Team:UCSD Software/SoftwareAchievements

From 2014.igem.org

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                <li id = "database"><a href = "#">Database</a></li>
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                <li id = "traversal"><a href = "#">Traversal algorithms</a></li>
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                <li id = "app"><a href = "#">Web application</a></li>
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                <li id = "parts"><a href = "#">Parts</a></li>
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                    <li><div class="btn btn-lg" id="achieve">Software Achievements</div></li>
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                     <div class="btn btn-lg" id="attributions">Attributions</div>
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                     <div class="btn btn-lg" id="achieve">Achievements</div>
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           <h1>Documentation</h1>
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           <h1>iGEM Gold Medal requirements</h1>
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          <p>
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We have documented each aspect of our project, ranging from the database to the traversal algorithms to the web application, in a very concise manner. We have discussed the project aims, methods, and success. Also, we have discussed the future directions of the project.
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We have also carved out a tutorial for our application that will make it easy for people to get started with SBiDER. This includes:
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<ul>
<ul>
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<li>Tutorial for using the web app.</li>
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<li>We did some modeling of circuits predicted by our tool, validation of search results, and complexity analysis work of our project. You can find details under the Validation section and Modeling section of the <a href = "https://2014.igem.org/Team:UCSD_Software/Project">Project</a> page. Using our tool, we were able to predict several novel circuit topologies recently published by <a href="http://www.nature.com/nbt/journal/v31/n5/pdf/nbt.2510.pdf">Piro et al</a></li>
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<li>FAQ fo navigating CyNetShare.</li>
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<li>We re-used and improved an existing database, & developed on it (<a href = "http://pubs.acs.org/doi/abs/10.1021/sb400139h">Linh's paper</a>). We also made use of SBOL visual (decribed in further detail under the "Web Application" section of the <a href = "https://2014.igem.org/Team:UCSD_Software/Project">Project</a> page). Furthermore, we utilize and extend the web-application architecture used by the <a href="http://cidar.bu.edu/owl/"> Owl Datasheet generator project</a> from iGEM 2013</li>
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</p>
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<li>We created a Python API for interacting with our database. The API documentation is available on the <a href = "https://2014.igem.org/Team:UCSD_Software/Documentation">Documentation</a> page as well as on <a href="https://github.com/igemsoftware/UCSD-iGEM_2014/tree/master/CircuitNetwork/web/doc">Github</a>. This way, other developers can use to build on our project or use it in novel ways for their own projects.</li>
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<li>As mentioned earlier, we made use of SBOLv standard.</li>
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           <h1>Re-Use and Best software development practices</h1>
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           <h1>iGEM Silver Medal requirements</h1>
           <ul>
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           <li>Our complete source code has been submitted to the iGEM GitHub repository.</li>
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           <li>We've demonstrated the relevance of our project to Synthetic Biology <a href = "https://2014.igem.org/Team:UCSD_Software/Project">here</a>.</li>
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           <li>We have also included comprehensive code documentation for outside developers.</li>
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           <li>We have a comprehensive and well-designed <a href = "https://2014.igem.org/Team:UCSD_Software/Documentation">Tutorial</a> for using our app.</li>
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          <li>We also used git versioning from the start of our project so that the commit history will be available on github.             </li>
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<li>We created a Python API for interacting with our database. The API documentation is available on the <a href = "https://2014.igem.org/Team:UCSD_Software/Documentation">Documentation</a> page as well as on <a href="https://github.com/igemsoftware/UCSD-iGEM_2014/tree/master/CircuitNetwork/web/doc">Github</a>. This way, other developers can use to build on our project or use it in novel ways for their own projects.</li>
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           <li>Use of SBOL and other standards. (Use and/or improvement of existing synthetic biology tools or frameworks; cite other iGEM teams).</li>
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           <li>We used QUnit, a JavaScript unit testing framework, for some of our work during the summer. In addition, we utilized a number of realistic test cases (pulled from published literature to validate our tool during development. <a href = "https://2014.igem.org/Team:UCSD_Software/Documentation">Look here</a></li>
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           <h1>Relevance and Validation</h1>
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           <h1>iGEM Bronze Medal requirements</h1>
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<p>
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<ul>
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This (provide link or info directly) is how our project is relevant to Synthetic Biology.  
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<li>Our team is all registered and ready to go! We're all immensely excited to represent UC San Diego at Boston.</li>
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</p>  
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<li>We've created a project description for our application <a href = "https://2014.igem.org/Team:UCSD_Software/Project">here</a>.</li>
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<p>
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<li>Find us ready with a Poster to talk about SBiDer at the Regional Jamboree and World Championship Jamboree, 2014.</li>
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We have also devised an experimental test for our program/algorithm/workflow (demonstrate/display here).  
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<li>Our code is well-documented and available via <a href = "https://github.com/igemsoftware/UCSD-iGEM_2014">The iGEM Software Registry</a> on GitHub.</li>
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<h1>Testing</h1>
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<p>In the early stages of our project, we had planned on and worked with testing frameworks such as QUnit, which is a JavaScript Unit Testing Framework. Although we ended up not using it eventually, it was something that a lot of our team members had worked on and/or considered using.  
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Latest revision as of 03:27, 18 October 2014


iGEM Gold Medal requirements

  • We did some modeling of circuits predicted by our tool, validation of search results, and complexity analysis work of our project. You can find details under the Validation section and Modeling section of the Project page. Using our tool, we were able to predict several novel circuit topologies recently published by Piro et al
  • We re-used and improved an existing database, & developed on it (Linh's paper). We also made use of SBOL visual (decribed in further detail under the "Web Application" section of the Project page). Furthermore, we utilize and extend the web-application architecture used by the Owl Datasheet generator project from iGEM 2013
  • We created a Python API for interacting with our database. The API documentation is available on the Documentation page as well as on Github. This way, other developers can use to build on our project or use it in novel ways for their own projects.
  • As mentioned earlier, we made use of SBOLv standard.

iGEM Silver Medal requirements

  • We've demonstrated the relevance of our project to Synthetic Biology here.
  • We have a comprehensive and well-designed Tutorial for using our app.
  • We created a Python API for interacting with our database. The API documentation is available on the Documentation page as well as on Github. This way, other developers can use to build on our project or use it in novel ways for their own projects.
  • We used QUnit, a JavaScript unit testing framework, for some of our work during the summer. In addition, we utilized a number of realistic test cases (pulled from published literature to validate our tool during development. Look here

iGEM Bronze Medal requirements

  • Our team is all registered and ready to go! We're all immensely excited to represent UC San Diego at Boston.
  • We've created a project description for our application here.
  • Find us ready with a Poster to talk about SBiDer at the Regional Jamboree and World Championship Jamboree, 2014.
  • Our code is well-documented and available via The iGEM Software Registry on GitHub.

Retrieved from "http://2014.igem.org/Team:UCSD_Software/SoftwareAchievements"