Team:Aalto-Helsinki/Cooperation

From 2014.igem.org

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     <h3>Devices We Used</h3>
     <h3>Devices We Used</h3>
         <ol>
         <ol>
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             <li>BBa_I20260 in pSB3K3</li>
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             <li>BBa_I20260 in pSB3K3 (sequencing data in a <a href="https://static.igem.org/mediawiki/2014/9/91/AaltoHelsinki_interlabs39.png">picture</a> or <a href="https://static.igem.org/mediawiki/2014/3/3e/AaltoHelsinki_interlabs39.pdf">text</a> format)</li>
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             <li>BBa_K823005 + BBa_E0240 in pSB1C3 (B0032-E0040-B0015) in pSB1C3</li>
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             <li>BBa_K823005 + BBa_E0240 in pSB1C3 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a <a href="https://static.igem.org/mediawiki/2014/8/8a/AaltoHelsinki_interlabs41.png">picture</a> or <a href="https://static.igem.org/mediawiki/2014/6/61/AaltoHelsinki_interlabs41.pdf">text</a> format)</li>
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             <li>BBa_K823012 + BBa_E0240 (B0032-E0040-B0015) in pSB1C3</li>
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             <li>BBa_K823012 + BBa_E0240 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a <a href="https://static.igem.org/mediawiki/2014/8/8b/AaltoHelsinki_interlabs42.png">picture</a> or <a href="https://static.igem.org/mediawiki/2014/c/cb/AaltoHelsinki_interlabs42.pdf">text</a> format)</li>
         </ol>
         </ol>
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    <p>
 
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        We sequenced all three devices and they were confirmed to be ok. You cand find the sequencing results by clicking the name of the device. (sekvenssitiedostot partsien nimiin, kuva/teksti?)
 
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    </p>
 
     <h3>Protocols</h3>
     <h3>Protocols</h3>
     <h4>Building the Devices</h4>
     <h4>Building the Devices</h4>

Revision as of 16:19, 13 October 2014

Cooperation

We wanted to give something to the iGEM Community and help other teams as much as possible.

Scroll down to read more
Seeker tools
Interlab Study
Interteam Cooperation

Photo © Tanja Maria

Seekers

Right from the start, we decided that we were going to develop software tools to make the work of our team easier. We also wanted to share the tools with the iGEM Community to help everyone, too!

We made two different Seeker brand tools (BioBrick Seeker and Team Seeker) for making the research part of iGEM projects a little easier. Both have tens of thousands of lines of data to search through, but the results update in real-time. Both get their content from JSON files that can be easily added to and which are completely separate from the code, so expanding the tools for the future can be done by just adding new data!

Both of the Seekers were written in JavaScript using the Angular.js library. They use Yeoman for scaffolding and deployment, and they are currently running on GitHub Pages. GitHub Pages is a free service and handles requests very quickly, so they will stay available for the foreseeable future.

All of the code is available as open source on GitHub and is free to be reused, modified and expanded. All of the projects can be found through our GitHub organization Quiet Sushi Force.

BioBrick Seeker

BioBrick Seeker was created to make searching for the needed BioBricks in the 2014 iGEM Distribution a bit easier. It can be used to find Bricks with a certain keyword or list all from a certain type. It even has a search for the part names to see if the Brick you need is in this year's distribution.

All of the code and installation instructions for future development are available on the BioBrick Seeker GitHub page.

Here's a screenshot of BioBrick Seeker and how it works if you want to search for BioBricks that have the word 'fluorescent' in their description.

BioBrick Seeker Reception

The tool was received very well and got a lot of mentions on Twitter and got even featured on the iGEM 2014 Help page. We put Google Analytics on the site to get a rough idea of where in the world the tool was actually used. Turned out it was used on 5 different continents and many many teams all around the world.

Here's a screenshot of the amount of sessions from different parts of the world. (12th October 2014)

Team Seeker

Team Seeker is a tool that you can use to search through the project abstracts of past teams. With this tool you don't need to use hours of research time to make sure that your idea hasn't been done yet in iGEM but you can just type in what you wish to find! With Team Seeker it's also easy to find all the projects that are close to your interests and this way the background research becomes a lot easier. Team Seeker has a smart phrase search; writing relevant phrases or words in the search bar brings up projects relating to them.

All of the code and installation instructions for future development are available at the project's GitHub page.

Here's a screenshot of Team Seeker.

Interlab Study

We participated in the Measurement Interlab Study arranged by iGEM. Here are our results.

Devices We Used

  1. BBa_I20260 in pSB3K3 (sequencing data in a picture or text format)
  2. BBa_K823005 + BBa_E0240 in pSB1C3 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a picture or text format)
  3. BBa_K823012 + BBa_E0240 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a picture or text format)

Protocols

Building the Devices

We built the test devices with the same ligation protocol that we have used for all our ligations. The protocol can be found here (click).

Testing Protocol

The samples were grown in LB broth, in E. coli Top10 and they were incubated in 37 C° (shaker 220 rpm) for 17 hours. Before measuring the GFP levels, the samples were diluted to achieve the same OD600 and 100 ul of each sample was pipetted onto a 96-well black microtiter plate. We had three samples of all three devices.

The microtiter plate was inserted in a Thermo Scientific Varioskan and the following parameters were set:

  • Excitation wavelength: 470 nm
  • Emission wavelength: 511 nm
  • Bandwidth: 5nm
  • Measurement time: 500 ms

We used BBa_K592009 (in pSB1C3, grown in Top10) in LB, and LB only as negative controls. We didn’t have a positive control for these measurements.

Results:

All measurement data () is in Relative Fluorescence Units (RFU).

. Measurement data.

Interteam Cooperation

ETH Zürich

Low Budget iGEM Challenge

We did some extraordinary intercountry collaboration with ETH Zürich team. Together, we participated to iGEM Colombia team's Low Budget iGEM Challenge. We planned, carried out and reported our experiments regarding an accessible, easy and low cost PCR method. You can find our entry here. Furthermore, we made a video describing our method in more detail. You can find the video featuring Oskari from Aalto-Helsinki and Sumana from ETH Zürich below:

We participated in the Low Budget iGEM Challenge together with ETH Zürich! Click to watch the video.

Complexity Survey

ETH Zürich team investigated the emergence of complex patterns. We helped their human practice part by filling out their survey about how we perceive complexity in everyday life as in biology and its emergence and how we react to it. We shared the survey for our friends and collected response on our Facebook page. As a result, we reached over 20 entries and received this awesome badge as a reward!

This is the badge we got for getting more than 20 entries for ETH-Zürich's complexity survey!

Colombia

Mathematical modeling Low Budget iGEM Challenge entry

Minttu, Oskari and Pietu skyping to Columbia.

Paris-Saclay

Paris-Saclay was the first iGEM team we got to talk to. It was great to hear of people doing the same kind of thing, though it was also kind of intimidating with such a big group and many advisors. It seemed like we'd need more knowledge to pull this off. Being a Finnish team, we appropriately Skyped from a sauna that was turned into a meeting room.

We got a lot of good tips about what to focus on and what to expect at Jamboree. They were doing bio art, so we contacted Aalto University's Biofilia project for them and they were very interested in talking to the Paris-Saclay team about their "Ceci n'est pas un citron"-project.

Paris-Saclay's view of us.

Virginia

Virginia's Survey

(more than 20 entries)

This badge we got for getting over 20 entries on Virginia's survey!

Amsterdam 2012

Meetings with a PhD student Tania from University of Helsinki, plenty of advice and feedback about our pitch etc.

Groningen 2012

Skype call, getting to know to the factors what makes an iGEM project successful one

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