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| - | <pageheader>Software Tools Used in Project Chimera</pageheader>
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| - | <th scope="col">Software tools used in Chimera... <br> </th>
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| - | <ul><h2>Eugene for Designing Devices</h2>
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| - | <tr> <th scope="col">Testing testing<br>
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| - | <ul><h2>Raven for Building Devices</h2>
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| - | <ul><h2>TASBE Tools for Testing Devices</h2>
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| - | <p>Using BBN Technologies <a href="https://synbiotools.bbn.com/">TASBE tools</a>, we were able to quickly and easily analyze the flow cytometry data obtained for our various devices. We collected data using a BD LSRFortessa outfitted with a high throughput sampler, allowing for the fast capture of cells in a 96-well format.<p>
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| - | <p>Below, you can see more details of our experimental design and the controls we used, which are required by the TASBE tools in order to convert the arbitrary fluorescence units obtained from the flow cytometer into absolute units in the form of molecules of equivalent fluorescein (MEFL). This allows the user to show their data in absolute units that then allow scientists to compare experiments across labs and machines.</p>
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| - | <p>The <a href="https://static.igem.org/mediawiki/2013/0/07/CST_Beads.pdf">Cytometer Setup and Tracking</a> beads offered by BD Biosciences were utilized to set the laser delay and optimize the cytometer settings prior to running any samples through the Fortessa.</p>
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| - | <p>We also used <a href="https://static.igem.org/mediawiki/2013/c/cf/Spherotech_beads.pdf">Spherotech's 8-peak particles</a> (RCP-30-5A) in order to obtain standard MEFL units for the FITC channel. They are also used to measure the long term performance of the flow cytometer and should be included in every experiment run through the flow cytometer.</p>
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| - | <br><p><center><img src="https://static.igem.org/mediawiki/2014/c/c1/BU2014_flow_Experimental_Design.png" width="85%"></center></p><br>
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| - | <br><p><center><img src="https://static.igem.org/mediawiki/2014/f/f6/BU2014Characterization_workflow.png" width="75%"></center></p><br>
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| - | <p>In order to obtain MEFL measurements for the RFP protein, we had to utilize a dual positive control that had a FITC channel fluorescent protein. We used GFP for our FITC control and RFP for our Texas Red control. We used the J23014 promoter in both devices, along with the BCD2 5'UTR element. The histograms show the similarity of expression between the two colors on our machine and the dot plot shows a agreement between them. The bottom figure is from the TASBE tools Color Translation model, which agrees with our dot plots and histograms. </p>
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| - | <ul><h2>SBOL for Sharing Devices</h2>
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| - | <!--Footer-->
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| - | <br><br><br><br><br><div class="sponsors" align="center"> <br><br><header1>Our Sponsors</header1><br><br><img src="https://static.igem.org/mediawiki/2014/c/c5/Sponsors_bu14.png" width="983" height="149"> </div>
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