Software

Welcome to iGEM 2013 Software Division

iGEM software development is based on an ecosystem of four concepts:

1. A repository of open source software tools.
2. Community driven data exchange standards.
3. Specific software frameworks built explicitly for synthetic biology.
4. Part information in the Registry of Standard Biological Parts.

These four concepts find a home in a revamped iGEM competition software track. The software track now complements the other tracks in iGEM with new goals, medal criteria, and awards to reflect the distinct requirements of tools in this domain.

The first concept will be supported by archiving each team's software in a centralized location. This will increase software reuse, interoperability, and collaboration. Ideally software will be reused in much the same way that the BioBrick parts are used by wet labs.

The second concept finds a home in the [http://www.sbolstandard.org Synthetic Biology Open Language (SBOL)] and the [http://biobricks.org/programs/technical-standards-framework/ BioBricks Foundation Request for Comments (RFC)] infrastructure.

Software frameworks include such efforts as [http://www.clothocad.org Clotho] and [http://www.genomecompiler.com/ Genome Compiler]. These tools aim to create open source, community driven software applications with a rapid development and deployment cycles.

Finally, the foundation of all of these efforts requires a steady stream of biological data and available parts. The [http://partsregistry.org/ Registry of Standard Biological Parts] provides this function.

Concepts

The Registry of Software Tools

The Registry of Software Tools is the computational analog to the Registry of Biological Parts. Driven by the large library of software tools generated by iGEM teams annually, the Registry of Software Tools will be a central location to store and access this growing resource.

[http://www.sbolstandard.org/ Synthetic Biology Open Language (SBOL)]

Synthetic Biology Open Language (SBOL) is a language for the description and the exchange of standard biological part designs. You can start using SBOL in your software by reading about the [http://www.sbolstandard.org/initiatives/serialization file format], checking out the library [http://github.com/SynBioDex/libSBOLj libSBOLj], and for more details see the [http://www.sbolstandard.org/sbolstandard/specification specification].

[http://biobricks.org/ BioBricks Foundation ]

The BBF is a public-benefit organization which looks to promote the standardizing of BioBrick parts. One such effort is through the Request for Comments (RFC) mechanism. RFCs are static documents or digital objects like videos intended to get an idea, proposed standard, or method out to the rest of the community for comment. RFCs are numbered, for ease of referencing, and the numbers are assigned by the BBF.

[http://openwetware.org/wiki/Computational_ToolsSoftware Frameworks]

There are a number of software efforts which look to make the specification, design, assembly, simulation, and data management activities in synthetic biology more efficient, automated, predictive, collaborative, and standardized. These efforts will allow us to develop more complex systems and incorporate advanced modeling methodologies. These frameworks are created by small research groups. iGEM provides an opportunity to improve upon these tools.

[http://partsregistry.org/ The Registry of Standard Biological Parts]

The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs.

Starting in 2011 it is our intention to elevate the development of software tools for synthetic biology to the same level of community support and participation currently experienced by the general iGEM competition. To this end, it is our goal to re-energize the software development of iGEM participants by:

• Reducing the amount of redundant code development.
• Increasing the size and scope of software development by leveraging previous projects and experiences.
• More closely couple the development of software with the experimental techniques and requirements of the wetlab.

This page will serve as the starting point for these efforts. So join us and help create the tools, algorithms, and infrastructure to power the next generation of Synthetic Biology. We can't wait to see what you create!!

[http://ddensmore.net Douglas Densmore], Boston University

[http://www.csail.mit.edu/user/886 Randy Rettberg], iGEM Headquarters

Software Competition Overview

iGEM traditionally has been a venue for teams to create designs in wetlabs. Starting in 2008, area awards for software tools were introduced. These efforts produced a number of truly unique [http://igem.synbioreview.com/ software projects]. However, there were a number of aspects which could be improved. Our goal is to begin the process of making the software aspects of iGEM more fully featured. This will include a centralized repository for the software tools developed. This will help to not only preserve the projects but also allow others to avoid building existing tools as well as extend them. Second, we hope to help create a community of users around specific design frameworks and community standards.

This page is the beginning of this process!

Organizing Committee

The Chairs of the iGEM Software track are: [http://ddensmore.net Douglas Densmore] and Randy Rettberg. Due to the truely international nature of the iGEM competition, we have an international organizing committee. These members are listed below:

• Anil Wipat Newcastle, Newcastle University

• Cesar Rodriguez, Autodesk

• Gil Alterovitz, Harvard, Wyss Institute

• Guevara Noubir Boston, Northeastern University

• Kaustubh Bhalerao, University of Illinois

• Michal Galdzicki, University of Washington

• Ming Chen, Zhejiang University

• HQ organizational support: Kim de Mora

If you want to contact the committee, please use the Software committee mailing list.

Calendar of Events

Please see the calendar of events for software teams on the iGEM wiki.

Past Software Projects

(provided by Michal Galdzicki)

[http://igem.synbioreview.com/ http://igem.synbioreview.com/] is a browsable collection of all the iGEM projects that created software. It has information about the Team, Year, Category, Availability (Free/Not available), and Software Dependencies.

We collected the information by crowd-sourcing the problem of collecting information about the iGEM projects. A group of volunteers browsed to every *.igem.org/* page that mentioned "software". We recorded a sample of pertinent information about each iGEM project. We hope to create a great reference to checkout what was done in the past.

The page is of course a work in progress. If you find something missing or incorrect please help. Please submit any feedback or comments here or use the Issues page on Github to submit feature requests (Enhancements) or bugs. https://github.com/mgaldzic/igemsoft/issues

You can also edit the data directly, look at bottom of iGEMsoft page for a link to the spreadsheet.

Software Division Judging

See the Software Judging Page for more information.

Software Division Awards

See the Software Division Awards page.

(currently under construction for the 2013 competition)

Software Division Resources

• [http://partsregistry.org/Registry_API Parts Registry]
  
• [http://www.clothocad.org/ Clotho] and [http://www.clothohelp.org Clotho Help]
  
• [http://www.eugenecad.org/ Eugene]
  
• [http://www.genomecompiler.com/ Genome Compiler]
  
• [http://www.sbolstandard.org/ Synthetic Biology Open Language (SBOL)]
  
• The Registry of Software Tools
  
• [http://igem.synbioreview.com/ iGEMsoft] - a complete collection of iGEM software projects 2007-2011