Difference between revisions of "Team:Queens Canada/Software"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1>Software</h1>
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<h3>Best Software Tool Special Prize</h3>
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>.
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You must also delete the message box on the top of this page to be eligible for this prize.
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<h5> Inspiration </h5>
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<img src="https://static.igem.org/mediawiki/2017/6/64/T--Queens_Canada--NavyNavBackground1.jpg" style="width:100%;height:30px">
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Here are a few examples from previous teams:
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<li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">2014 Aachen</a></li>
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<p class="big"><font size="5" color="black">
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This summer QGEM created a unique ratiometric application program. <br><br>
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Our program outlines the steps required to build specific bifunctional E.coli biofilms, based on designated conditions - as deemed by the user. As such, the user inputs the designated ratio of the two proteins to be found in the biofilm, as well as the protein coding sequences, and organism/plasmid. The program then outputs the required promoter sequences and RBS sequences necessary to achieve such a ratio under the given conditions.<br><br>
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Various components of the program were modeled, predominately by ordinary differential equations, as outlined on QGEM's "Mathematic Theory" wiki-page. These models were then directly integrated into our program's code, to ensure reliable results.<br><br>
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QGEM also had the opportunity to integrate the Salis Lab's RBS Calculator code directly into our program, thanks to the gracious help and support from Dr. Howard Salis. Dr. Salis provided QGEM with the Python helper script necessary to access the web-based API. Given the nature of the system, QGEM was given an authentication token for the file. Thus, it is not accessible to be run externally without contacting Dr. Salis. <br>
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<br>
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The program is run in Python 2.7, and can be found on our GitHub page.
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  <p><font face="Corbel">contact us: <a href="director@qgemteam.com">director@qgemteam.com</a></p></font>
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Revision as of 03:52, 28 October 2017

This summer QGEM created a unique ratiometric application program.

Our program outlines the steps required to build specific bifunctional E.coli biofilms, based on designated conditions - as deemed by the user. As such, the user inputs the designated ratio of the two proteins to be found in the biofilm, as well as the protein coding sequences, and organism/plasmid. The program then outputs the required promoter sequences and RBS sequences necessary to achieve such a ratio under the given conditions.

Various components of the program were modeled, predominately by ordinary differential equations, as outlined on QGEM's "Mathematic Theory" wiki-page. These models were then directly integrated into our program's code, to ensure reliable results.

QGEM also had the opportunity to integrate the Salis Lab's RBS Calculator code directly into our program, thanks to the gracious help and support from Dr. Howard Salis. Dr. Salis provided QGEM with the Python helper script necessary to access the web-based API. Given the nature of the system, QGEM was given an authentication token for the file. Thus, it is not accessible to be run externally without contacting Dr. Salis.

The program is run in Python 2.7, and can be found on our GitHub page.


contact us: director@qgemteam.com