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<h2> iGEM 2015 Tracks - Software</h2>
 
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<p>
 
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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.
 
−
</p><p>
 
−
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!).
 
−
</p><p>
 
−
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.
 
−
</p>
 
  
−
<h2><a class="anchor" id="Track Details"></a>Information about the track</h2>
 
  
 +
<h1><u><a id="Track Details"></a>SynBio Needs Software</u></h1>
 +
<p>
 +
<p>
 +
<p>If you are going to design a new life form, chances are you’ll need a computer to design the smallest genetic circuits and deal with genome-scale complexity. </p>
 +
<p>Software development is a valuable skill set for any synthetic biology team to have. In previous iGEM competitions, software has often been built by wetlab teams to solve specific problems. Recognising the utility of these software tools, and the importance of software development skills, the software track has been set up for computer scientists and developers to nurture their knowledge of biology, and for computational biologists, bioinformaticians and biologists to enhance their aptitude for building software.</p>
 +
<p>Whether you are a wet lab team that has decided to build a software tool, or a software group looking to get involved in iGEM, we encourage you compete in the dedicated software track 2015. </p>
 
<p>
 
<p>
−
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.
 
−
</p><p>
 
−
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.
 
−
</p>
 
−
 
−
<h3>Team Projects from previous years</h3>
 
−
<h4>UT Tokyo 2012</h3>
 
 
<p>
 
<p>
−
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.
 
−
</p>
 
−
<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>
 
  
−
<h4>SYSU-Software 2013</h3>
+
<h2><u><a id="Track Details"></a>Deadlines for this track</u></h2><p>
 +
<ol>
 +
  <li>Installability Test</li>
 +
  <li>Submission of Code</li>
 +
</ol> 
 +
<p>
 +
<p>
 +
1) IF you are creating an application that requires direct installation onto a hard drive, you must provide the software committee with a version of the program by September 11th. This is so that we can test to see if the tool is installable. The contact person for this will be our co-chair, Raik Greunberg. You must email (Raik.Gruenberg [at] gmail.com) with an installable version of your code so that it can be tested thoroughly ahead of the next deadline.
 +
<p>
 +
<p>
 +
2) The deadline for submission of code to the iGEM Github Repository is the same date as the Wiki Freeze for conventional iGEM teams. You MUST submit your code to iGEM by September 18th - the judges will use this code as the basis of evaluating your project at the jamboree. Any code submitted after this deadline will be ignored and may subject your team to severe penalties.
 +
<p>
 
<p>
 
<p>
−
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.
 
−
</p>
 
 
<p>
 
<p>
−
SYSU-Software won the Best Software Project Award in 2013.
 
−
</p>
 
  
−
<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>
+
<h2><u><a id="Track Details"></a>Information about the track</u></h2>
 +
<h4><u>Work Together &amp; Solve Challenges in SynBio Software</u></h4>
  
−
<h2><a class="anchor" id="Resources"></a>iGEM Software Resources</h2>
+
<p>Wetlab teams have lots of problems. Software teams can provide solutions. This year, iGEM is encouraging software and wet lab teams to work together and assist each other. If you need software for your wetlab project, or are a software team looking for a problem reach out to each other, by using the iGEM Reddit, contacting other teams on Twitter, or encouraging computer science departments to start teams.</p>  
−
<ul>
+
  
−
<li><a href="http://igem.synbioreview.com/"> iGEMsoft: an iGEM software project aggregator</a></li>
 
  
−
<li><a href="https://github.com/igemsoftware"> iGEM software on GitHub</a></li>
+
<h4><u>Two Teams are Better than One</u></h4>
  
−
<li><a href="http://www.sbolstandard.org/"> Synthetic Biology Open Language (SBOL) </a></li>
+
If you have a large ambitious wet lab project that includes a lot of computational 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 prize!).
  
−
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API"> iGEM Parts Registry API</a></li>
 
  
 +
<h4><u>Learn to be a Professional Biocoder</u></h4>
 +
iGEM encourages software teams to learn the best practices of professional software developers. As software development is about solving problems in way that is useful for the users and for other developers, students, the software track focuses on teaching students the importance of:
 +
 +
<ul>
 +
<li>Quality of codebase documentation</li>
 +
<li>Automated testing practices</li>
 +
<li>Version control (Git &amp; Github)</li>
 +
<li>Professional software development practices (Agile, Scrum etc)</li>
 +
<li>Making use of previous iGEM teams’ work</li>
 +
<li>Documenting code to enable other teams to pick up from where they will leave</li>
 +
<li>Conducting user experience testing</li>
 
</ul>
 
</ul>
−
<h2><a class="anchor" id="Requirements"></a>Requirements</h2>
 
  
 +
<h4><u>Tools that Stand the Test of Time</u></h4>
 +
<p>Many tools built by iGEM teams have been of professional-level quality, and others have shown great potential to be improved upon by future teams. Software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. iGEM would love to see that happen again this year.</p>
 +
 +
<p>Since 2012 there has been a centralised repository for software projects on Github. iGEM is currently exploring ways to host the work products and codebases of the 2015 competition for synthetic biologists and developers to access and improve in the future. Stay tuned for updates.</p>
 +
<p>
 
<p>
 
<p>
−
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:
+
<h2><u>Picking a Project</u></h2>
−
</p>
+
<p>iGEM software developers should work closely with experimental synthetic biologists and iGEM teams to build tools that are genuinely useful to the synthetic biology and iGEM communities. Software tools could directly help synthetic biologists in the lab, at their desktops, or even in how they communicate with each other and access information. You may wish to build a tool that:</p>
  
 
<ul>
 
<ul>
−
  <li>Wiki documentation must contain project aims, methods and success</li>
+
<li>Improves design, assembly and testing of biological circuits</li>
−
  <li>Use git (from beginning of project)</li>
+
<li>Makes bioengineering more predictive </li>
−
  <li>Submission of complete source code and any auxiliary files to GitHub</li>
+
<li>Helps biologists discover parts and exchange information about them</li>
−
  <li>Basic code documentation for outside developers</li>
+
<li>Improves parts registry navigation</li>
−
  <li>Detailed installation or setup instructions for users (if applicable)
+
<li>Helps the iGEM community communicate with one another / identify problems</li>
−
  <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>  
+
<li>Serve as a better biobrick database API</li>
−
  <li>If your institution requires it, seek Institutional Review Board (IRB) approval before conducting software testing.</li>
+
<li>Parses information from one form to another</li>
 
</ul>
 
</ul>
  
−
<h2><a class="anchor" id="Medal Criteria"></a>Medal Criteria</h2>
+
<p>The track is open to all sorts of projects but teams should make sure that they are not repeating work that has been done by the community already. If the team believes they can improve an existing software solution, they should ensure that their tool has significant performance or feature advantages over the existing one. </p>
  
 
<p>
 
<p>
−
<b>Bronze. </b>The following 4 goals must be achieved:<br>
+
<p>
−
<ol id="criterialist">
+
<h2><u>Requirements</u></h2>
−
<li>Register the team, have a great summer, and have fun attending the Jamboree in Boston.</li>
+
<p>There is no constraint on languages, libraries or other software developments tools in the track, except that the use of Git/Github for version control is mandatory. 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.</p>
−
<li>Create and share a description of the team's project via the iGEM wiki.</li>
+
<p>All teams must be part of the iGEM github repository run by HQ - teams must contact the committee chair (see below), who will create a new account for you to get started.  
−
<li>Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.</li>
+
 
−
<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>
+
−
</li></ol>
+
−
</p>
+
  
 
<p>
 
<p>
−
<b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br>
+
<p>
−
<ol id="criterialist">
+
<h2><u>Medal Criteria</u></h2>
−
<li>Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</li>
+
−
<li>Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</li>
+
−
<li>Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc). </li>
+
−
<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>
+
−
</ol>
+
−
</p>
+
  
 +
Medal criteria have been announced for some tracks <a href="https://2015.igem.org/Judging/Medals#software">here</a>. Check back for final details soon.
 +
 +
<p>
 +
<p>
 +
<p>
 +
<h2><u>Team Projects from previous years</u></h2>
 +
The committee is working to put together a list of projects from previous years along a buildup of why they were successful. Watch this space.
 +
<p>
 
<p>
 
<p>
−
<b>Gold</b>: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: <br>
+
<h2><u>Track Awards</u></h2>
−
<ol id="criterialist">
+
 
−
<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>
+
<p>iGEM is moving to a nominations system for awards. That means the top 3 - 5 software teams will get recognition for their work. Think of the nominations as you would the academy awards. Being nominated amongst a very strong field of competitors is still recognition that you did a great job.</p>
−
</ol>
+
 
−
And the second goal can be any one of the following:
+
<h4><u>Best Software Track Project</u></h4>
−
<ol id="criterialist">
+
<p>The best software track project, based on nominations and achieving Gold Medal Criteria, will receive the best Software Track Project award.
−
<li>Make your software interact / interface with the Registry. </li>
+
 
−
<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>
+
<h4><u>Best Software Tool for all teams in the competition.</u></h4>
−
<li>Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)</li>
+
<p>Examples of the best software tools from the last few years (and the reasons why they were so good) are being gathered from previous judges. Watch this space.</p>
−
<li>Support and use the SBOL and / or SBOLv standard.</li>
+
 
−
<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>
+
<h4><u>Special Prizes / Grand Prize</u></h4>
−
</li></ol>
+
The Software teams are eligible for all the special prizes on top of the software track prize, including best model, best poster, best wiki, best applied design, etc. Software teams can also win the entire iGEM competition,
−
</p>
+
−
+
  
 
<p>
 
<p>
−
Please feel free to contact us with any question or concern:
+
<p>
−
<img src="https://static.igem.org/mediawiki/2014/0/07/Softwaretrack_email.png">
+
<h2><u>iGEM Software Resources</u></h2>
−
</p>
+
<p>The requirements for medals in the software track are in line with standards and expectations required of professional software development teams and are supposed to give teams a taste for building useful computational synbio tools. iGEM appreciates that the requirements are tough, and we are working to put together more and more educational materials for teams to use.</p>
 +
<p>Software teams should not necessarily start from scratch; over the years, libraries, design frameworks, and software tools have been built for you to use, abuse and improve wherever possible. In particular  teams should make use of the SBOL standard for synthetic biology data exchange as well as SBOL Visual.</p>  
  
 +
<h4><u>Git Resources</u></h4>
 +
<ul>
 +
<li><a href="http://git-scm.com/downloads">Git</a></li>
 +
<li><a href="https://www.codeschool.com/courses/try-git">Git Codeschool Lessons</a></li>
 +
<li><a href="http://training.github.com/resources/videos/">Git training videos</a></li>
 +
<li><a href="http://gitref.org">Git Reference</a></li>
 +
</ul>
  
 +
<h4><u>Synthetic Biology Resources</u></h4>
 +
<ul>
 +
<li><a href="http://parts.igem.org/Registry_API?title=Registry_API">Registry API</a></li>
 +
<li><a href="http://www.sbolstandard.org/">SBOL Standard</a></li>
 +
<li><a href="https://github.com/igemsoftware">iGEM Software Repository</a></li>
 +
<li><a href="http://igem.synbioreview.com/">iGEMsoft project aggregator</a></li>
 +
</ul>
  
 +
<h4><u>Python Resources</u></h4>
 +
<ul>
 +
<li><a href="https://store.continuum.io/cshop/anaconda/">The anaconda distribution of python</a></li>
 +
</ul>
 +
 +
 +
<h4>Bioinformatics Development Guidelines</h4>
 +
<ul>
 +
<li><a href="https://github.com/pjotrp/bioinformatics">Bioinformatics small tools manifesto</a></li>
 +
</ul>
 +
 +
<h4><u>Development Frameworks &amp; Team Management</u></h4>
 +
<ul>
 +
<li><a href="http://en.wikipedia.org/wiki/Scrum_%28software_development%29Agile">Scrum</a></li>
 +
<li><a href="http://en.wikipedia.org/wiki/Agile_software_development">Agile Development Framework</a></li>
 +
<li><a href="https://trello.com/">Trello</a></li>
 +
</ul>
 +
 +
 +
<h4><u>Other Resources</u></h4>
 +
<ul>
 +
<li><a href="http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html">The Java IDK</a></li>
 +
<li><a href="https://netbeans.org/downloads/Netbeans">Netbeans - be sure to get either the Java EE version or the "All" option</a></li>
 +
</ul>
 +
 +
<div class="clear"></div>
 +
 +
<h2><u>Committee</u></h2>
 +
 +
<p>If students, mentors or other interested parties have any questions about the iGEM 2015 software track, the track committee can be contacted by emailing software (at) igem (dot) org.</p>
 +
 +
<ul>
 +
<li>Edward Perello - Founder &amp; CBO @ Desktop Genetics | Software Committee Chair</li>
 +
<li>Raik Grünberg -  X @ Y | Software Committee Co-chair</li>
 +
<li>Gil Alterovitz - Assistant Professor @ Center for Biomedical Informatics, Harvard Medical School</li>
 +
<li>Evan Appleton - Research Assistant, CIDAR Lab @ Boston University</li>
 +
<li>Cory Li - Sizigi Studios</li>
 +
<li>Jenhan Tao - Graduate Student Researcher, Glass Lab @ UCSD</li>
 +
<li>Sean Ward - Founder &amp; CEO @Synthace</li>
 +
</ul>
 +
 +
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Latest revision as of 12:54, 19 July 2015

SynBio Needs Software

If you are going to design a new life form, chances are you’ll need a computer to design the smallest genetic circuits and deal with genome-scale complexity.

Software development is a valuable skill set for any synthetic biology team to have. In previous iGEM competitions, software has often been built by wetlab teams to solve specific problems. Recognising the utility of these software tools, and the importance of software development skills, the software track has been set up for computer scientists and developers to nurture their knowledge of biology, and for computational biologists, bioinformaticians and biologists to enhance their aptitude for building software.

Whether you are a wet lab team that has decided to build a software tool, or a software group looking to get involved in iGEM, we encourage you compete in the dedicated software track 2015.

Deadlines for this track

  1. Installability Test
  2. Submission of Code

1) IF you are creating an application that requires direct installation onto a hard drive, you must provide the software committee with a version of the program by September 11th. This is so that we can test to see if the tool is installable. The contact person for this will be our co-chair, Raik Greunberg. You must email (Raik.Gruenberg [at] gmail.com) with an installable version of your code so that it can be tested thoroughly ahead of the next deadline.

2) The deadline for submission of code to the iGEM Github Repository is the same date as the Wiki Freeze for conventional iGEM teams. You MUST submit your code to iGEM by September 18th - the judges will use this code as the basis of evaluating your project at the jamboree. Any code submitted after this deadline will be ignored and may subject your team to severe penalties.

Information about the track

Work Together & Solve Challenges in SynBio Software

Wetlab teams have lots of problems. Software teams can provide solutions. This year, iGEM is encouraging software and wet lab teams to work together and assist each other. If you need software for your wetlab project, or are a software team looking for a problem reach out to each other, by using the iGEM Reddit, contacting other teams on Twitter, or encouraging computer science departments to start teams.

Two Teams are Better than One

If you have a large ambitious wet lab project that includes a lot of computational 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 prize!).

Learn to be a Professional Biocoder

iGEM encourages software teams to learn the best practices of professional software developers. As software development is about solving problems in way that is useful for the users and for other developers, students, the software track focuses on teaching students the importance of:
  • Quality of codebase documentation
  • Automated testing practices
  • Version control (Git & Github)
  • Professional software development practices (Agile, Scrum etc)
  • Making use of previous iGEM teams’ work
  • Documenting code to enable other teams to pick up from where they will leave
  • Conducting user experience testing

Tools that Stand the Test of Time

Many tools built by iGEM teams have been of professional-level quality, and others have shown great potential to be improved upon by future teams. Software projects from previous years have resulted in long-term efforts and have even led to several start-up companies. iGEM would love to see that happen again this year.

Since 2012 there has been a centralised repository for software projects on Github. iGEM is currently exploring ways to host the work products and codebases of the 2015 competition for synthetic biologists and developers to access and improve in the future. Stay tuned for updates.

Picking a Project

iGEM software developers should work closely with experimental synthetic biologists and iGEM teams to build tools that are genuinely useful to the synthetic biology and iGEM communities. Software tools could directly help synthetic biologists in the lab, at their desktops, or even in how they communicate with each other and access information. You may wish to build a tool that:

  • Improves design, assembly and testing of biological circuits
  • Makes bioengineering more predictive
  • Helps biologists discover parts and exchange information about them
  • Improves parts registry navigation
  • Helps the iGEM community communicate with one another / identify problems
  • Serve as a better biobrick database API
  • Parses information from one form to another

The track is open to all sorts of projects but teams should make sure that they are not repeating work that has been done by the community already. If the team believes they can improve an existing software solution, they should ensure that their tool has significant performance or feature advantages over the existing one.

Requirements

There is no constraint on languages, libraries or other software developments tools in the track, except that the use of Git/Github for version control is mandatory. 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.

All teams must be part of the iGEM github repository run by HQ - teams must contact the committee chair (see below), who will create a new account for you to get started.

Medal Criteria

Medal criteria have been announced for some tracks here. Check back for final details soon.

Team Projects from previous years

The committee is working to put together a list of projects from previous years along a buildup of why they were successful. Watch this space.

Track Awards

iGEM is moving to a nominations system for awards. That means the top 3 - 5 software teams will get recognition for their work. Think of the nominations as you would the academy awards. Being nominated amongst a very strong field of competitors is still recognition that you did a great job.

Best Software Track Project

The best software track project, based on nominations and achieving Gold Medal Criteria, will receive the best Software Track Project award.

Best Software Tool for all teams in the competition.

Examples of the best software tools from the last few years (and the reasons why they were so good) are being gathered from previous judges. Watch this space.

Special Prizes / Grand Prize

The Software teams are eligible for all the special prizes on top of the software track prize, including best model, best poster, best wiki, best applied design, etc. Software teams can also win the entire iGEM competition,

iGEM Software Resources

The requirements for medals in the software track are in line with standards and expectations required of professional software development teams and are supposed to give teams a taste for building useful computational synbio tools. iGEM appreciates that the requirements are tough, and we are working to put together more and more educational materials for teams to use.

Software teams should not necessarily start from scratch; over the years, libraries, design frameworks, and software tools have been built for you to use, abuse and improve wherever possible. In particular teams should make use of the SBOL standard for synthetic biology data exchange as well as SBOL Visual.

Git Resources

Synthetic Biology Resources

Python Resources

Bioinformatics Development Guidelines

Development Frameworks & Team Management

Other Resources

Committee

If students, mentors or other interested parties have any questions about the iGEM 2015 software track, the track committee can be contacted by emailing software (at) igem (dot) org.

  • Edward Perello - Founder & CBO @ Desktop Genetics | Software Committee Chair
  • Raik Grünberg - X @ Y | Software Committee Co-chair
  • Gil Alterovitz - Assistant Professor @ Center for Biomedical Informatics, Harvard Medical School
  • Evan Appleton - Research Assistant, CIDAR Lab @ Boston University
  • Cory Li - Sizigi Studios
  • Jenhan Tao - Graduate Student Researcher, Glass Lab @ UCSD
  • Sean Ward - Founder & CEO @Synthace