Blue Collar Bioinformatics

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Biopython projects for Google Summer of Code 2010

with 5 comments

Google Summer of Code provides the unique opportunity for students to spend a summer working on open source projects and getting paid. Biopython was involved with two great projects last summer, and it’s time to apply for this year’s program: the student application period is from next Monday, March 29th to Friday, April 9th, 2010.

If you are a student interested in biology and open source work, there are two community organizations to look at for mentors and project ideas:

  • NESCent Phyloinformatics — NESCent is a GSoC mentoring organization for the 4th year, focusing on projects related to phylogenetics and open source code.
  • Open Bioinformatics Foundation — The umbrella organization that manages BioPerl, Biopython, BioJava, BioRuby and several other popular open source bioinformatics projects is involved with GSoC for the first time.

This year, I’ve collaborated on three project ideas centering around the idea of tool integration. An essential programming skill for dealing with large heterogeneous data sets is combining a set of tools in a way that abstracts out the implementation details, instead allowing you to focus on the high level biological questions. Bradford Cross, a machine learning and data crunching expert at FlightCaster, describes this process brilliantly in an interview at Data Wrangling.

These three project ideas allow a student to develop essential toolkit integration skills, while having the flexibility to work on biological questions relevant to their undergrad or graduate research:

All involve taking two or more different toolkits and combining the functionality into a higher level interface focused around ease of use. They are intentionally broad and flexible ideas, and a student proposal should concentrate on functionality most relevant to their biological questions. Ideally the work would be both a publicly available resource, and contribute directly to the student’s daily research.

If you’re interested in these ideas and in working with a set of great mentors, definitely get in touch with me either through the project mailing lists or directly. If none of these ideas strike your fancy but you would like to be involved with GSoC, get in touch with a mentor from one of the other project ideas at NESCent and OpenBio. It’s a unique opportunity to develop new coding skills, work with great mentors, and give back to the open source community.

Written by Brad Chapman

March 26, 2010 at 8:02 am

Posted in OpenBio

Tagged with , ,

5 Responses

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  1. Hi Brad. I’m a PhD student interested in your project idea about integrating Python with R phylogenetic libraries. Where can I contact you?


    David Suarez

    April 2, 2010 at 12:24 am

  2. David;
    Great to hear. The best way to ask questions is directly on the NESCent mailing list if you are interested in taking the project in a phylogenetic direction:

    or the Biopython mailing list if you have other biological libraries you’d be interested in working with:

    The first step is putting together a proposal, which we’d be happy to help with. Let us know what questions you have and what direction you are thinking about taking it, and we can work from there.

    Brad Chapman

    April 2, 2010 at 6:06 am

    • Brad:
      I will put together a draft of my proposal. It certainly will take a phylogenetic direction.


      David Suarez

      April 2, 2010 at 3:53 pm

  3. Hi Brad-

    Sorry for the off topic post, but I wanted to let you and the readers of your blog know that SciPy 2010 is rapidly approaching and will be held in Austin, TX this year ( I’m chairing the bioinformatics/biomedical track ( and I am looking for presenters that would like to talk about how they are using python in their bioinformatics research.



    Glen Otero

    April 13, 2010 at 12:54 am

  4. […] was also selected as the 2010 Google summer code with the following contributed […]

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