Blue Collar Bioinformatics

Note: new posts have moved to Please look there for the latest updates and comments

Biopython projects for Google Summer of Code

leave a comment »

Google Summer of Code is a brilliant program that provides a summer stipend for students to work on open source projects. This year, I have been evaluating Biopython student proposals under the watchful eye of The National Evolutionary Synthesis Center (NESCent). Biopython was lucky enough to have interest from several students, resulting in some excellent proposals. Two of these were selected for funding:

  • Eric Talevich’s proposal on adding support to Biopython for PhyloXML, an XML format for representing phylogenetic trees and associated data. I will be the primary mentor for this project, with Christian Zmasek, the author of PhyloXML, providing plenty of capable secondary mentoring.
  • Nick Matzke’s proposal on Biogeographical Phylogenetics. This is an integrated project that involves extracting biodiversity data from the web, merging it with phylogenetic data, and providing analysis and display libraries. Nick helped assemble a full team of mentors, and I will be providing input on integrating his code with Biopython while learning about Biogeography along the way.

This is my first year working with summer of code, and I could not be more impressed by the professionalism and hard work of the organizers at both Google and NESCent. The program is designed from the ground up to be simultaneously inclusive and rigorously selective. Students are asked to prepare detailed project plans to demonstrate they understand the subject, are able programmers, and can communicate effectively. There is also a strong eye given to students who are likely to continue on in their open source communities after the summer; after all, open source work is really built on the free labor of many dedicated people.

Having worked on open source projects for several years, it is invigorating and heartening to see a program designed to encourage the next generation of open source leaders. My time on the program thus far has been a great learning experience, and I am looking forward to a productive summer.

Written by Brad Chapman

April 20, 2009 at 5:38 pm

Posted in OpenBio

Tagged with , ,

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: