http://2014.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Raik2014.igem.org - User contributions [en]2024-03-28T16:46:18ZFrom 2014.igem.orgMediaWiki 1.16.5http://2014.igem.org/Tracks/SoftwareTracks/Software2014-10-11T15:07:11Z<p>Raik: </p>
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<h1>iGEM 2014 Software Track</h1><br />
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<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
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This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
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Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
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<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
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<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
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<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
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<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
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SYSU-Software won the Best Software Project Award in 2013. <br />
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<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
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<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
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<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
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<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
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<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
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<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
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<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
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<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
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<ul><br />
<li>Wiki documentation must contain project aims, methods and success</li><br />
<li>Use git (from beginning of project)</li><br />
<li>Submission of complete source code and any auxiliary files to GitHub</li><br />
<li>Basic code documentation for outside developers</li><br />
<li>Detailed installation or setup instructions for users (if applicable)<br />
<li>for web servers: ensure another developer can easily set up an independent copy of your web server. Preferably provide a Docker container of your web server. A virtual machine snapshot or Vagrant configuration file and / or simple step by step installation instructions may be an alternative.</li> <br />
<li>If your institution requires it, seek Institutional Review Board (IRB) approval before conducting software testing.</li><br />
</ul><br />
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<h2><a class="anchor" id="Medal Criteria"></a>Medal Criteria</h2><br />
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<p><br />
<b>Bronze. </b>The following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Register the team, have a great summer, and have fun attending the Jamboree in Boston.</li><br />
<li>Create and share a description of the team's project via the iGEM wiki.</li><br />
<li>Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.</li><br />
<li>Develop and make available, via <a href="https://github.com/igemsoftware">The iGEM Software Registry</a>, an open source software that supports Synthetic Biology based on Standard Parts. </li><br />
</li></ol><br />
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<b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</li><br />
<li>Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</li><br />
<li>Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc). </li><br />
<li>Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of <a href="http://martinfowler.com/bliki/TestCoverage.html"> test coverage </a>, bug tracking facilities, documentation of releases and changes between releases.</li><br />
</ol><br />
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<p><br />
<b>Gold</b>: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: <br><br />
<ol id="criterialist"><br />
<li>Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.</li><br />
</ol><br />
And the second goal can be any one of the following:<br />
<ol id="criterialist"><br />
<li>Make your software interact / interface with the Registry. </li><br />
<li>Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks. </li><br />
<li>Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)</li><br />
<li>Support and use the SBOL and / or SBOLv standard.</li><br />
<li>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. <b>Describe</b> an approach that your team used to address at least one of these questions. <b>Evaluate</b> your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.</li><br />
</li></ol><br />
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<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
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<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
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<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
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<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
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</html></div>Raikhttp://2014.igem.org/Judging/AwardsJudging/Awards2014-09-05T18:48:18Z<p>Raik: </p>
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<!--<p style="color:red;"> <b> Please note that all information on this page is currently in a draft version. Please check back often for details. </b> </p>--><br />
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<p>The following is a list of Awards given by the iGEM Judges and some general information about how Award decisions are made. For examples of award-winning work, see <br />
<a href="https://igem.org/Results?year=2013&region=All&division=igem">the 2013 Jamboree Results</a>. </p><br />
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<h3>iGEM Medals</h3> <br />
<p><i><br />
<strong>New Track teams must meet medal criteria specific to their track. Please see your <a href="https://2014.igem.org/Tracks#New_Tracks">New Track pages </a> for more details on what you need to accomplish to be awarded a medal. </strong><br />
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<p><br />
All teams can earn medals. Teams must nominate themselves using the Judging Form, which will be available later. The three levels of medals, from lowest to highest are Bronze, Silver, and Gold. Requirements for each medal are:<br><br />
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<b>Bronze. </b>The following 6 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Team registration.</li><br />
<li>Complete Judging form.</li><br />
<li>Team Wiki.</li><br />
<li>Present a poster and a talk at the iGEM Jamboree.</li><br />
<li>The description of each project must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services. Please see the <a href="https://2011.igem.org/Team:Imperial_College_London/Team">iGEM 2011 Imperial College Acknowledgements page</a> for an example. </li><br />
<li>Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). Please note you must submit this new part to the iGEM Parts Registry. Please see the <a href="http://parts.igem.org/Help:Adding_Parts">Registry help page</a> on <a href="http://parts.igem.org/Help:Adding_Parts">adding new parts</a>. A new application and/or outstanding documentation (quantitative data showing the Part’s/ Device’s function) of a previously existing BioBrick part also counts. Please see the <a href="http://parts.igem.org/Help:Contributions">Registry help page</a> on <a href="http://parts.igem.org/Help:Contributions">how to document your contributions</a>. To fulfill this criteria, you will also need to submit the part with its original part name to the Registry, following the <a href="http://parts.igem.org/cgi/dna_transfer/index.cgi">submission guidelines</a>.</li></ol><br />
</p><br />
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<p><br />
<b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.</li><br />
<li>Document the characterization of this part in the “Main Page” section of that Part’s/Device’s Registry entry.</li><br />
<li>Submit this new part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).</li><br />
<li>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Articulate at least one <b>question</b> encountered by your team, and describe how your team considered the(se) question(s) within your project. Include attributions to all experts and stakeholders consulted.</li></ol><br />
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<p><br />
<b>Gold</b>: In addition to the Bronze and Silver Medal requirements, any one or more of the following: <br><br />
<ol id="criterialist"><br />
<li>Improve the <b>function</b> OR <b>characterization</b> of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry. Please see the <a href="http://parts.igem.org/Help:Contributions">Registry help page</a> on <a href="http://parts.igem.org/Help:Contributions">how to document a contribution</a> to an existing part. <br><i>The growth of the Registry depends on having a broad base of reliable parts. This is why the improvement of an existing part is just as important as the creation and documentation of a new part. An "improvement" is anything that improves the functionality and ease-of-use of a part, so that it is more likely to be used by the community. "Characterization" is a measurement of a functional parameter of a part, preferably in absolute units, that can precisely and repeatably be performed in other labs.</i></li><br />
<li>Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.</li><br />
<li>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. <b>Describe</b> an approach that your team used to address at least one of these questions. <b>Evaluate</b> your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.<br />
</p><br />
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<p> <h3> Special Prizes</h3> </p><br />
<p>Special prizes are awarded to honor specific innovative and unique contributions to iGEM. The iGEM 2014 judging committee hopes to award the following Special prizes, conditional on the accomplishments presented by the teams.</p><br />
<br />
<ol><br />
<li><b>Best Policy and Practices Advance</b>: iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. <b>Describe</b> an approach that your team used to address at least one of these questions. <b>Evaluate</b> your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.<br />
<br />
</li><br />
<li><b>Best Innovation in BioBrick Measurement</b>: There are a lot of exciting Parts in the Registry, but many Parts have still not been characterized. Designing great measurement approaches for characterizing new parts or developing and implementing an efficient new method for characterizing thousands of parts are good examples. Teams interested in competed for the Measurement prize are <b><i>strongly</i></b> encouraged to participate in the <a href ="https://2014.igem.org/Tracks/Measurement/Interlab_study">measurement interlab study</a>.</li><br />
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<li><b>Best Model</b>: Mathematical models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. </li><br />
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<b>Best New Standard</b>: Standards help to make sharing biological parts easier. For example, the BioBrick DNA assembly standard makes it easier to construct parts from pre-existing parts created by the entire BioBrick community. What other sorts of standards can you create? How about a standard system for measuring promoter activity, a standard method for reporting compatible/ incompatible parts, a standard to help describe and control post-translational modifications (such as phosphorylation), or chassis-specific standards (for instance, a system for describing and sharing transgenic yeast)?<br></li><br />
<i>Your New Standard should be clearly presented and easy to find in your <b>Wiki</b>.</i></li>--><br />
</ol><br />
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<p><br />
<ol start="4" id="criterialist"><br />
<li><b>Best New Basic BioBrick Part</b>: Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are *many* opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. To be eligible for this award, this part must adhere to Bronze medal requirement #6 and have been sent to the Registry of Standard Biological Parts.<br><br />
<i>Your best Basic BioBrick Part(s) should be visible on your Wiki’s <b>Data Page</b> (see <a href="https://igem.org/Sample_Data_Page">https://igem.org/Sample_Data_Page</a>).</i></li><br />
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<li><b>Best New Composite BioBrick Part</b>: New BioBrick devices can be made by combining existing BioBrick Parts. For example, Inverters, Amplifiers, Smell Generators, Protein Balloon Generators, Senders, Receivers, Actuators, and so on. To be eligible for this award, this part must adhere to Bronze medal requirement #6 and have been sent to the Registry of Standard Biological Parts.<br><br />
<i>Your best new Composite BioBrick Part(s) should be visible on your Wiki’s <b>Data Page</b>.</i></li><br />
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<li><b>Best Wiki</b>: The team Wiki is the “face” of your iGEM project. The team Wikis serve as the main project information resource for future iGEM students and teams, as well as the rest of the world. This award honors the “model” Wiki page, which exemplifies what the following year’s Wikis should strive for.</li><br />
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<li><b>Best Poster</b>: Posters should be attractive, clear, and concisely present your team's work.</li><br />
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<li><b>Best Presentation</b>: Presentations should be clear, engaging, and communicate your project to a broad audience.</li><br />
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<li><b>Best Two-Page Communication</b>: We're introducing a new requirement in 2014. Teams are required to make a two page summary of their project in the style of a lab report. </li><br />
</ol></p><br />
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<ol start="10" id="criterialist"><br />
<li><b>NEW! Best Parts Collection</b>: Did your team make a lot of great parts? Is there a team that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection or a collection of awesome pigment parts? Tell the judges you should be evaluated for the Best Parts Collection award! To be eligible for this award, these parts must adhere to Bronze medal requirement #6 and have been sent to the Registry of Standard Biological Parts.</li><br />
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<li><b>NEW! Best Supporting Software</b>: Regardless what's the topic, iGEM projects often create or adapt computational tools to move the bigger project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can even prove surprisingly useful for others. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honour such "nuggets" of computational work. To be eligible, your software has to be documented and made available under an <a href="http://opensource.org/licenses">OSI approved</a> open source license.<br />
</li><br />
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<li><b>NEW! Best Art & Design Installation</b>: </li><br />
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<!--<li><b>Most Improved Registry Part</b></li>--><br />
</ol><br />
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<p> <h3> Grand Prizes</h3> </p><br />
<p>A small number of iGEM teams will be selected by the judges as iGEM Finalists. These teams will be selected based on the overall excellence of their entire project, from choice of project, to new Parts and Devices, to the quality of the Project Description, Poster, and Presentation, to the success and impact of the project, to consideration of issues of Policy and Practices, and so on. There will be three finalists from both the undergraduate section and the overgraduate section.</p><br />
<br />
<p><br />
<ol id="criterialist"><br />
<li><b>Grand Prize Undergraduate</b>: also known as the aluminum BioBrick Trophy; best overall undergraduate team project</li><br />
<li><b>First Runner-up Undergraduate</b>: the next highest ranking undergraduate team project</li><br />
<li><b>Second Runner-up Undergraduate</b>: the next highest ranking undergraduate team project</li></ol><br />
</p><br />
<br />
<p><br />
<ol id="criterialist"><br />
<li><b>Grand Prize Overgraduate</b>: also known as the aluminum BioBrick Trophy; best overall overgraduate team project</li><br />
<li><b>First Runner-up Overgraduate</b>: the next highest ranking overgraduate team project</li><br />
<li><b>Second Runner-up Overgraduate</b>: the next highest ranking overgraduate team project</li></ol><br />
</p><br />
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<p> <h3>Track Prizes</h3> </p><br />
<br />
<p>The iGEM 2014 judging committee hopes to award the following Area prizes, conditional on the accomplishments presented by the teams. Each prize will be awarded at the discretion of the judges. Below are brief descriptions for each Area prize:</p><br />
<br />
<p><br />
<ol id="criterialist"><br />
<br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Energy">Energy</a> Project</b>: World energy consumption has increased by roughly a factor of six since 1950. In May 2013, atmospheric C02 readings taken at the Mauna Loa Observatory in Hawaii surpassed 400 ppm for the first time, an unsustainably high concentration of CO2. Can we use synthetic biology to create energy technologies that produce less CO2, make energy using feedstock and waste materials or otherwise sustainably generate energy? </li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Environment">Environment</a> Project</b>: The quality of the air, water, and land, both on Earth and other heavenly bodies, limits the happiness of humans and other creatures. Can biotechnology be used to help clean the air, provide fresh drinking water, restore or enhance soil quality, terraform a near-Earth asteroid, or protect, preserve, or enhance natural biological diversity?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Food_Nutrition">Food & Nutrition</a> Project</b>: People need to eat. Can biotechnology be responsibly used to produce food or nutritional molecules without causing widespread shortages of either, and without harming the environment that future generations will inherit?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Foundational_Advance">Foundational Advance</a> Project</b>: Just thirty-five years ago, scientists could not cut and paste pre-existing fragments of genetic material like we can today. The discovery and application of DNA recombination allowed us to assemble new genes. The synthetic biology community needs other enabling technologies that help to make new accomplishments possible. What are other types of basic tricks does nature use? Have you discovered and applied one that could revolutionize synthetic biology?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Health_Medicine">Health & Medicine</a> Project</b>: Many health and medical problems might best be addressed by improved biological technologies. What can synthetic biology do?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Information_Processing">Information Procressing</a> Project</b>: The diversity and abundance of biological properties, behaviors, and parts presents a huge information processing challenge. Has your project led to an innovative system that allows us to navigate and use lots of information quickly and effectively?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/Manufacturing">Manufacturing</a> Project</b>: Have you ever heard of nanotechnology? Well, biology is a nanotechnology that already exists, and that actually works. The ribosome is a programmable nanoassembler embedded within a reproducing machine. Could we responsibly use biology to manufacture useful products, from the nanoscale (atoms) to the decascale (buildings and bridges)? What can biology be programmed to manufacture?</li><br />
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<li><b>Best <a href="https://2014.igem.org/Tracks/New_Application">New Application</a> Project</b>: We're guessing that you have great ideas that nobody has ever thought about, or if they have they forgot to tell somebody else. Can you imagine an entirely new application area for biological technology?</li><br />
</ol><br />
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<p> <h3>New Track Prizes</h3> </p><br />
<br />
<p><br />
We are introducing seven new tracks to the iGEM 2014 competition. On top of our regular tracks such as Foundational Advance and Health and Medicine, we also have the new tracks listed below. Each of the following new tracks is eligible for a best in track award. New Track teams have the same eligibility for awards as all other iGEM teams, pending confirmation from the judging committee. For example, this makes them eligible for (but not limited to) the Best Poster, Best Presentation, Best Wiki, Best New Basic BioBrick Part awards as well as the Undergraduate and Overgraduate BioBrick Trophies. <br />
</p><br />
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<br />
<ol><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Art_Design">Art and Design</a> Project</b>: Teams of art and design students with input from scientific advisors can use art to drive their iGEM projects, while also making scientific contributions. We are looking for projects that use art and design to consider and explore current and future implications of synthetic biology (including stakeholders, communication, pedagogy, thinking outwards).<br />
</li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Community_Labs">Community Labs</a> Project</b>: The Community Lab Track will have the same focus on bench research as the traditional iGEM track, however we are also looking for projects that increase the accessibility of synthetic biology. These might include kits such as Genomikon, or equipment hacks such as the Open PCR. We especially want to encourage teams that may not be able to conduct genetic engineering experiments within their labs due to local regulations, but who might innovate in the areas of equipment, software, outreach, education, etc...</li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Entrepreneurship">Entrepreneurship</a> Project</b>: Entrepreneurship in iGEM is about fostering the development of a new industry where Synthetic Biology is the underlying technological platform. As with any new industry, it is not clear which business plans will be the most successful. But, there are also more fundamental questions: What Business models will succeed, how will intellectual property affect company formation and funding, what skills are required at each stage of company’s life cycle, how will government policies promote or hinder new companies, what will be the social contract with Synthetic Biology companies?</li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Measurement">Measurement</a> Project</b>: With all the instruments in our laboratories, why isn't measurement a solved problem in synthetic biology? Part of the problem is knowing what to measure and in what context. The iGEM Measurement Track will aim to address some of these problems.</li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Microfluidics">Microfluidics</a> Project</b>: Microfluidic, or “lab-on-a-chip” technology, is a maturing field of research involving miniaturized systems where fluids are manipulated on the scale of nanoliters and picoliters. With microfluidics it is possible to perform high-throughput biological experiments integrating multiple functions in devices no larger than a postage stamp. </li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Policy_Practices">Policy and Practices</a> Project</b>: In previous years, iGEM teams that have made significant contributions to integrating broader social considerations into the design of their synthetic biology devices, have been awarded with the Special Prize for Best Human Practices Advance. This year we are introducing a dedicated ‘Policy & Practices’ track for teams looking to contribute detailed work grounded in the humanities and social sciences. The new name of ‘Policy & Practices’ is intended to reflect a broadened and matured vision for activities in this track - and across iGEM as a whole - that has evolved from the strong track record of Human Practices at iGEM.</li><br />
<li><b>Best <a href="https://2014.igem.org/Tracks/Software">Software</a> Project</b>: Computers have been around for a long time. Why don't we have more, great software tools to help everyone engineer synthetic biological systems based on standard biological parts?<br><br />
See the <a href="https://2014.igem.org/Tracks/Software">Software Track Page</a> for details.<br><br />
</ol><br />
<br />
<br />
<p>Please send us any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. </p><br />
<br />
<br><br />
<br><br />
<br />
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</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-07-21T16:37:06Z<p>Raik: </p>
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<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<ul><br />
<li>Wiki documentation must contain project aims, methods and success</li><br />
<li>Use git (from beginning of project)</li><br />
<li>Submission of complete source code and any auxiliary files to GitHub</li><br />
<li>Basic code documentation for outside developers</li><br />
<li>Detailed installation or setup instructions for users (if applicable)<br />
<li>for web servers: ensure another developer can easily set up an independent copy of your web server. Preferably provide a Docker container of your web server. A virtual machine snapshot or Vagrant configuration file and / or simple step by step installation instructions may be an alternative.</li> <br />
<li>If your institution requires it, seek Institutional Review Board (IRB) approval before conducting software testing.</li><br />
</ul><br />
<br />
<h2><a class="anchor" id="Medal Criteria"></a>Medal Criteria</h2><br />
<br />
<p><br />
<b>Bronze. </b>The following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Register the team, have a great summer, and have fun attending the Jamboree in Boston.</li><br />
<li>Create and share a description of the team's project via the iGEM wiki.</li><br />
<li>Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.</li><br />
<li>Develop and make available via <a href="http://parts.igem.org/2014SWTools">The Registry of Software Tools</a>, an open source software tool that supports Synthetic Biology based on Standard Parts. </li><br />
</li></ol><br />
</p><br />
<br />
<p><br />
<b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</li><br />
<li>Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</li><br />
<li>Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc). </li><br />
<li>Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of <a href="http://martinfowler.com/bliki/TestCoverage.html"> test coverage </a>, bug tracking facilities, documentation of releases and changes between releases.</li><br />
</ol><br />
</p><br />
<br />
<p><br />
<b>Gold</b>: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: <br><br />
<ol id="criterialist"><br />
<li>Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.</li><br />
</ol><br />
And the second goal can be any one of the following:<br />
<ol id="criterialist"><br />
<li>Make your software interact / interface with the Registry. </li><br />
<li>Show how your software affects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security. </li><br />
<li>Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks. </li><br />
<li>Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)</li><br />
<li>Support and use the SBOL and / or SBOLv standard.</li><br />
</li></ol><br />
</p><br />
<br />
<br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-07-10T22:18:55Z<p>Raik: Make validation obligatory for Gold</p>
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<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Medal Criteria"></a>Medal Criteria</h2><br />
<br />
<p><br />
<b>Bronze. </b>The following 5 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Register the team, have a great summer, and have fun attending the Jamboree in Boston.</li><br />
<li>Create and share a description of the team's project via the iGEM wiki.</li><br />
<li>Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.</li><br />
<li>Develop and make available via The Registry of Software Tools </a>an open source software tool that supports synthetic biology. </li><br />
</li></ol><br />
</p><br />
<br />
<p><br />
<b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br><br />
<ol id="criterialist"><br />
<li>Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</li><br />
<li>Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</li><br />
<li>Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc). </li><br />
<li>Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of <a href="http://martinfowler.com/bliki/TestCoverage.html"> test coverage </a>, bug tracking facilities, documentation of releases and changes between releases.</li><br />
</ol><br />
</p><br />
<br />
<p><br />
<b>Gold</b>: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: <br><br />
<ol id="criterialist"><br />
<li>Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.</li><br />
</ol><br />
And the second goal can be any one of the following:<br />
<ol id="criterialist"><br />
<li>Make your software interact / interface with the Registry. </li><br />
<li>Show how your software affects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security. </li><br />
<li>Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks. </li><br />
<li>Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)</li><br />
<li>Support and use the SBOL and / or SBOLv standard.</li><br />
</li></ol><br />
</p><br />
<br />
<br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
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</html></div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:54:47Z<p>Raik: /* Bronze Medal */</p>
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''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Jamboree in Boston.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide [https://www.docker.io/ Docker] container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
None of the bonus points are a strict requirement but you have to collect at least one or three of them in order to earn the Silver or Gold medal, respectively.<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-06-04T21:44:56Z<p>Raik: </p>
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<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Detailed requirements for Bronze, Silver and Gold medals are being fleshed out on the <a href="Software/Judging">judging page</a>. Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
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''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide [https://www.docker.io/ Docker] container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
None of the bonus points are a strict requirement but you have to collect at least one or three of them in order to earn the Silver or Gold medal, respectively.<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:43:04Z<p>Raik: /* Bronze Medal */</p>
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<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide [https://www.docker.io/ Docker] container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
None of the bonus points are a strict requirement but you have to collect at least one or three of them in order to earn the Silver or Gold medal, respectively.<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:42:11Z<p>Raik: /* Bonus points */</p>
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<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
None of the bonus points are a strict requirement but you have to collect at least one or three of them in order to earn the Silver or Gold medal, respectively.<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:36:49Z<p>Raik: /* 2014 Software Track Judging */</p>
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''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:35:00Z<p>Raik: /* 2014 Software Track Judging */</p>
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</html><br />
<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it<br />
<br />
Please note, these requirements are preliminary and will still be changed and fine-tuned by the software committee. Please feel free to contact the software committee to ask for clarification or participate in the discussion.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:32:49Z<p>Raik: </p>
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<div class="grid_9"><br />
</html><br />
<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:32:02Z<p>Raik: </p>
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</div> <br />
</div><br />
</div><br />
</html><br />
<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-06-04T21:30:47Z<p>Raik: </p>
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<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Detailed requirements for Bronce, Silver and Gold medals are being fleshed out on the <a href="Software/Judging">judging page</a>. Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
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</body><br />
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<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Detailed requirements for Bronce, Silver and Gold medals are being fleshed out on the <a href="Tracks/Software/Judging">judging page</a>. Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:27:30Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:27:16Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:26:49Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-06-04T21:25:43Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Detailed requirements for Bronce, Silver and Gold medals are being fleshed out on the [Tracks/Software/Judging judging page]. Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="https://bcl.med.harvard.edu/?page_id=42">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:22:34Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:21:39Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal (Note: changed from last year!)===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* collect one bonus point (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* good test coverage<br />
* excellent installation-, user- and developer documentation<br />
* collect 3 bonus points (see below)<br />
<br />
<br />
===Bonus points===<br />
<br />
* 2-3 points for: experimental validation of your software or algorithm (experiments can be outsourced to other teams, labs or companies)<br />
* 1 point for: use and support of [http://www.sbolstandard.org SBOL]<br />
* 1 point for: re-use and further development of previous iGEM software projects (or parts thereof)<br />
* 1 point for: use and/or improvement of existing synthetic biology tools or frameworks<br />
* 1 point for: development of a well documented library for other developers rather than "only" stand-alone Apps for end users<br />
* 1-2 points for: surprising us with something that is so cool or new that we would have never thought of it</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:05:20Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
** for web servers: provide Docker container of your server (details are being worked on by iGEM headquarters)<br />
* Basic user guide<br />
<br />
===Silver Medal (Note: changed from last year!)===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* fulfill one bonus point requirement (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
<br />
===Bonus points===<br />
<br />
* use and support of SBOL and other standards<br />
* re-use and further development of previous iGEM software projects (or parts thereof)<br />
* use and/or improvement of existing synthetic biology tools or frameworks<br />
* development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T21:02:15Z<p>Raik: /* Gold Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
* Basic user guide<br />
<br />
===Silver Medal (Note: changed from last year!)===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* fulfill one bonus point requirement (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation, testing the performance of their development -- experimental or by other teams. Note, even if the algorithm turns out not to work, they can still get Gold if their test is good and the analysis convincing.<br />
#Show how their software effects Human Practices in Synthetic Biology. This may include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
===Bonus points===</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T20:58:25Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Detailed installation or setup instructions for users (if applicable)<br />
* Basic user guide<br />
<br />
===Silver Medal (Note: changed from last year!)===<br />
<br />
In addition to the Bronze Medal requirements:<br />
<br />
#Follow best practises in software development so that other developers can modify, use and re-use your code.<br />
#Provide a comprehensive and well-designed User Guide.<br />
#Demonstrate the relevance of your development for Synthetic Biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)<br />
* more than one realistic test case<br />
* automated unit tests, documentation of test coverage<br />
* fulfill one bonus point requirement (see below)<br />
<br />
===Gold Medal===<br />
<br />
To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:<br />
<br />
#Provide a convincing validation testing the performance of their development -- experimental or by other teams. Note, even if your algorithm turns out not to work, you can still get Gold if your test is good and the analysis convincing.<br />
#Discuss how your software effects Human Practices in Synthetic Biology. Such topics include: ethics, sharing, innovation and creative process, ownership, safety, or security.<br />
<br />
===Bonus points===</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T20:34:17Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
''Detailed Technical Requirements:''<br />
<br />
* Wiki documentation of project aims, methods and success<br />
* Use git (from beginning of project)<br />
* Submission of complete source code and any auxiliary files to GitHub<br />
* Basic code documentation for outside developers<br />
* Installation or setup instructions for users (if applicable)<br />
* Basic user guide</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:10:13Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{ombox | text = Detailed technical requirements.}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:09:52Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{ombox <br />
| text = Detailed technical requirements<br />
}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:09:16Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{ambox <br />
| text = Detailed technical requirements<br />
}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:08:22Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{ambox | text = Detailed technical requirements}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:03:56Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{This workaround may harm accessibility.}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:03:40Z<p>Raik: /* Bronze Medal */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{Note|<translate><br />
This workaround may harm accessibility.</translate>}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T19:03:26Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>''Status of this document:'' '''Draft for discussion'''<br />
<br />
==2014 Software Track Judging==<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.<br />
<br />
===Bronze Medal===<br />
<br />
#Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree.<br />
#Create and share a description of the team's project via the iGEM wiki.<br />
#Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
#Develop and make available via the [[The Registry of Software Tools|The Registry of Software Tools]] an open source software tool that supports synthetic biology.<br />
<br />
{{Note|<translate><!--T:58--><br />
This workaround may harm accessibility.</translate>}}</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T18:54:02Z<p>Raik: /* 2014 Software Track Judging */</p>
<hr />
<div>==2014 Software Track Judging==<br />
<br />
Status of this document: '''Draft for discussion'''<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.</div>Raikhttp://2014.igem.org/Tracks/Software/JudgingTracks/Software/Judging2014-06-04T18:53:31Z<p>Raik: Created page with "==2014 Software Track Judging== Status of this document: ```Draft for discussion``` Judging for the Software track will have area-specific requirements for medals as detailed b..."</p>
<hr />
<div>==2014 Software Track Judging==<br />
<br />
Status of this document: ```Draft for discussion```<br />
<br />
Judging for the Software track will have area-specific requirements for medals as detailed below. These criteria evolve together with the iGEM competition, so please read carefully. Software Tools teams are also eligible for selection as Finalists, Grand Prizes, and Special Prizes at the iGEM 2014 World Championship Jamboree.</div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-04-23T21:59:51Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biology</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Lixin Zhang, Chinese Academy of Sciences, Beijing, China</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-03-06T17:06:51Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
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</style><br />
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<br />
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<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc)</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-23T19:29:00Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
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<br />
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<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<p><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png"><br />
</p><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-23T19:27:28Z<p>Raik: add contact mail</p>
<hr />
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{{NavBar}}<br />
<html><br />
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<style type="text/css"><br />
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<html><br />
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</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<br><br />
Please feel free to contact us with any question or concern:<br />
<img src="https://2014.igem.org/File:Softwaretrack_email.png"><br />
<br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/File:Softwaretrack_email.pngFile:Softwaretrack email.png2014-02-23T19:24:50Z<p>Raik: software track contact address</p>
<hr />
<div>software track contact address</div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-23T19:22:20Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
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<style type="text/css"><br />
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</style><br />
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<br />
<div class="container_12"><br />
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<html><br />
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<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>A well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
<br><br />
<br><br />
<br><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T20:04:32Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "500px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T20:03:53Z<p>Raik: </p>
<hr />
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{{NavBar}}<br />
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</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project. Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T20:01:17Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
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<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
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<div id="contentcontainer"><br />
<br />
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<html><br />
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<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: <a href="http://www.raiks.de/research.html">Raik Grünberg</a> and co-Chair <a href="http://bcl.med.harvard.edu/people/gil">Gil Alterovitz</a>.<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T19:59:38Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams. The Chairs of the iGEM Software track are: [http://www.raiks.de/research.html Raik Grünberg] and co-Chair [http://bcl.med.harvard.edu/people/gil Gil Alterovitz].<br />
</p><br />
<br />
<ul><br />
<li>Gil Alterovitz, Wyss Institute / Harvard Medical School, Boston, US</li><br />
<li>Evan Appleton, Boston University, US</li><br />
<li>Raik Grünberg, IRIC / University of Montreal, Canada</li><br />
<li>HaiYan Liu, USTC, Hefei, China</li><br />
<li>Edward Perello, Desktop Genetics, Cambridge, UK</li><br />
<li>Sally Radwan, Canonical, London, UK</li><br />
<li>Jenhan Tao, UCSD, San Diego, US</li><br />
<li>Sean Ward, Synthase, London, UK</li><br />
<li><emph>HQ organizational support:</emph> Kim de Mora</li><br />
</ul><br />
<br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T19:44:08Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h4>End User Documentation</h4><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h4>Re-Use and Best software development practices</h4><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h4>Relevance and Validation</h4><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T19:41:40Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
</p><br />
<br />
<h3>End User Documentation</h3><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h3>Re-Use and Best software development practices</h3><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h3>Relevance and Validation</h3><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<p><br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T19:40:55Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
<br />
<h3>End User Documentation</h3><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h3>Re-Use and Best software development practices</h3><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h3>Relevance and Validation</h3><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
<br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-20T19:39:42Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Software teams are not be required to contribute parts to the Registry (but instead are expected to contribute to the GitHub software repository). Key requirements for software teams are:<br />
<br />
<h3>End User Documentation</h3><br />
Core requirements are:<br />
<ul><br />
<li>Wiki documentation of project aims, methods and success -- in line with the general iGEM requirements</li><br />
<li>Detailed installation or setup instructions (if applicable)</li><br />
<li>An well-designed User Guide explaining how to use of your program or tool</li><br />
</ul><br />
<br />
<h3>Re-Use and Best software development practices</h3><br />
Core requirements are:<br />
<ul><br />
<li>submission of your complete source code and any auxiliary files to the iGEM github repository</li><br />
<li>Use git versioninig from the start of your project so that the commit history is / will be available on github</li><br />
<li>Comprehensive code documentation for outside developers</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>more than one realistic test case</li><br />
<li>automated unit tests, documentation of test coverage</li><br />
<li>API documentation, preferably automatically built from source code documentation</li><br />
</ul><br />
Bonus points for:<br />
<ul><br />
<li>use of SBOL and other standards</li><br />
<li>re-use and further development of previous iGEM software projects (or parts thereof)</li><br />
<li>use and/or improvement of existing synthetic biology tools or frameworks</li><br />
<li>development of well documented libraries for other developers rather than "only" stand-alone Apps for end users</li><br />
</ul><br />
<br />
<h3>Relevance and Validation</h3><br />
Core requirement:<br />
<ul><br />
<li>Demonstrate the relevance of your development for Synthetic Biolgy</li><br />
</ul><br />
Highly recommended:<br />
<ul><br />
<li>Devise an experimental test for your program/algorithm/work flow</li><br />
</ul<br />
The experimental validation of software/computational projects is <emph>not</emph> expected to result in a super fancy engineering project (that's what all the wet lab tracks are for). Instead we would like to see simple and straightforward experiments (for example: gene synthesis, expression, fluorescence of x constructs) which can be delegated to external labs or collaborating teams. <br />
iGEM/software will try to support teams who want to outsource experimental testing to academic or commercial labs. Details will follow.<br />
<br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-19T23:23:32Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
The iGEM software track started in 2008. Since 2012, there is a centralized repository for iGEM software projects on GitHub. Please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will not only preserve the projects but also help others to avoid re-inventing the wheel. <br />
</p><p><br />
iGEM software developers often work closely with experimental synthetic biologists to improve design, assembly and testing of biological circuits, make bio engineering more predictive or help discovering and exchanging information about standard biological parts. Of course we are open to all kind of cool projects but please make sure that they are relevant to real-world Synthetic Biology. For some things, there is no need to start from scratch. Over the years, the Synthetic Biology community has already created many interesting libraries, design frameworks, and software tools. Please use, abuse and improve them wherever possible. There is also a nascent standard for synthetic biology data exchange (SBOL) which you should probably have a look at.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Requirements for Software teams will differ from other tracks, as you will not be required to contribute parts to the Registry. However, there will be additional elements to a software team. <br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-19T22:52:07Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
Starting in 2008, area awards for software tools were introduced. These efforts produced a number of truly unique software projects. Last year, we introduced a centralized repository for iGEM software projects on GitHub. BTW, please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will help to not only preserve the projects but also allow others to avoid building existing tools as well as extend them. Moreover, we hope to help create a community of users around specific design frameworks and community standards.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Requirements for Software teams will differ from other tracks, as you will not be required to contribute parts to the Registry. However, there will be additional elements to a software team. <br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raikhttp://2014.igem.org/Tracks/SoftwareTracks/Software2014-02-17T14:21:05Z<p>Raik: </p>
<hr />
<div>{{CSS/Main}}<br />
{{NavBar}}<br />
<html><br />
<br />
<style type="text/css"><br />
#software {display: block;}<br />
</style><br />
<br />
<div id="contentcontainer"><br />
<br />
<div class="container_12"><br />
<br />
<div class="grid_3"><br />
</html><br />
{{HTML/TrackMenu}}<br />
<html><br />
<div class="contentpara" style="margin-top: 60px;"><br />
<p style="width: 160px; margin: auto; color:#7d7d7d; font-size:80%;"></p><br />
</div> <br />
</div><br />
<br />
<div class="grid_9"><br />
<br />
<h1>iGEM 2014 Software Track</h1><br />
<br />
<body><br />
<br />
<p><br />
Computational work and software development are a very important part of Synthetic Biology. The iGEM competition again has a track for teams that want to focus on exactly that. <br />
</p><p><br />
This year, we want to create a yet closer link to the wet lab side of iGEM. We therefore encourage software/computational teams to validate their tools and algorithms with some experiments. These experiments can be "outsourced", that is, performed in some other lab or by a collaborating iGEM team. We are working on supporting software teams to find partner labs -- stay tuned! Moreover, if you have a large ambitious project that includes both a lot of computational and a lot of wet lab work, think about registering two teams -- students can be members of both the computational and the wet lab team at the same time. This gives more exposure to the hard computational work which will be judged by experts (and you can win one more price!). <br />
</p><p><br />
Software projects will also be judged by the quality of documentation (both for users and for other developers), by how much they embrace best practices (e.g. modern tools, testing, agile development) and by how well they make use of previous iGEM teams' work and by how well they enable other teams to pick up from where they will leave. Many software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. We would love to see that happen again this year.<br />
</p><br />
<br />
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2><br />
<br />
<p><br />
Starting in 2008, area awards for software tools were introduced. These efforts produced a number of truly unique software projects. Last year, we introduced a centralized repository for iGEM software projects on GitHub. BTW, please, use git right from the start of your project -- knowing the history of your commits is very helpful for other developers who want to build on your hard work. This will help to not only preserve the projects but also allow others to avoid building existing tools as well as extend them. Moreover, we hope to help create a community of users around specific design frameworks and community standards.<br />
</p><br />
<br />
<h3>Team Projects from previous years</h3><br />
<h4>UT Tokyo 2012</h3><br />
<p><br />
In 2012, the UT Tokyo team created an innovative BioBrick search page. Their project was web accessible and allowed users to search the Registry for parts using many different keywords, approaches, years and other parameters. They also created a rating system for parts based on the number of uses. <br />
</p><br />
<a href="https://2012.igem.org/Team:UT-Tokyo-Software"><img src="https://static.igem.org/mediawiki/2014/e/e7/BioBrick_Search-UT_Tokyo2012.jpg" width = "700px"></a><br />
<br />
<h4>SYSU-Software 2013</h3><br />
<p><br />
SYSU-Software created a program called CAST (Computer Aided Synbio Tool), to address specific technical challenges in synthetic biology. Their software can automatically perform regulatory network and gene circuits design, modeling, vector design and actually build the proposed circuit. All designs can be stored in a database to be shared through CAST. In addition, they incorporated wetlab experimentation into the project to validate their new simulation model. <br />
</p><br />
<p><br />
SYSU-Software won the Best Software Project Award in 2013. <br />
</p><br />
<br />
<a href="https://2013.igem.org/Team:SYSU-Software"><img src="https://static.igem.org/mediawiki/2014/7/71/SYSU-2013.png" width = "700px"></a><br />
<br />
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2><br />
<ul><br />
<br />
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li><br />
<br />
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li><br />
<br />
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li><br />
<br />
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li><br />
<br />
</ul><br />
<h2><a class="anchor" id="Requirements"></a>Requirements</h2><br />
<br />
<p><br />
Requirements for Software teams will differ from other tracks, as you will not be required to contribute parts to the Registry. However, there will be additional elements to a software team. <br />
</p><br />
<br />
<h2><a class="anchor" id="Committee"></a>Track Committee</h2><br />
<br />
<p><br />
We have a great committee to help out 2014 software teams:<br />
</p><br />
<br />
<ul><br />
<li>Edward Perello</li><br />
<li>Evan Appleton</li><br />
<li>Sally Radwan</li><br />
<li>Raik Grunberg</li><br />
<br />
</ul><br />
<br />
</ul><br />
</body><br />
</div><br />
</div><br />
</html></div>Raik