button.png|right|150px]]<br />
<br />
== Classification ==<br />
<span class="anchor" id="classification"></span><br />
<br />
=== Smoothness Index ===<br />
<br />
For position prediction in virtual environments, jitter or noise in the output signal is not wanted though often present.<br />
Since discovering smooth areas is a similar problem to jitter detection, a simple method for determining jitter can be used to measure non-jitter, smoothness (Joppich, Rausch and Kuhlen, 2013).<br />
It is assumed that jitter-free areas of a position signal do not differ in velocity.<br />
<br />
Smooth areas do not differ in intensity, and therefore only low changes in velocity (intensity change) can be recorded.<br />
For the reduction of noise, this operation is performed on the smoothed input image.<br />
Then the smoothness $s$ of a pixel $p$ in its k-neighbourhood $\mathcal{N}_k$ can be determined as:<br />
\begin{equation}<br />
s(p) = \sum\limits_{p' \in \mathcal{N}_k} \nabla(p') / \arg\max\limits_{p} s(p)<br />
\end{equation}<br />
<br />
Using thresholding, $TS_l \leq s(p) \leq TS_u \wedge TI_l \leq I \leq TI_u$, different areas, such as background or pathogen, can be selected.<br />
<br />
For the empirical choice of thresholds, it can be argued that these are tailored to the specific case.<br />
While this surely is true to a certain extent, the here presented method has been successfully tested on images from a completely different domain, and no changes to the thresholds have been made to make it work.<br />
A proper theoretical evaluation is emphasized, however, is probably not the aim of the iGEM competition.<br />
<br />
Finally, selecting for the red region, this delivers the location of possible pathogens.<br />
Since the size of the agar chips is variable but fixed a quantitative analysis can be performed by counting pixels for instance.<br />
<br />
=== Empirical Evaluation ===<br />
<br />
Using our MATLAB code we found the lower threshold for the smoothness index to be $TS_l = 0.85$ and the upper threshold $TS_u = \infty$.<br />
Similarly, for $TI_l = 235$ and $TI_u = \infty$.<br />
<br />
Using these settings, we can find a response already in images taken after 42&nbsp;minutes.<br />
<br />
Ideally, one would rate the quality of the image segmentation using some ground truth, such as manual delineations. This still has to be done for our method.<br />
However, from visual observations, our method is showing promising results.<br />
<br />
* image of smoothness index<br />
<br />
=== Automatic Classification ===<br />
<br />
<br />
<html><br />
<div class="codediv"><br />
<pre><code class="matlab"><br />
function [mask, seg] = automaticseeds(im)<br />
<br />
imc = im;<br />
<br />
%% to grayscale and filtering<br />
Z = double(rgb2gray(im));<br />
Z = 255 * Z / max(max(Z));<br />
<br />
filtertype = 'disk';<br />
Z = filter2(fspecial(filtertype), Z);<br />
Z = filter2(fspecial(filtertype), filter2(fspecial(filtertype), Z));<br />
Z = 255 * Z / max(max(Z)); <br />
<br />
%% calculating similarity score/smoothness index<br />
k=4;<br />
sSI = similarity(Z,k);<br />
sSI = sSI / max(max(sSI)); <br />
<br />
%% classify<br />
pathogene = ((sSI > 0.85) == 1) & ((Z > 235) == 1); <br />
<br />
mask = ones( size(imc) );<br />
seg = zeros( size(imc) );<br />
<br />
<br />
%% output<br />
for i=1:size(im,1)<br />
for j=1:size(im,2)<br />
<br />
if (pathogene(i,j) == 1)<br />
seg(i,j,1:3) = [255 0 0];<br />
mask(i, j, 1:3) = [0 0 0];<br />
end<br />
end<br />
end<br />
end<br />
</code></pre><br />
</div><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="measurartyachievements"></span><br />
<br />
''Measurarty'' is the image analysis logic behind our project.<br />
It is comprised of simple constructs put together into a pipeline, that is clearly laid out, easily maintainable and - if needed - easily adaptable.<br />
For example, changing from green to red fluorescence, only means to change the ''createMask'' function to select another target area.<br />
<br />
Overall the results look convincing. We have not yet performed a comparison to a manual delineation, however, by eye the results look promising and have a low error.<br />
<br />
Talking about computational complexity, the MATLAB code of course performs better than our own C++ implementation, which must be regarded as a proof-of-principle.<br />
<br />
Space-wise, the code depends heavily on the image size $O( x \cdot y)$ (width $x$, height $y$, which also limits the number of edges in SRM between regions, as each pixel is one region to start with. However, it cannot take less memory, as the image is stored in an uncompressed format.<br />
<br />
On the computational side, the thresholding, image conversion and gradient steps are linear in the number of pixels, and are thus in $O(x \cdot y)$.<br />
Unfortunately, the summation of the gradient for the smoothness index adds a heavy factor to it (k-neighbourhood for smoothness index).<br />
Due to the merging step in our C++-SRM algorithm implementation, our code has to do $O(x^2 \cdot y^2)$ comparisons, which then finally results in a runtime complexity of $O( x^2 \cdot y^2)$.<br />
<br />
*include image here<br />
<br />
From the above figure it can also be seen that the detected amount of pathogenic-area correlates with time after induction.<br />
The lag-phase can be explained first by the lag-phase of the cells, which first need to generate a response to the pathogen, and on the other hand, by too low fluorescence which is not detectable.<br />
The pixel count also meets the expectation when looking at the sample files by eye.<br />
<br />
It can be concluded that the ''Measurarty'' pipeline defines a robustly working chip-analysis algorithm which can detect pathogens from images supplied by ''WatsOn''.<br />
Therefore, this algorithm closes the gap between our biology, detection hardware and the user who wants easy-to-interpret results.<br />
<br />
For future prospects, it would be interesting to do a proper performance analysis on our code, to find hotspots and optimize the code. Many ''for''-loops leave plenty of room for vectorization and loop-unrolling. Parallelization, specifically with respect to embedded hardware such as the Raspberry Pi or Odroid U3, is limited to the extend that the overhead created would probably eliminate the improvements.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== Source Code ==<br />
<span class="anchor" id="source"></span><br />
<br />
Measuarty is the image analysis logic behind our project. It has been prototyped and developed in [http://www.mathworks.de/academia/student-competitions/igem/ MATLAB], and only later been ported into our WatsOn GUI.<br />
<br />
We are happy to provide you with a zip-ped download of our MATLAB code here, as well as on the iGEM softwarerepository on [https://github.com/orgs/igemsoftware/teams/aachen2014 github].<br />
<br />
* MATLAB code<br />
* link [https://github.com/orgs/igemsoftware/teams/aachen2014 github]<br />
<br />
For the C++ conversion please see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware our WatsOn Software] section.<br />
<br />
=== Using the MATLAB Code ===<br />
<br />
In general, please follow the included ''README.MD'' file. Our package comes with a set of test files from one of our experiments.<br />
After installing the Statistical Region Merging code (see readme), you can simply run ''igem_srm_demo.m''. Select your current folder, and MATLAB will automatically segment and classify the included jpg-images.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== References ==<br />
<span class="anchor" id="measurartyrefs"></span><br />
<br />
* Boltz, S. (2009, October 20). Image segmentation using statistical region merging - File Exchange - MATLAB Central. Image segmentation using statistical region merging. Retrieved December 12, 2013, from http://www.mathworks.com/matlabcentral/fileexchange/25619-image-segmentation-using-statistical-region-merging<br />
<br />
* Joppich, M., Rausch, D., & Kuhlen, T. (2013). Adaptive human motion prediction using multiple model approaches.. Virtuelle und erweiterte Realität (p. 169–180). 10. Workshop der GI-Fachgruppe VR/AR: Shaker.<br />
<br />
* Nock, R., & Nielsen, F. (2004). Statistical region merging. IEEE Transactions on Pattern Analysis and Machine Intelligence, 26(11), 1452-1458.<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T15:28:59Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. On the one hand, this competition depends on the mentioned financial profits and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market resulting in intensitief price wars. On the Asian market personnel and production costs are much less and thus the same product can be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. However, for a company it is important to chose a good '''price-performance ratio''' because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment|subtitle=(Thermo Fisher Scientific, 2013)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find that in this branche there are really low costs for research and development, restruction and amorthilisation. In contrast, general expenses and costs for administartion, revenues, and sales are high. Lastly, financial profit is a big cost point cause businesses have to be self-financing. In general, these factors are making '''technical equipment for labs really expensive''', and therefore unaffordable for low budget instutions. <br />
<br />
One of the world's biggest producers of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometers and other equipment. The image on the left side shows all costs and operating expenses listed in the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx Annual Report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. '''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. One weakness of our device is the low reliability compared to commercial devices. This is because of the used low cost materials. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
Annual report. (2013). Thermo Fisher Scientific. Available at http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T15:19:50Z<p>J.plum: /* Hardware */</p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
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<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
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<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
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<b>Hardware</b><br />
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</li><br />
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<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
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</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
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</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
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</ul><br />
</center><br />
</html><br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37&nbsp;°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information on ''WatsOn'' and on the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''WatsOn''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-17T15:18:07Z<p>J.plum: /* Hardware */</p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
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<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
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<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
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<b>Hardware</b><br />
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<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
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<b>Software</b><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
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<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=WatsOn|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
''Download the laser cutting plan here: [https://2014.igem.org/File:Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Eletronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The Raspberry Pi is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The Arduino board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37&nbsp;°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': An 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide a user interface and manage the connection to the hardware.<br />
The scheme below shows the different components of the software:<br />
<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
Features of the GUI include:<br />
* Change settings (1):<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
* Take image/s (2): <br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image (3). Previous images can be selected with the arrow buttons.<br />
* Analyze image (4):<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Afterwards, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://2014.igem.org/File:Aachen_Device_Backend.zip Download]<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/1/1e/Aachen_WatsOn_arduino.ino.zip Download] <br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information on ''WatsOn'' and on the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''WatsOn''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section ‘Raspberry Pi - Setup’[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<br />
By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Project/Measurement_DeviceTeam:Aachen/Project/Measurement Device2014-10-17T15:15:55Z<p>J.plum: /* WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
{{Team:Aachen/FigureFloatRight|Aachen_Device_11.jpg|title=WatsOn|subtitle= |width=230px}}<br />
Part of the biosensor system ''Cellock Holmes'' are our agar chips. They contain our engineered sensing cells that fluoresce in the presence of the pathogen ''Pseudomonas aeruginosa''. However, bacteria are small and the fluorescent signal cannot be seen with the naked eye. Thus the central question '''"What's on the chip?"''' remains.<br />
<br />
To answer this question we present our measurement device '''''WatsOn'''''. <br />
<br />
The device can incubate the sensing cells, take images and analyze them.<br />
<br />
''WatsOn'' is designed such that it can be easily copied. Our work heavily emphasizes the '''Open Source''' concept. Therefore, the construction manual and all technical detailes are [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy published on our wiki]. Analogous to our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device], we used low-cost and easily available parts. <br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/thumb/c/c7/Aachen_WatsOn_easy.png/600px-Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonhardware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Hardware</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonsoftware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Software</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonmeasurarty" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measurarty</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/21/Aachen_14-10-16_Measurarty_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== Application ==<br />
<span class="anchor" id="watsonapplication"></span><br />
<br />
{{Team:Aachen/Figure|How_two_use_watsOn_flowsheet_V7_ipo.png|title=How to use ''WatsOn''|subtitle=This scheme illustrates handling WatsOn when testing the 2D biosensor chip for a fluorescent signal.|width=1000px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Hardware_button_iNB.png|right|150px]]<br />
<br />
== Hardware ==<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Elektronikkomponenten1.jpg|title=Hardware components|subtitle=From top left to bottom right: Arduino, Peltier element, Raspberry Pi, relay, cables, MOSFET, temperature display, camera, LEDs and resistors.|width=520px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen in the first section was build from laser cutted acrylic glass.<br />
<br />
The electronic circuit is a combination of the components displayed in the image above. We combined the Raspberry Pi - a small single-board computer running a Linux operating system - and an Arduino board which is a programmable microcontroller. The Arduino operates the excitation LEDs and a Peltier heater for incubation. For taking images of the sensor chips we used the Raspberry Pi camera module which is directly connected to the board.<br />
<br />
A detailed description of all components and the wiring can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware Engineering section of our Notebook].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Software_button_iNB.png|right|150px]]<br />
<br />
== Software ==<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
[[File:Aachen_WatsOn_igem_GUI_originalImage.png||650px]]<br />
<br />
The software is responsible for presenting a user interface on the display of the device and to take images with the LED wavelength selected by the user. Therefore it is separated into three single components: the graphical user interface (GUI) with a backend script running on the Raspberry Pi and the code on the Arduino board.<html><br/></html><br />
The GUI(left image) provides the user with the option to take a single image or a time lapse shooting and specify parameters for the camera and the wavelength of the LEDs. The wavelength used in our device are 480nm for GFP and 450nm for iLOV. Furthermore the images are analysed for the presence or absence of P. aeruginosa by analysing the image and providing the user with a visual feedback (right image). All taken images can be saved to disk manually for single images and automatically for time lapse shootings.<html><br/></html><br />
Further details on the software including the backend which gives the possibility of using the GUI remotely on a different device (e.g. notebook) in the same local network can be found here [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Measurarty_button_iNB.png|right|150px]]<br />
<br />
== Measurarty ==<br />
<span class="anchor" id="watsonmeasurarty"></span><br />
<center><br />
{{Team:Aachen/Figure|Aachen_srm_regions_3.PNG|title=SRM component of our image analysis component ''Measurarty''|subtitle=SRM is one of the core components of our image analysis approach. This image shows the different regions created.|width=500px}}<br />
</center><br />
<br />
Measurarty is the '''image analysis software''' of our device and is designed to allow an automatic segmentation and classification of our '''agar chip pictures'''.<br />
Therefore, it expects as input an image from WatsOn, and produces an output image with pathogenic regions marked in red.<br />
<br />
This component mainly focuses on recognizing pathogens early, such that pure thresholding is not necessary.<br />
We therefore designed a pipeline and established a smoothness index to make statements about the pathogenity of a chip as early as possible, but also with as much certainty as possible.<br />
<br />
A sample output of the segmentation is presented below, showing that the pipeline works as intended.<br />
<br />
{{Team:Aachen/Figure|Aachen_Pseudomonas_aeruginosa_Measurarty_slower.gif|title=Detection of ''Pseudomonas aeruginosa''|subtitle=Measurarty is able to reliably identify the fluorescence response of the sensor cells which is produced in a response to ''Pseudomonas aeruginosa''.|width=480px}}<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="watsonachievements"></span><br />
<br />
When developing ''WatsOn'' our goal was to build a system that<br />
*incubates the sensing cells and the sampling chip <br />
*illuminates the chip with the right excitation wavelength for our fluorescence proteins<br />
*takes photos and time lapse shootings of the chips<br />
*uses cheap filter slides to block the light emitted from the LEDs<br />
*analyzes the fluorescence signal<br />
*gives feedback to the user about the presence or absence of ''P. aeruginosa'' through a GUI (graphical user interface)<br />
*prevents escape of potentially sampled pathogens and our genetically engineered cells<br />
*is portable and fast in analyzing the images<br />
<br />
<br />
++++++++++++ hier kommt noch was hin +++++++++++++<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Project/Measurement_DeviceTeam:Aachen/Project/Measurement Device2014-10-17T15:14:40Z<p>J.plum: /* Application */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
{{Team:Aachen/FigureFloatRight|Aachen_Device_11.jpg|title=WatsOn|subtitle= |width=230px}}<br />
Part of the biosensor system ''Cellock Holmes'' are our agar chips. They contain our engineered sensing cells that fluoresce in the presence of the pathogen ''Pseudomonas aeruginosa''. However, bacteria are small and the fluorescent signal cannot be seen with the naked eye. Thus the central question '''"What's on the chip?"''' remains.<br />
<br />
To answer this question we present our measurement device '''''WatsOn'''''. <br />
<br />
The device can incubate the sensing cells, take images and analyze them.<br />
<br />
''WatsOn'' is designed such that it can be easily copied. Our work heavily emphasizes the '''Open Source''' concept. Therefore, the construction manual and all technical detailes are [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy published on our wiki]. Analogous to our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F device], we used low-cost and easily available parts. <br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonapplication" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/thumb/c/c7/Aachen_WatsOn_easy.png/600px-Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonhardware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Hardware</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonsoftware" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Software</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonmeasurarty" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Measurarty</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/2/21/Aachen_14-10-16_Measurarty_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#watsonachievements" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== Application ==<br />
<span class="anchor" id="watsonapplication"></span><br />
<br />
{{Team:Aachen/Figure|How_two_use_watsOn_flowsheet_V7_ipo.png|title=How to use ''WatsOn''|subtitle=This scheme illustrates handling WatsOn when testing the 2D biosensor chip for a fluorescent signal.|width=1000px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Hardware_button_iNB.png|right|150px]]<br />
<br />
== Hardware ==<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Elektronikkomponenten1.jpg|title=Hardware components|subtitle=From top left to bottom right: Arduino, Peltier element, Raspberry Pi, relay, cables, MOSFET, temperature display, camera, LEDs and resistors.|width=520px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen in the first section was build from laser cutted acrylic glass.<br />
<br />
The electronic circuit is a combination of the components displayed in the image above. We combined the Raspberry Pi - a small single-board computer running a Linux operating system - and an Arduino board which is a programmable microcontroller. The Arduino operates the excitation LEDs and a Peltier heater for incubation. For taking images of the sensor chips we used the Raspberry Pi camera module which is directly connected to the board.<br />
<br />
A detailed description of all components and the wiring can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware Engineering section of our Notebook].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Software_button_iNB.png|right|150px]]<br />
<br />
== Software ==<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
[[File:Aachen_WatsOn_igem_GUI_originalImage.png||650px]]<br />
<br />
The software is responsible for presenting a user interface on the display of the device and to take images with the LED wavelength selected by the user. Therefore it is separated into three single components: the graphical user interface (GUI) with a backend script running on the Raspberry Pi and the code on the Arduino board.<html><br/></html><br />
The GUI(left image) provides the user with the option to take a single image or a time lapse shooting and specify parameters for the camera and the wavelength of the LEDs. The wavelength used in our device are 480nm for GFP and 450nm for iLOV. Furthermore the images are analysed for the presence or absence of P. aeruginosa by analysing the image and providing the user with a visual feedback (right image). All taken images can be saved to disk manually for single images and automatically for time lapse shootings.<html><br/></html><br />
Further details on the software including the backend which gives the possibility of using the GUI remotely on a different device (e.g. notebook) in the same local network can be found here [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Measurarty_button_iNB.png|right|150px]]<br />
<br />
== Measurarty ==<br />
<span class="anchor" id="watsonmeasurarty"></span><br />
<center><br />
{{Team:Aachen/Figure|Aachen_srm_regions_3.PNG|title=SRM component of our image analysis component ''Measurarty''|subtitle=SRM is one of the core components of our image analysis approach. This image shows the different regions created.|width=500px}}<br />
</center><br />
<br />
Measurarty is the '''image analysis software''' of our device and is designed to allow an automatic segmentation and classification of our '''agar chip pictures'''.<br />
Therefore, it expects as input an image from WatsOn, and produces an output image with pathogenic regions marked in red.<br />
<br />
This component mainly focuses on recognizing pathogens early, such that pure thresholding is not necessary.<br />
We therefore designed a pipeline and established a smoothness index to make statements about the pathogenity of a chip as early as possible, but also with as much certainty as possible.<br />
<br />
A sample output of the segmentation is presented below, showing that the pipeline works as intended.<br />
<br />
{{Team:Aachen/Figure|Aachen_Pseudomonas_aeruginosa_Measurarty_slower.gif|title=Detection of ''Pseudomonas aeruginosa''|subtitle=Measurarty is able to reliably identify the fluorescence response of the sensor cells which is produced in a response to ''Pseudomonas aeruginosa''.|width=480px}}<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
== Achievements ==<br />
<span class="anchor" id="watsonachievements"></span><br />
<br />
When developing ''WatsOn'' our goal was to build a system that<br />
*incubates the sensing cells and the sampling chip <br />
*illuminates the chip with the right excitation wavelength for our fluorescence proteins<br />
*takes photos and time lapse shootings of the chips<br />
*uses cheap filter slides to block the light emitted from the LEDs<br />
*analyzes the fluorescence signal<br />
*gives feedback to the user about the presence or absence of ''P. aeruginosa'' through a GUI (graphical user interface)<br />
*prevents escape of potentially sampled pathogens and our genetically engineered cells<br />
*is portable and fast in analyzing the images<br />
<br />
<br />
++++++++++++ hier kommt noch was hin +++++++++++++<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T15:03:45Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on the mentioned financial profits, on the one hand, and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market so that price wars happened. On the asian market personal and production costs are much more less and so one products could be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. Besides, for a company it is important to chose a good price-performance ratio because this factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The image on the left side shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. '''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. One weakness of our device is the low reliability compared to commercial devices. This is because of the used low cost materials. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T15:02:21Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested in satisfying and dealing with all customer needs for better sales figures, in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on the mentioned financial profits, on the one hand, and, on the other hand, on the following factors: technical improvement followed by price wars. Due to globalization products from the Asian market are increasingly competing with the American and European market so that price wars happened. On the asian market personal and production costss are much more less and so one products could be sold with higher profits. Some of these products are less expensive but are often of lower quality, too. Besides, for a company it is important to chose a good price-performance ratio because thi factor always catch customers and influence their purchase decision. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The image on the left side shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. '''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. One weakness of our device is the low reliability compared to commercial devices. This is because of the used low cost materials. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/Project/2D_BiosensorTeam:Aachen/Project/2D Biosensor2014-10-17T14:53:07Z<p>J.plum: /* Detecting Pseudomonas&nbsp;aeruginosa with K131026 in our Sensor Chip with WatsOn */</p>
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= 2D Biosensor =<br />
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With our 2D biosensor technology we are able to detect the pathogen ''Pseudomonas aeruginosa'' on solid surfaces. The sensor system is comprised of '''two distinct but inseparable modules''', a biological and a technical part:<br />
<br />
* Sensing chips containing '''''Cellocks''''', our '''engineered detective cells''' that fluoresce in the presence of the pathogen, make up the biological part of ''Cellock Holmes''.<br />
* Our '''measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn'']''' and the complementary '''software [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty'']''' complete our sensing technology on the technical side. <br />
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<a href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensorpoo" style="color:black"><br />
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<div class="menukachel">Principle of Operation</div><br />
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<a href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensordevelopment" style="color:black"><br />
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<div class="menukachel">Development & Optimization</div><br />
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<a href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensorachievements" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<div class="menukachel">Achievements</div><br />
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<a href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensoroutlook" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
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[[File:Aachen_15-10-14_Principle_of_operation_2D_sensor_ipo.png|right|150px]]<br />
<br />
== Principle of Operation ==<br />
<span class="anchor" id="biosensorpoo"></span><br />
<br />
''Cellock Holmes'' is designed upon a SynBio approach comprising a '''two-dimensional biosensor and a measurement unit'''. The two-dimensional biosensor is devised to recognize quorum sensing molecules secreted by the pathogen cells and to generate a distinct fluorescence signal; while the measurement device recognizes and analyzes the produced signal. <br />
<br>On the molecular side, we use the '''[https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct]''' to transform regular ''E. coli'' cells into ''Cellocks''.<br />
<br />
{{Team:Aachen/Figure|Aachen 17-10-14 The basics of quorum sensing ipo.png||title=The principle of quorum sensing|subtitle=Microorganisms can sense the presence of their own kind based on quorum sensing which is a form of chemical communication. Depending on their cell density, quorum sensing allows these cells to activate or deactivate certain gene expression cascades for a specific function. (Waters and Bassler, 2005).|width=1000px}}<br />
<br />
Our '''sensor cells, ''Cellocks'', are immobilized in agar chips'''. To make the chips, we mix the ''Cellocks'' with liquid LB agar. <br />
In the course of our project, we designed a casting mold specifically for the production of our agar chips. When the agar has cooled down, the chips are cut out of the mold and are ready to use. Storage of the readily usable sensor chips is possible for up to 2 days at 4 °C when using LB medium or up to 5 days if TB medium is used. A detailed description of the sensor chip manufacturing can be found in our [https://2014.igem.org/Team:Aachen/Notebook/Protocols/detection Protocols] section.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part1 ipo.png|title=Assay to detect ''P.&nbsp;aeruginosa'' using ''Cellock Holmes''|subtitle=This flow sheet shows the procedure to sample and detect ''P.&nbsp;aeruginosa'': A sampling chip is briefly put onto the potentially contaminated surface, added onto one of our sensor chips and inserted into ''WatsOn''.|width=1000px}}<br />
<br />
Using ''Cellock Holmes'', we developed a simple assay to detect ''P.&nbsp;aeruginosa''. <br />
* First, a sampling chip is placed on a solid surface that is potentially contaminated with the pathogen. <br />
* Second, the sampling chip is removed from the surface and put onto one of our sensor chips. (Theorectically, the sensor chips could be directly used for sampling, however, this was avoided in our project to '''match [https://2014.igem.org/Team:Aachen/Safety biosafety regulations]''' and to prevent the spread of GMOs into the environment.) <br />
* Third, the two layered chip-stack is put into a petri dish which is inserted into our measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for evalutation.<br />
<br />
{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part2 ipo.png|title=Mode of action inside ''WatsOn''.|subtitle=Chips are incubated at 37 °C to stimulate cell growth and then illuminated with blue light to excite fluorescence. A picture is taken and analyzed for fluorescence signals using the software ''Measurarty''.|width=1000px}}<br />
<br />
Inside ''WatsOn'', the chips are incubated at 37&nbsp;°C and the sampled populations of microorganisms attached on the sampling chip start to grow and multiply. During incubation the chips can be '''illuminated with blue light''' at any time, and a '''photo of the chips''' is taken. The '''software ''Measurarty''''' then analyzes any fluorescent signal. ''P.&nbsp;aeruginosa'' secrets an increasing number of quorum sensing molecules that are recognized by ''Cellocks'', thereby producing a fluorescence signal. For detection of ''P.&nbsp;aeruginosa'', we focused on a quorum sensing molecule called N-3-oxo-dodecanoyl-L-homoserine lactone (for short: 3-oxo-C<sub>12</sub>-HSL), which is involved in virulence regulation of ''P.&nbsp;aeruginosa'' (Jimenez, Koch, Thompson et al., 2012). The incorporation of the 3-oxo-C<sub>12</sub>-HSL detection system into the ''Cellocks'' is explained in detail in the [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh Construct] section.<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
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<!-- ==A Novel Molecular Approach==<br />
<span class="anchor" id="biosensormolecularapproach"></span><br />
<br />
For our biosensor, our team genetically modified ''E. coli'' cells to be able to elecit a '''fluorescent response to autoinducers''' produced by the pathogen ''Pseudomonas aeruginosa'' during quorum sensing. In the case of ''P.&nbsp;aeruginosa'', these autoinducers are N-3-oxo-dodecanoyl-L-homoserine lactone, or 3-oxo-C-12-HSL for short. The quorum sensing system of this pathogen contains the '''LasR activator''' which binds 3-oxo-C-12-HSL, and the '''LasI promoter''', which is activated by the LasR-HSL complex. Both LasR activator and LasI promoter are available as BioBricks [http://parts.igem.org/Part:BBa_C0179 C0179] and [http://parts.igem.org/Part:BBa_J64010 J64010].<br />
<br />
As a reporter gene, we use '''GFP'''. However, expression of GFP is not simply controlled through the LasI promoter activity in our approach. Instead, our sensor cells contain genes for a constitutively expressed fusion protein consisting of GFP and a dark quencher, and an '''HSL-inducible protease'''. We use the REACh protein as dark quencher for GFP and the TEV protease to cleave the complex; [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter here] you can read more about the REACh construct and the TEV protease. <br />
<br />
{{Team:Aachen/Figure|align=center|Aachen_REACh_approach.png|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=500px}}<br />
<br />
When ''P.&nbsp;aeruginosa cells'' are stuck on our agar chip and come close to our sensor cells, the latter take up the HSL molecules secreted by the pathogens. Inside the sensor cells, the autoinducer binds to the LasR gene product and activate the expression of the TEV protease. The protease then cleaves the GFP-REACh construct. When '''illuminated with light of 480&nbsp;nm''', the excitation wavelenght of GFP, our sensor cells in the vicinity of ''P.&nbsp;aeruginosa'' give a '''fluorescence signal'''. On the other hand, sensor cells that were not anywhere close to the pathogens do not express the protease. Therefore, the GFP will still be attached to the dark quencher in these cells, and no fluorescence is produced.<br />
<br />
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[[File:Aachen_14-10-16_Iterative_Process_iNB.png|right|150px]]<br />
<br />
== Development & Optimization ==<br />
<span class="anchor" id="biosensordevelopment"></span><br />
<br />
=== Medium ===<br />
{{Team:Aachen/FigureFloat|Aachen_ILOV_GFP_HM_1,5h.png|title=iLOV and GFP in the Gel Doc<sup>TM</sup>|subtitle=Sensor cells producing iLOV (A) and GFP (B) 1.5&nbsp;h after induction.|left|width=500px}}<br />
Prior to using our own device for detection of fluorescence emitted by the sensor chips we used equipment readily available in the lab. A Molecular Imager&reg; Gel Doc™ XR+ from BIO-RAD was available which uses UV and white light illuminators. However, only two different filters were available for the excitation light wavelength, which resulted in very limitted possibilities for the excitation of fluorescent molecules. For example, it was possible to detect the expression of iLOV in our sensor chips but the detection of GFP was not possible. It was thus determined that the '''Gel Doc™ was not suitable for our project'''.<br />
<br />
<!--Regarding the medium used for our sensor chips, LB medium showed a high background fluorescence when exposed to UV light in the Gel Doc. Surprisingly, the background fluorescence resulting from the LB medium was too high to detect a signal emitted by our sensor cells. Hence, minimal media (NA, M9, Hartman (HM)) was used to minimize background fluorescence, but this approach resulted in less to no growth of our sensor cells.<br />
In our device ''WatsOn'', optimized wavelengths of 450&nbsp;nm and 480&nbsp;nm were used for excitation of iLOV and GFP, respectively. When exposed to either excitation wavelength TB medium, which is basically an improved LB medium and highly supports cell growth, showed strong background fluorescence in our own device. High background fluorescence was also observed for TB medum when using the Gel Doc. In contrast to the Gel Doc LB medium showed minimal fluorescence in our device ''WatsOn'' and no difficulties in cultivation of our ''Cellocks'' were observed. Because of the reduced fluorescence compared to TB medium when using ''Watson'' for sensor chip evaluation and because of sufficient cultivation conditions for our 'Cellocks'' LB medium was chosen over TB mediium for sensor chip manufacturing. --><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Chip_medium_geldoc.png|title=Differend medium in the Gel Doc™|subtitle=complex media exhibited high background fluorescence while less back-ground fluorescence was observed with the minimal media (HM, M9, NA).|right|width=500px}}<br />
<br />
{{Team:Aachen/FigureFloat|Aachen_5days_K131026_neb_tb_1,5h.jpg |title=Testing our chips' shelf-life.|subtitle= [http://parts.igem.org/Part:BBa_K131026 K131026] in NEB induced after 5 days of storage at 4&nbsp;°C. The right chip was induced with 0.2&nbsp;µL of 500&nbsp;µg/mL HSL, and the image was taken after 1.5&nbsp;h.|left|width=500px}}<br />
<br />
To determine which medium enables fast and reliable fluorescence response detection of our chip system, the growth behavior on as well as the fluorescence properties of several media have been investigated. The complex media LB, TB and NA and the minimal media M9 and HM were tested.<br />
Because of the reduced background fluorescence compared to TB medium when using Watson for sensor chip evaluation and because of sufficient cultivation conditions for our 'Cellocks, LB medium was chosen for sensor chip manufacturing (table below).<br />
<br />
<br />
<center><br />
{| class="wikitable"<br />
! !! LB !! TB !! NA !! M9 !! HM <br />
|-<br />
| Growth of Cellock || <div style="text-align: center;">'''x'''</div> || <div style="text-align: center;">'''x'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|-<br />
| Background fluorescence in GelDoc || <div style="text-align: center;">'''x'''</div> || <div style="text-align: center;">'''x'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|-<br />
| Background fluorescence in ''WatsOn'' || <div style="text-align: center;">-</div> || <div style="text-align: center;">'''x'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|}<br />
</center><br />
<br />
<br />
Further experiments were conducted to test long-time storage of the sensor chips. Storage at -20 °C resulted in the loss of our sensor cells. Adding 5-10% (v/v) glycerol ensured survival of the sensor cells, but resulted in an expression stop of fluorescence proteins. Thus, the idea of long time storage of the sensor chips had to be passed on. However, it was possible to store ready-to-use sensor chips for 2 days at 4&nbsp;°C when using LB medium and storage for 5 days was possible with chips made from TB medium.<br />
<br />
=== Agar Concentration ===<br />
For the sensor chip manufacturing, a concentration of 1.5% agarose was found to be optimal. When agarose concentrations below 1.5% (w/v) were used the sensor chips were easily damaged and were not transportable. Agar concentrations over 1.5% (w/v) had to be avoided, because the agarose started to solidify before it could be poured into the chip casting mold.<br />
Agarose was chosen over agar, because of a more even linkage between molecules resulting in a better chip homogenity. In addition, agarose reduced diffusion of inducer molecules through the chip. A reduction in diffusion was desired in order to achieve distinct fluorescent spots on the sensor chips.<br />
<br />
=== Chip Form ===<br />
Various approaches were tried for production of sensor chips with reproducable quality. The first approach was to cast every sensor chip individually. In order to achieve a plain chip surface, which was required for high quality images, we tried to cast the sensor chips between four microscope slides. This approach had to be rejected, because the agar was too liquid. In a second try, we produced a closed mold into which liquid agar was injected using a pipette, but we encountered a high number of bubbles in the chips when using this method. Bubbles in the sensor chips resulted in problems during fluorescence evalutaion.<br />
<br />
{{Team:Aachen/Figure|Aachen_2_chipform.jpg|title=Chips made using the closed mold|subtitle=With this method we encounter problems due to frequent bubble formation.|width=600px}}<br />
<br />
Finally, we used an open mold into which the agar was poured right after mixing with the sensor cells. When the agar had solidified the chips were cut out along precast indentations in the casting mold. An advantage of the open mold was the ability to simultaneously produce nine sensor chips while the surface tension of the liquid agar ensured a plane chip surface.<br />
<br />
{{Team:Aachen/Figure|Aachen_Final_chipform.jpg|title=Final chip mold.|subtitle=We found the above shown casting mold to be ideal for our purposes.|width=600px}}<br />
<br />
=== Induction ===<br />
For artificially induction of our molecular detection constructs we simluated the presence of ''P.&nbsp;aeruginosa'' by use of IPTG or 3-oxo-C12 HSL. <br />
A minimal pipetting volume was desired for induction, because initial experiments showed that diffusion of the inducers through the chip hindered formation of distinct spots on the chips. Due to the pipetts available the lowest volume we could pipett was limitted to 0.2 &nbsp;µL .<br />
Sensor cells based on ''E. coli'' BL21, which incorporated the [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042] construct were able to detect IPTG concentrations down to 1&nbsp;mM (0.2&nbsp;µL), so were sensor cells based on ''E. coli'' BL21, which incorporated the REACh constructs.<br />
Sensor cells based on ''E. coli'' BL21, which incorporated the [http://parts.igem.org/Part:BBa_K131026 K131026] construct were able to detect HSL concentrations down to 500&nbsp;µg/mL (0.2&nbsp;µL). Further more, detection of growing ''Pseudomonas aeruginosa'' cells based on secreted HSLs was possible using the [http://parts.igem.org/Part:BBa_K131026 K131026] construct. A detailed description including pictures of the experiments leading to the just mentioned findings can be found in the [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensorachievements Achievements] section.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_Medal_Cellocks_iNB.png|right|150px]]<br />
<br />
==Achievements==<br />
<span class="anchor" id="biosensorachievements"></span><br />
<br />
We are able to detect IPTG, 3-oxo-C{{sub|12}} HSL and ''Pseudomonas aeruginosa''. To prove that the sensor constructs produce the flourescence signal and not the medium or ''E. coli'' in its own we have [http://parts.igem.org/Part:BBa_B0015 B0015] in NEB as a negativ control for IPTG, HSL and ''Pseudomonas aeruginosa'' induction.<br />
<br />
<br />
{{Team:Aachen/Figure|Aachen_B0015_IPTG_HSL_Pseudomonas.png|title=Negativ control |subtitle=B0015 in NEB as negativ control induced with A) 0.2&nbsp;µl of 100&nbsp;mM IPTG, image taken after 2.5&nbsp;h; B) 0.2&nbsp;µl of 500&nbsp;µg/ml HSL (3-oxo-C12), image after 2.5&nbsp;h; C) with 5 spots of ''Pseudomonas aeruginosa'' on the left and one big spot on the right, image taken after 2&nbsp;h|width=900px}}<br />
<br />
=== Testing our Sensor Chips in a Plate Reader ===<br />
{{Team:Aachen/FigureFloat|Aachen_K1319042_Platereader.gif|title=Testing K1319042 in our sensor chips|subtitle=K1319042 in our sensor chip induced with 2&nbsp;µL IPTG and measured with a plate reader. Blue color indicates no fluorescence, red color indicates fluorescence. Top chip is not induced, bottom chip is induced with IPTG.|width=300px}}<br />
<br />
<br />
<br />
<br />
<br />
<br />
To establish a prove of principle we used our construct [http://parts.igem.org/Part:BBa_K1319042 K1319042] an IPTG inducible iLOV. They were introduced into our sensor chips and then fluorescence was measured every 15 minutes after an induction with 2&nbsp;µl 100&nbsp;mM IPTG.<br />
<br />
There is a clear difference in fluorescence between the not induced chip (top) and the induced chip (bottom). It is distinctively visible that the middle of the bottom chip start to exhibit fluorescence and then the fluorescence increases over time and spreads outward. The top chip also shows a slight increase in measured fluorescence but it is nowhere near the level of the induced chip and is primarily attributable to a leaky promoter and the background fluorescence. <br />
<br />
This demonstrates a general proof of principle of the sensor chip design. Therefore the next was testing the detection of 3-oxo-C{{sub|12}} HSL.<br />
<html></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br><br />
</html><br />
<br />
=== Detecting 3-oxo-C{{sub|12}} HSL with Sensor Chips ===<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_K131026_Platereader.gif|title=Testing K131026 in our sensor chips|subtitle=K131026 in our sensor chip induced with 0.2&nbsp;µL 3-oxo-C{{sub|12}} HSL and measured with a plate reader. Blue color indicates no fluorescence, red color indicates fluorescence. Top chip is not induced, bottom chip is induced with IPTG.|width=300px}}<br />
<br />
As a next step, we used [http://parts.igem.org/Part:BBa_K131026 K131026] from the 2008 iGEM Team Calgary in our sensor chips to detect 3-oxo-C{{sub|12}} HSL which is produced by ''Pseudomonas&nbsp;aeruginosa'' during quorum sensing. First, we tested them by direct induction with purified 3-oxo-C{{sub|12}} HSL (0.2&nbsp;µL, 500&nbsp;µg/mL). A fluorescence measurement was taken every 15&nbsp;min with an excitation wavelength of 496&nbsp;nm and an emission wavelength of 516&nbsp;nm (for GFP).<br />
<br />
The measured fluorescence again showed a distinct signal on the induced chip (bottom) compared to the uninduced chip (top). The fluorescence clearly starts in the middle of the chip (point of induction) and then extends outwards, still showing an ever increasing signal of fluorescence. The base level of fluorescence is attributed to leakiness of the promoter and general background fluorescence of growing ''E. coli'' cells. In the induced chip (bottom), the background fluorescence is a lot lower than in the uninduced chip (top) because the signal masks the noise. The difference between the induced and uninduced chips indicates a clear response to the HSL and a proof for the ability of our sensor chip design to detect the HSL produced by ''Pseudomonas&nbsp; aeruginosa''.<br />
<br />
<html></br></br></br></br></br></br></br></br></html><br />
<br />
=== Detecting IPTG with Sensor Chips ===<br />
{{Team:Aachen/FigureFloat|Aachen_I746909_slower_reduced.gif|title=IPTG inducible superfolder GFP (I746909) in sensor chips|subtitle=IPTG inducible superfolder GFP (I746909) is induced with IPTG (2 µl, 100mM) on the right chip with a non induced chip on the left|width=480px}}<br />
<br />
<br />
<br />
This video shows the construct [http://parts.igem.org/Part:BBa_I746909 I746909] from the 2007 iGEM Team Cambridge. This BioBrick is a producer of superfolder GFP under the control of a T7 promoter. It was introduced into BL21(DE3) cells making the expression IPTG inducible through the T7 RNA Polymerase encoded in the genome of BL21(DE3) under the control of a lacI promoter. <br />
<br />
The left chip does not show visible fluorescence and the right chip exhibits a strong fluorescence signal showing clearly the ability of the sensor chip technology to detect IPTG. On top of that, the fluorescence response is strong enough to be detected and analyzed by the measurement device WatsOn.<br />
<html></br></br></br></br></br></br></br></br></br></br></br></br></br><br />
</html><br />
<br />
===Detecting the 3-oxo-C{{sub|12}} HSL with K131026 in our Sensor Chips with WatsOn===<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_K131026_HSLdetection_slow.gif|title=Detection of 3-oxo-C{{sub|12}} HSL with K131026|subtitle=0.2 µL of 3-oxo-C{{sub|12}} HSL was placed in the middle of the chip and then incubated at 37&nbsp;°C in WatsOn.|width=480px}}<br />
<br />
The next step towards the final goal to detect ''Pseudomonas&nbsp;aeruginosa'' was to replicate the detection of 3-oxo-C{{sub|12}} HSL, which was established in the plate reader, in our own [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] device. Therefore, we again used K131026 as our construct in ''E. coli'' BL21(DE3) cells and induced with 0.2&nbsp;µL 3-oxo-C{{sub|12}} HSL with a concentration of 500&nbsp;µg/mL. The right chip was induced and - as a negative control - the left chip was not induced. Pictures were taken every 4&nbsp;min.<br />
<br />
The result was a clear replication of the success of the plate reader experiment. The induced chip shows a clear fluorescence response eminating from the center where the induction with HSL took place. This demonstrates the ability of not only our sensor chips but also our measurement device WatsOn to successfully detect 3-oxo-C{{sub|12}} HSL.<br />
<br />
<html></br></br></br></br></br></br></br></br><br />
</html><br />
<br />
===Detecting ''Pseudomonas&nbsp;aeruginosa'' with K131026 in our Sensor Chip with WatsOn===<br />
{{Team:Aachen/FigureFloat|Aachen_K131026_Pseudomonas_aeruginosa_detection.gif|title=Detection of ''Pseudomonas aeruginosa'' with K131026|subtitle=Direct detection of ''Pseudomonas aeruginosa'' on our sensor chips. Sensor cell used were K131026.|width=480px}}<br />
<br />
After establishing the successful detection of 3-oxo-C{{sub|12}} with our sensor chips the next step was the detection of ''Pseudomonas aeruginosa'' with our measurement device WatsOn. Therefore sensor chips with K131026 were again prepared and the right chip was induced with 0.2&nbsp;µl of a ''Pseudomonas aeruginosa'' culture while the left chip was not induced. <br />
<br />
The results clearly demonstrate our ability to detect ''Pseudomonas aeruginosa'' with our measurement device WatsOn. On the induced chip a definite fluorescence response is visible in response to ''Pseudomonas aeruginosa''. The fluorescence eminates outward from the induction point and shows a significant difference to the non induced chip. Therefore detection of ''Pseudomonas aeruginosa'' is possible with our sensor chip technology in our measurement device ''WatsOn''!<br />
<br />
<html></br></br></br></br></br></br></br></br><br />
</html><br />
<br />
=== Comparing the REACh Construct with K731520 and I746909 ===<br />
<br />
More information about the kinetic differences between these construct in our sensor chips, look under <br />
[https://2014.igem.org/Team:Aachen/Project/FRET_Reporter The REACh Construct] Achievements.<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
<br />
== Outlook ==<br />
<span class="anchor" id="biosensoroutlook"></span><br />
<br />
After successfully detecting ''P.&nbsp;aeruginosa'', the next step in developing our sensor chip platform further is an '''improvement of the sampling chip'''. The current technique of using a simple agarose chip is not sufficient to collect all microorganisms from the sampled surface. Therefore, the aim is to improve the sampling chip by trying different, more adhesive material. <br />
<br />
Furthermore, diffusion in the sensor chips will be reduced to '''limit the spread of the fluorescence signal'''. Currently, the fluorescence spot grows at lot beyond the point of detection and makes it difficult to successfully differentitate between multiple points of induction. By introducing different diffusion barriers into our chips, the growth of the fluorescence spots might be limited, thus enabling the detection of multiple sources of fluorescence lying close together. <br />
<br />
Additionally, the application of our sensor chips in combination with our ''WatsOn'' device is currently being evaluated for the detection of signals other than fluorescence. '''Detecting bio- and chemiluminescence''' has been identified as an area of potential future application. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==References==<br />
<br />
* Waters, C. M., & Bassler, B. L. (2005). QUORUM SENSING: Cell-to-Cell Communication In Bacteria. Annual Review of Cell and Developmental Biology, 21(1), 319-346. Available online at http://www.annualreviews.org/doi/full/10.1146/annurev.cellbio.21.012704.131001.<br />
<br />
* Jimenez, P. N., Koch, G., Thompson, J. A., Xavier, K. B., Cool, R. H., & Quax, W. J. (2012). The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa. Microbiology and Molecular Biology Reviews, 76(1), 46-65. Available online at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294424/#B63.<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T14:51:21Z<p>J.plum: /* Cellock Holmes - A Case of Identity */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
= Cellock Holmes - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''''WatsOn'''''] , our measurement device. ''WatsOn'' is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we provide the OD/F Device. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all technical details as well as construction manuals are published on our wiki. We demonstrate immediate application of the OD/F Device '''in schools, community labs and in the bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T14:50:46Z<p>J.plum: /* Cellock Holmes - A Case of Identity */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
= Cellock Holmes - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
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</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] , our measurement device. ''WatsOn'' is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we provide the OD/F Device. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all technical details as well as construction manuals are published on our wiki. We demonstrate immediate application of the OD/F Device '''in schools, community labs and in the bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T14:50:02Z<p>J.plum: /* Cellock Holmes - A Case of Identity */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
= Cellock Holmes - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''WatsOn'''] , our measurement device. ''WatsOn'' is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we provide the OD/F Device. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all technical details as well as construction manuals are published on our wiki. We demonstrate immediate application of the OD/F Device '''in schools, community labs and in the bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/ProjectTeam:Aachen/Project2014-10-17T14:48:01Z<p>J.plum: /* Cellock Holmes - A Case of Identity */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
= Cellock Holmes - A Case of Identity =<br />
<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/2D_Biosensor" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">2D Biosensor</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5a/Aachen_14-10-14_cellock_liegend_panel_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/FRET_Reporter" style="color:black"><br />
<div class="menuright-item menuright-info" ><div class="menukachel">REACh Construct</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/b/ba/Aachen_14-10-13_REACh_construct_tile_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Gal3" style="color:black"><br />
<div class="menuright-item menuright-info" ><br />
<div class="menukachel">Galectin-3</div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/7/74/Aachen_14-10-13_Galectin-3-YFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>WatsOn</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c7/Aachen_WatsOn_easy.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<br />
</ul></html><br />
<br />
<br />
'''"What's living on the table in front of you?"''' seems to be an easy question to answer: microoganisms. <br />
<br />
However, '''"''Which'' microorganisms are there?"''' is not such a trivial question anymore, especially in environments where you only want to have a non-pathogenic microflora or no microorganisms at all, such as lab spaces or health care institutions. <br />
<br />
'''Our project ''Cellock Holmes'' solves this case of identy.'''<br />
<br />
''Cellock Holmes'' encompasses our '''[https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensing technology]''' with which can detect bacteria on solid surfaces. ''Cellock Holmes'' is mainly devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method.<br />
<br />
We demonstrate the '''proof-of-concept''' for ''Cellock Holmes'' by detecting an opportunistic pathogen ''Pseudomonas&nbsp;aeruginosa''. This gram-negative prokaryote infects patients with open wounds and burns as well as immunodeficient people. ''P.&nbsp;aeruginosa'' cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, our team engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of ''P.&nbsp;aeruginosa'' and elicit a distinct fluorescence signal. Further, the response time of our sensor cells has been highly enhanced by the use of our special [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter '''REACh construct'''].<br />
<br />
While ''Cellocks'' are specifically designed to detect ''P.&nbsp;aeruginosa'', with a modular composition of our genetic device, it is possible to easily engineer ''Cellocks'' to detect autoinducers of other bacteria. Even more flexibility is introduced when using our [https://2014.igem.org/Team:Aachen/Project/Gal3 '''alternative molecular approach using Galectin-3'''].<br />
<br />
Hand in hand with the biological side of our project, our IT crew built the [https://2014.igem.org/Team:Aachen/Project/Measurement_Device '''WatsOn'''] , our measurement device. WatsOn is able to read and analyze the fluorescent signal emitted by the 2D biosensor. For an Open access, we publish DIY construction manual and technical details of our devices.<br />
<br />
To learn more about the different parts of our 2D biosensor, click on the respective panels on the right.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= The OD/F Device - A Project Spin-Off =<br />
<html><ul class="menuright-grid" style="width:215px;"><br />
<!-- Overview --><br />
<li style="margin-top:6px; margin-bottom:4px;margin-right:10px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device" style="color:black"><br />
<div class="menuright-item menuright-info" > <div class="menukachel"><i>OD/F Device</i></div></div><br />
<div class="menuright-item menuright-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul></html><br />
<br />
<br />
Last but not the least, we provide the OD/F Device. This device is designed to '''measure optical density and fluorescence''' of a liquid sample in cuvettes. The measurement values are subsequently displayed to the user.<br />
<br />
The OD/F Device is as well designed in accordance with the '''Open Source''' principle and all technical details as well as construction manuals are published on our wiki. We demonstrate immediate application of the OD/F Device '''in schools, community labs and in the bio-hacker scene'''.<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T14:43:26Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested to satisfy and deal with all customer needs for better sales figures, and in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on these financial profits: technical improvement followed by '''price wars'''. Besides, good price-performance ratios always catch customers and influence their purchase decision. Especially since globalization takes place products from the asian market which are often reasonably but for that they often have a lower quality. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The image on the left side shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. '''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. One weakness of our device is the low reliability compared to commercial devices. This is because of the used low cost materials. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T14:42:32Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested to satisfy and deal with all customer needs for better sales figures, and in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on these financial profits: technical improvement followed by '''price wars'''. Besides, good price-performance ratios always catch customers and influence their purchase decision. Especially since globalization takes place products from the asian market which are often reasonably but for that they often have a lower quality. <br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title=Costs and operating expenses for companies producing technical laboratory equipment (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The following image shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. '''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. One weakness of our device is the low reliability compared to commercial devices. This is because of the used low cost materials. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T14:37:31Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested to satisfy and deal with all customer needs for better sales figures, and in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on these financial profits: technical improvement followed by '''price wars'''. Besides, good price-performance ratios always catch customers and influence their purchase decision. Especially since globalization takes place products from the asian market which are often reasonably but for that they often have a lower quality. <br />
<br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The following image shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title='''Costs and operating expenses for companies producing technical laboratory equipment''' (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy for creating access to technical equipment|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
'''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T14:35:23Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested to satisfy and deal with all customer needs for better sales figures, and in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on these financial profits: technical improvement followed by '''price wars'''. Besides, good price-performance ratios always catch customers and influence their purchase decision. Especially since globalization takes place products from the asian market which are often reasonably but for that they often have a lower quality. <br />
<br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The following image shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title='''Costs and operating expenses for companies producing technical laboratory equipment''' (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<center><br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|title=Social vision as economical strategy|width=800px}}<br />
</center><br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
'''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPracticesTeam:Aachen/PolicyPractices2014-10-17T14:32:53Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= Policy & Practices =<br />
<br />
During the past summer, we not only refined the technical and biological sides of ''Cellock Holmes'' but also considered other aspects of our iGEM project such as '''social acceptance''', '''biosafety''' and '''economical relevance'''. Will society accept the technology we develop? How can we convince skeptics that synthetic biology is safe? Does our product have economical relevance and how can we best market what we built? What is the target group that might benefit from our devices, and can we make our developments available to not only the privileged population but to everybody in the world? At the meetup of the German iGEM teams in Munich earlier this summer, we also prepared a suggestion on how to handle '''intellectual proporty rights on BioBricks'''.<br />
<br />
These are only a few of the questions we discussed within our team. To read more about the different aspects of our Policy & Practices work, please click on a panel below: <br />
<br />
<center><br />
<html><ul class="team-grid" style="width:1040px"><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppsocialacceptance" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Social Acceptance</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_14-10-13_Love_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbiosafety" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Biosafety</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/11/Aachen_14-10-13_Pathogen_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppeconomics" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Economical View</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/bd/Aachen_14-10-13_Money_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbbaip" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Intellectual Property on BioBricks</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9b/Aachen_14-10-14_IP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppblog" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Blog</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b8/Aachen_14-10-13_Blogger_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Love_Cell_iNB.png|right|150px]]<br />
<br />
== Spreading the Idea of Synthetic Biology ==<br />
<span class="anchor" id="ppsocialacceptance"></span><br />
<br />
How can we convince people that the technology we develop is safe to use and that the problems we tackle with our project concern everybody? Unfortunately, a lot people around the world are scared of genetically modified organisms and any application related to them. Though we believe that '''natural skepticism''' towards new and unproved technologies is not just good but especially desirable, the current fear some people encounter gene technology with is a bit disproportionate and might be counterproductive to technological and scientific advance in related fields.<br />
<br />
However, as reported, for example, in an [http://www.rundschau-online.de/magazin/gentechnik--risiko-oder-chance-,15184902,15929266.html article] published in a major local newspaper's magazine, Kölner Stadtanzeiger, the social acceptance of biotechnological products could be higher if people felt informed better and understood the underlying science. Following up on this, we thought about how we can inform people '''factually but in a comprehensible way''' about gene technology and synthetic biology. Before we talk about fancy devices in synthetic biology, how can we '''get down to the underlying issue''' of social rejection of gene technology in general? <br />
<br />
At the same time, '''young students''' interested in science and engineering are the most valuable future source of innovation. One day, they might be the researchers who develop the solutions to the most pressing issues of our world. For that reason, informing this group of people is of utmost importance and was therefore prioritized in our Policy & Practices work.<br />
<br />
Combining these two thoughts, we visited '''two schools''', the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] in Aachen and the [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] in Hilden, where we talked to students about synthetic biology and the iGEM competition, but also explained the scientific background and social aspects of our project. A delegation of our team also visited the [https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire MakerFaire] in Hannover, a family-friendly '''exhibition for tinkerers''' of all kinds, to spread the idea of synthetic biology and to discuss our project with the public. When we organized the [https://2014.igem.org/Team:Aachen/Meetup Aachen iGEM Meetup 2014], we also made sure to include a '''public part''' where all teams who participated in our meetup had the opportunity to present their project to a general audience.<br />
<br />
To read more about our different public projects, please click on the respective logo below.<br />
<br />
<html><ul class="team-grid" style="width:1064px;"><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b> Kaiser-Karls-Gymnasium</b><br />
<br/><br/><br />
Teaching Module "Synthetic Biology" for High Schools<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/f/f7/Aachen_14-10-10_Logo_Kaiser-Karls-Gymnasium.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> NEAnderLab </b><br />
<br/><br/><br />
In Cooperation with the Gymnasium an Neandertal<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/d/d8/Aachen_14-10-10_Logo_NEAnderLab.jpg); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> MakerFaire </b><br />
<br/><br/><br />
Visit of a DIY Exhibition<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/53/Aachen_14-10-10_Logo_MakerFaire.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Meetup" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> Aachen iGEM Meetup 2014 </b><br />
<br/><br/><br />
Including Public Presentations<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5b/Aachen_14-10-10_Meetup_Logo_white_background_iVA.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
</ul></html><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
== Biosafety ==<br />
<span class="anchor" id="ppbiosafety"></span><br />
<br />
Our iGEM team is committed to reflect all aspects of the entire project, including biosafety. From the beginning on, the team thoroughly discussed safety issues that could potentially arise with the implementation of ''Cellock Holmes''. The results of these discussions fundamentally influenced the design of [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''Watson''] and the choice of potential application fields. Read more about our safety considerations on our [https://2014.igem.org/Team:Aachen/Safety Safety] page.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Money_Cell_iNB.png|right|150px]]<br />
<br />
== Economical View ==<br />
<span class="anchor" id="ppeconomics"></span><br />
<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific advance'''<br />
<br />
For both our [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] and our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device], we are following an economical strategy focused on the open source principle. Low cost and the use of easily available parts have '''heavily influenced the design choices''' made when developing our devices. You can find more information on our page [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View].<br />
<br />
{{Team:Aachen/Figure|Aachen Team Social vision.png|width=800px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-14_IP_iNB.png|right|150px]]<br />
<br />
== Intellectual Property on BioBricks ==<br />
<span class="anchor" id="ppbbaip"></span><br />
<br />
During the meetup of the German iGEM teams from 23rd to 25th May also workshops took place in which amongst others we discussed the topic of bioethics. Moral questions were addressed, regarding the value of life and human influence on it, as well as questions dealing with the possible socioeconomic effects of synthetic biology.<br />
<br />
Especially the topic of an '''open source vs. patent''' controlled field accounted for a large part of the discussion. During the discussion one student brought up the point that the legal status of parts in registry remains unclear, and that there are parts where only upon a closer look it becomes clear that the rights are company–owned. Because the issue of '''uncertain legal status of parts''' in the registry persists, the German iGEM teams '''wrote a proposal''' on how to deal with intellectual property rights in the Registry of Standard Biological Parts.<br />
<br />
For for information on intellectual property on BioBricks, read the [https://2014.igem.org/Team:Aachen/PolicyPractices/BioBrickIntellectualProperty full proposal] the German iGEM teams composed.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Blogger_Cell_iNB.png|right|150px]]<br />
<br />
== Blog ==<br />
<span class="anchor" id="ppblog"></span><br />
<br />
On our [https://2014.igem.org/Team:Aachen/Blog Blog] we post entries about recent news concerning our team's work and activities. We also write about general news from the field of synthetic biology, biotechnology and medicine. <br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPracticesTeam:Aachen/PolicyPractices2014-10-17T14:31:03Z<p>J.plum: /* Economical View */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= Policy & Practices =<br />
<br />
During the past summer, we not only refined the technical and biological sides of ''Cellock Holmes'' but also considered other aspects of our iGEM project such as '''social acceptance''', '''biosafety''' and '''economical relevance'''. Will society accept the technology we develop? How can we convince skeptics that synthetic biology is safe? Does our product have economical relevance and how can we best market what we built? What is the target group that might benefit from our devices, and can we make our developments available to not only the privileged population but to everybody in the world? At the meetup of the German iGEM teams in Munich earlier this summer, we also prepared a suggestion on how to handle '''intellectual proporty rights on BioBricks'''.<br />
<br />
These are only a few of the questions we discussed within our team. To read more about the different aspects of our Policy & Practices work, please click on a panel below: <br />
<br />
<center><br />
<html><ul class="team-grid" style="width:1040px"><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppsocialacceptance" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Social Acceptance</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_14-10-13_Love_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbiosafety" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Biosafety</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/11/Aachen_14-10-13_Pathogen_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppeconomics" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;" > <div class="menukachel" style="top: 25%;line-height: 1.5em;">Economical View</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/bd/Aachen_14-10-13_Money_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppbbaip" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Intellectual Property on BioBricks</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9b/Aachen_14-10-14_IP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/PolicyPractices#ppblog" style="color:black"><br />
<div class="menusmall-item menusmall-info" style="height: 180px; width: 180px;"> <div class="menukachel" style="top: 25%;line-height: 1.5em;">Blog</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b8/Aachen_14-10-13_Blogger_Cell_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"><br />
</div><br />
</a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Love_Cell_iNB.png|right|150px]]<br />
<br />
== Spreading the Idea of Synthetic Biology ==<br />
<span class="anchor" id="ppsocialacceptance"></span><br />
<br />
How can we convince people that the technology we develop is safe to use and that the problems we tackle with our project concern everybody? Unfortunately, a lot people around the world are scared of genetically modified organisms and any application related to them. Though we believe that '''natural skepticism''' towards new and unproved technologies is not just good but especially desirable, the current fear some people encounter gene technology with is a bit disproportionate and might be counterproductive to technological and scientific advance in related fields.<br />
<br />
However, as reported, for example, in an [http://www.rundschau-online.de/magazin/gentechnik--risiko-oder-chance-,15184902,15929266.html article] published in a major local newspaper's magazine, Kölner Stadtanzeiger, the social acceptance of biotechnological products could be higher if people felt informed better and understood the underlying science. Following up on this, we thought about how we can inform people '''factually but in a comprehensible way''' about gene technology and synthetic biology. Before we talk about fancy devices in synthetic biology, how can we '''get down to the underlying issue''' of social rejection of gene technology in general? <br />
<br />
At the same time, '''young students''' interested in science and engineering are the most valuable future source of innovation. One day, they might be the researchers who develop the solutions to the most pressing issues of our world. For that reason, informing this group of people is of utmost importance and was therefore prioritized in our Policy & Practices work.<br />
<br />
Combining these two thoughts, we visited '''two schools''', the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] in Aachen and the [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] in Hilden, where we talked to students about synthetic biology and the iGEM competition, but also explained the scientific background and social aspects of our project. A delegation of our team also visited the [https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire MakerFaire] in Hannover, a family-friendly '''exhibition for tinkerers''' of all kinds, to spread the idea of synthetic biology and to discuss our project with the public. When we organized the [https://2014.igem.org/Team:Aachen/Meetup Aachen iGEM Meetup 2014], we also made sure to include a '''public part''' where all teams who participated in our meetup had the opportunity to present their project to a general audience.<br />
<br />
To read more about our different public projects, please click on the respective logo below.<br />
<br />
<html><ul class="team-grid" style="width:1064px;"><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;" ><br />
<br/><br/><br />
<b> Kaiser-Karls-Gymnasium</b><br />
<br/><br/><br />
Teaching Module "Synthetic Biology" for High Schools<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/f/f7/Aachen_14-10-10_Logo_Kaiser-Karls-Gymnasium.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> NEAnderLab </b><br />
<br/><br/><br />
In Cooperation with the Gymnasium an Neandertal<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/d/d8/Aachen_14-10-10_Logo_NEAnderLab.jpg); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> MakerFaire </b><br />
<br/><br/><br />
Visit of a DIY Exhibition<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/53/Aachen_14-10-10_Logo_MakerFaire.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
<li style="width:220px;margin-left: 23px;margin-right: 23px;margin-bottom: 23px;margin-top: 23px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Meetup" style="color:black"><br />
<div class="team-item team-info" style="width:214px;height:214px;"><br />
<br/><br/><br />
<b> Aachen iGEM Meetup 2014 </b><br />
<br/><br/><br />
Including Public Presentations<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/5b/Aachen_14-10-10_Meetup_Logo_white_background_iVA.png); norepeat scroll 0% 0% transparent; background-size:100%;width:214px;height:214px;"> </div></a><br />
</li><br />
<br />
</ul></html><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
== Biosafety ==<br />
<span class="anchor" id="ppbiosafety"></span><br />
<br />
Our iGEM team is committed to reflect all aspects of the entire project, including biosafety. From the beginning on, the team thoroughly discussed safety issues that could potentially arise with the implementation of ''Cellock Holmes''. The results of these discussions fundamentally influenced the design of [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''Watson''] and the choice of potential application fields. Read more about our safety considerations on our [https://2014.igem.org/Team:Aachen/Safety Safety] page.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Money_Cell_iNB.png|right|150px]]<br />
<br />
== Economical View ==<br />
<span class="anchor" id="ppeconomics"></span><br />
<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific advance'''<br />
<br />
For both our [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] and our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device], we are following an economical strategy focused on the open source principle. Low cost and the use of easily available parts have '''heavily influenced the design choices''' made when developing our devices. You can find more information on our page [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View].<br />
<br />
{{Team:Aachen/Figure|Aachen_Team_social_vision.png|width=800px}}<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-14_IP_iNB.png|right|150px]]<br />
<br />
== Intellectual Property on BioBricks ==<br />
<span class="anchor" id="ppbbaip"></span><br />
<br />
During the meetup of the German iGEM teams from 23rd to 25th May also workshops took place in which amongst others we discussed the topic of bioethics. Moral questions were addressed, regarding the value of life and human influence on it, as well as questions dealing with the possible socioeconomic effects of synthetic biology.<br />
<br />
Especially the topic of an '''open source vs. patent''' controlled field accounted for a large part of the discussion. During the discussion one student brought up the point that the legal status of parts in registry remains unclear, and that there are parts where only upon a closer look it becomes clear that the rights are company–owned. Because the issue of '''uncertain legal status of parts''' in the registry persists, the German iGEM teams '''wrote a proposal''' on how to deal with intellectual property rights in the Registry of Standard Biological Parts.<br />
<br />
For for information on intellectual property on BioBricks, read the [https://2014.igem.org/Team:Aachen/PolicyPractices/BioBrickIntellectualProperty full proposal] the German iGEM teams composed.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-13_Blogger_Cell_iNB.png|right|150px]]<br />
<br />
== Blog ==<br />
<span class="anchor" id="ppblog"></span><br />
<br />
On our [https://2014.igem.org/Team:Aachen/Blog Blog] we post entries about recent news concerning our team's work and activities. We also write about general news from the field of synthetic biology, biotechnology and medicine. <br />
<br />
{{Team:Aachen/Footer}}</div>J.plumhttp://2014.igem.org/File:Aachen_Team_Social_vision.pngFile:Aachen Team Social vision.png2014-10-17T14:29:17Z<p>J.plum: </p>
<hr />
<div></div>J.plumhttp://2014.igem.org/Team:Aachen/PolicyPractices/EconomicsTeam:Aachen/PolicyPractices/Economics2014-10-17T14:10:29Z<p>J.plum: /* OD/F Device */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_open_access.png|right|300px]]<br />
<br />
= Economical View =<br />
The economical considerations regarding our project were carried out according to the motto: <br />
<br />
'''Make the world a better place - Open access for scientific progress'''<br />
<br />
In the center of every economic analysis are the customers and their needs and desires. Every commercial company is interested to satisfy and deal with all customer needs for better sales figures, and in order to maintain regular clientele. Both measures aim for '''higher financial profits'''. On the global seller’s market of technical laboratory equipment there is a permanent competition between the existing providers. This competition depends on these financial profits: technical improvement followed by '''price wars'''. Besides, good price-performance ratios always catch customers and influence their purchase decision. Especially since globalization takes place products from the asian market which are often reasonably but for that they often have a lower quality. <br />
<br />
Take a look at cost calculations for technical laboratory equipment including development, production, transport, warehousing and sale. Usually, you will find in this branche on one hand low costs for research and development, restruction, amorthilisation and other costs. On th other hand you will find really high costs of revenues and also selling, general and administartion expenses. At least financial profit is a big cost point cause buisinesses have to self-financing. In general, these factors are making '''technical equipment for labs really expensive''' and so one unattractive for low budgets. One off the world's biggest producer of laboratory products is [http://www.thermofisher.com/en/home.html Thermo Fisher Scientific]. They also offer photometer and other equipment stuff. The following image shows all costs and operating expenses out off the [http://ir.thermofisher.com/investors/financial-information/annual-reports/default.aspx annual report 2013] from Thermo Fisher Scientific.<br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|TeamAachen DiagrammThermoScientific.png|title='''Costs and operating expenses for companies producing technical laboratory equipment''' (annual report. (2013). Thermo Fisher Scientific)|width=600px}}<br />
</center><br />
<br />
We follow a strategy to circumvent unnecessary costs for customers by realizing a '''social vision'''. In accordance with the principle of open source including both '''open hardware''' and open software, information where to get the necessary components, quantities, a step-by-step technical construction manual and circuit diagrams could be published online for free. Potential customers can follow our given building instructions and download needed informations from our [https://2014.igem.org/Team:Aachen/Notebook/Engineering engineering website]. So our profit is not of financial nature but is instead based on recognition and on motivating other iGEM teams and companies to spread the idea of open hardware, too. In accordance with the motto do-it-yourself we offer '''low budget versions''' while '''reducing''' all '''potential costs''' exept for the basic costs where material costs are falling under it. Customers with a little technical skill, willingness to try something new and keen to experiments could follow our step-by-step building instructions and creat their own devices. <br />
<br />
To make our whole idea more user-friendly we thought over the offering of device kits. With this theoretical method customers don't have to order a lot of separate device parts from diffrent componies but still were not able of '''flexibility'''. Flexible with regard to potential new modifications of the devices including the choise of other building parts or a replenishment. Especially in natural science changes are lying under a daily agenda. New improvements are so direct assimili- and realizable in our concept devices.<br />
<br />
At least we want to mention that our vision is limited in getting acceptance by companies on the global seller market and we know about this problem. These companies, parts of them global players, are profit orientated and following another firm strategy. Our vision is standing against this as '''non-profit-idea''' finding acceptance in other groups of customers with lower budgets and just open view of fiancial aspects. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== ''WatsOn'' ==<br />
<span class="anchor" id="economicswatson"></span><br />
<br />
The measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for our [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D biosensor], too, has been designed accordingly. So far, no comparable devices could be found on the commercial market. Here, we definitely have a pioneer role. Following our do-it-yourself method everybody can create his own ''WatsOn'' for 310 $ using the given [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn building instructions]. Starting with the order of needed components followed by assembling the different parts. Components for rebuliding are easy availible all over the world using the folowing links.<br />
<center><br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1||spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15&nbsp;mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480&nbsp;nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450&nbsp;nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40&nbsp;Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100&nbsp;Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||total||-||-||243.88||309.70<br />
|}<br />
</center><br />
<br />
Such low prices with the acceptance of '''self-building''' opens a grand new customer market and offers competition to commercial saleable products. Especially in developing counties our ''WatsOn'' could help and its low rebuilding costs are making purchase possible. Such those low material costs and the high technical flexibility are making ''WatsOn'' to an adequate device for developing countries, community labs and the biohacker scene. In particular for developing countries such a low budget device version bids a good alternative to regular devices for detecting pathogens. With our device institutions in such those countries have an access to modern technology and working methods.<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Team_WatsOn_3.png|title=''WatsOn's'' self-made concept makes it available for low budged institutions|width=800px}}<br />
</center><br />
Also for this device we are offering the building plan and also the needed software Measuraty for use. This makes it for institutions and also for amateurs possible to modify the device according to personal progress including for example the '''range of detectable micro-organisms'''. As an example it could be possible to detect not just the fluorescent of GFP and iLOV but also important reporter-proteins YFP, CFP or RFP. This would just be possible by changing the filter slides or LEDs.<br />
<br />
However, please always remind yourself of the respective [https://2014.igem.org/Team:Aachen/Safety safety aspects] when dealing with GMOs and human pathogens.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== OD/F Device ==<br />
<span class="anchor" id="economicsodf"></span><br />
<br />
One of our greater visions we share with the synthetic biology community is that everyone interested in biological work should have access to basic laboratory equipment. With our OD/F Device we are able to offer a low cost solution for community labs, biohackers and high schools. <br />
<br />
<center><br />
{{Team:Aachen/FigureFloat|Netdiagramm_ODF_Device.png|title= Advantages and Disadvantes of our OD/F Device compared to commercial availiable devices|width=400px}}<br />
</center><br />
<br />
In general we have to make a difference between our OD and our F device. The reason for this is the bad comparability to commercial devices. These don't combine the measure of fluorescence and OD. With our OD/F we offer a solution to combine both measurement methods in one device. With our given instructions it is also possible to build two separate devices one for OD and one for F. In this context we offer the user a higher flexibility of choice during the user is also able to modify our device according to his own ideas and wishes. <br />
<br />
Commercially obtainable spectrophotometers like [http://www.opticsplanet.com/unico-model-s-1205-spectrophotometer-5-nm-bandpass.html UNICO S-1205], for example, costs 1.249&nbsp;$ or more, and can measure optical density only. At the same time they are heavy, not portable and therefore not easy to handle. Specially the portability is beside the low costs a big poitive point which allows new rages of applications. But compared to our device it is able to work with a broader range of wavelengths and it has a higher accuracy and precision. Besides commercial [http://www.moleculardevices.com/systems/microplate-readers/fluorescent-readers/gemini-xps plate reader] are also available on the market, too. To compare our device with this comercial devices is really difficult because no portable devices like ours could be found which can also measure at a wave-band of 480 nm.<br />
<br />
Comparable to our developed device in the points measuring range and portability is the OD-meter [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php CO 8000]. This device measures also the OD at 600&nbsp;nm but still costs almost 920&nbsp;$. Our [https://2014.igem.org/Team:Aachen/OD/F_device OD/F Device] can measure OD as well as fluorescence for less than [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy 60&nbsp;$] like the following chart is showing. Prices are given in $ and € for better accoutability and conversion.<br />
<br />
<center><br />
'''All needed components their quantities and prices for creating your own OD/F device'''<br />
{| class="wikitable"<br />
! align="center" |'''OD/F device'''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|-<br />
! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] <br />
|-<br />
| 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 <br />
|-<br />
| 1||[http://www.mouser.com/ProductDetail/ams/TSL235R-LF/%3Fqs%3D14HO7rLZPQsjmBHaoYCzkA%253D%253D&sa=U&ei=3fA8VN3sN8T0OuLPgLAJ&ved=0CCUQ2yk&sig2=WOchotQO4XDym0jpXDjtzw&usg=AFQjCNGNr9DthURC_BKhgthh8EuJhjqutg TSL 235R]||2.47||3.14||2.47||3.14 <br />
|-<br />
| 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDzxHNysWBp Display 16x2]||2.58||3.28||2.58||3.28 <br />
|-<br />
| 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 <br />
|-<br />
| 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 <br />
|-<br />
| 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 <br />
|-<br />
| 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 <br />
|-<br />
| 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 <br />
|-<br />
| 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893#.VDzzMNysWBo power supply]||2.20||2.80||2.20||2.80<br />
|-<br />
| 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18<br />
|-<br />
| 1||3&nbsp;mm acrylic glas (black)||7.98||10.14||7.98||10.14<br />
|-<br />
| 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913#.VDz3ttysWBo Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88<br />
|-<br />
| 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VDz4HtysWBo Male Headers]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600&nbsp;nm]||0.99||1.11||0.87||1.11<br />
|-<br />
! Total OD !!!!!!!! 45.94 !! 58.37 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total F !!!!!!!! 46.06 !! 58.52 <br />
|-<br />
| 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.99||1.11||0.87||1.11 <br />
|-<br />
| 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480&nbsp;nm]||0.99||1.26||0.99||1.26<br />
|-<br />
! Total OD/F !!!!!!!! 47.05 !! 59.78 <br />
|-<br />
|}<br />
</center><br />
<br />
'''Cost saving''' lies here round about '''850&nbsp;$'''. Money that could definetly be given some better utilizations like into other projects. All you have to do is to order the needed parts from the list above, invest some time and have technnical skills to construct our OD/F Device. It's still this aspect which could also have simultanious a positive learning effect for people in schools and universities and so on. Therefore, we present a solution for '''low budget institutions''' like schools, universities, community labs and the biohacking scene. <br />
<br />
<center><br />
{{Team:Aachen/Figure|Team_Aachen_OD F device.png|title= Possible application of our OD/F device|width=800px}}<br />
</center><br />
<br />
In our cooperation with the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and with [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] one of our target groups gathered first experience using our OD/F Device. As result we received the answer of our question if the device is useable in daily practice with teenagers. And we got a positive feedback for this. Even young people are able to use and understand our device without any security risk like mentioned on our [https://2014.igem.org/Team:Aachen/Safety safty page].<br />
<br />
<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>J.plum