Evolving Bits

After we participated in the Google Summer of Code™ program as a mentoring organization in 2007, we pulled together an application for this year, too — and we got accepted again! So the Phyloinformatics Summer of Code, as we are calling our program in reference to the emphasis on phyloinformatics, has been on for 2008 since March 17, when Google published the list of accepted organizations. The period during which students can apply opened on March 24, and was originally slated to end only one week later, on March 31.

The latest news is that Google may extend the application deadline for students by one week. We’ll hear the final decision on this early tomorrow morning (Pacific Time, obviously – so probably no news on this on the East Coast before noon). So if you are a student enrolled at a university in a graduate or undergraduate program, you are interested in evolutionary or comparative biology, and you have always wanted to get involved in a bioinformatics open-source software project or even possibly help found one, here is your chance for likely another week, and Google will even pay you a stipend.

I’m serving again as the organization administrator. Last year, our participation originated out of the spur of the moment, when I came across a Google Summer of Code announcement on some mailing list (I don’t even remember which one) and thought this would be a great program to continue some of the activities started as well as the energy galvanized at the Phyloinformatics Hackathon that had taken place 3 months earlier. Despite a lot of skepticism and having had barely 2 weeks to pull together a competitive ideas page and application, we made it and became one of the 131 out of ~330 of applying organizations that got accepted.

The rest is history. The turn-out of applications was overwhelming (we received 65 in total), which gave us an even higher allocation of students (11) than we had anticipated in our wildest dreams (Google bases the allocation roughly on the number of applications an organization received, with adjustments for past performance and other things). Most of the top applications came from students with a strong background in evolutionary biology who wanted to gain or broaden their programming skills in a real-life context. Most of the students we accepted had not contributed in any significant way to open-source software before.

The applications showed that there is an audience for exactly this kind of program in our field. How successful were we in training the students, who are going to be the future researchers in our field, to not only (re-)use open-source software, but to be able to contribute to it? I’ll let you decide for yourself, for example based on the statistics I compiled for this year’s application (check section 5, Did your organization participate in previous GSoC years).

There is a nice overview of all of our 2007 Summer of Code projects in the Fall 2007 issue of the NESCent newsletter, which also has a group photo from the end-of-summer meet-up that we organized as an add-on. Moreover, one of the students (Mark Okada, if I recall correctly) assembled the mentors and students into a cladogram and every mentor received this motif on a mousepad. Isn’t that cool?

I can’t resist to highlight at least two of the projects here. One is PhyloWidget, developed by Greg Jordan (currently at the EBI), who has continued to work on it even after the end of the Summer of Code program. PhyloWidget is a Java applet based on Processing (an MIT spin-off initiated by Ben Fry) to allow navigating and manipulating even large phylogenetic trees; lately it has started to receive a lot of attention, for example in the AToL community, and Rod Page has covered it as well.

The other one is PhyloGeoViz, a project started from scratch and developed by Yi-Hsien Erica Tsai. Erica is my personal hero of the program and exemplifies what kind of empowerment the program makes possible. Though she had attended some programming classes before, she didn’t have any prior experience in the programming languages she ended up using (PHP and JavaScript) or the Google Maps API, and those were only a few of the obstacles she had to, and did surmount to finish reaching all her project goals! For me, her accomplishment alone was enough reward for the time I put into the program.

So I’m looking forward to enjoying this year’s Summer at least as much as last year’s. We have even received some blog coverage already (Panda’s Thumb, Your Bones Got a Little Machine, and TreeTapper) and if you can add to that please feel encouraged I have to say that based on our experience I disagree with Andrew Perry’s (over at Your Bones) suggestion that coding for a bioinformatics project is less interesting to Summer of Code students. The variety of interests among the students is huge, and so the observation that not all of them are into bioinformatics is no surprise (even if not fully understandable ). I also have no evidence to believe that Google limited the admission of bioinformatics projects in any way — unfortunately, and that is a surprise, aside from those admitted I really don’t know of any bioinformatics project that made the effort to apply (including, sadly, the O|B|F projects). Maybe bioinformatics is funded too well? Actually, believe it or not, almost everyone I speak to either isn’t aware of the program, or hasn’t thought that it might be for them too.

That said, I’ve been really pleased to see some new organizations there, such as quite a few related to grid and workflow computing (among them Taverna), and the Squeak development environment, which includes project ideas for Croquet. These examples also show that in reality more bioinformatics projects may be represented than one might think, as some listed organizations in reality act as umbrellas. In fact, two of our own project ideas (phyloXML support in BioPerl and BioRuby) are Bio* projects, so in a sense they are here.

Update 1 (March 31, 1.54pm): The student application period has now officially been extended to April 7.

Update 2: Added blog coverage by TreeTapper in the text.

Update 3: Failed to mention Plazi who I am positively surprised to see participate, as it is from the intersection of biodiversity informatics and digital archiving.