Google Summer of Code 2010 Org Application

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Organization name

Open Bioinformatics Foundation


The OBF is a nonprofit volunteer run organization focused on supporting open source programming in bioinformatics. It acts as an umbrella organization for the BioPerl, BioPython, BioJava, BioRuby, BioSQL, and BioLib projects, and organizes conferences and workshops to promote and support open-source bioinformatics.

Home page


Main organization license

GPL v2

Why is your organization applying to participate in GSoC 2010? What do you hope to gain by participating? (required)

There are a lot of good reasons to apply for GSoC, but the most important for us is the opportunity to hopefully recruit and retain new, competent contributors for our projects. In fact, even if a student does not go on to be a regular contributor, they would still be much more likely to consider a career in bioinformatics or medical informatics after a summer working with us. And if there's one thing that bioinformatics needs, it is more good software developers! But not just good developers, ones with biological domain knowledge, or enough intellectual curiosity to develop the necessary domain knowledge.

A program like GSoC is a great opportunity to cultivate some of the next generation of bioinformatics developers. Based on our experience with a few GSoC students we've had work on our projects (through NESCent), they do good work.

Did your organization participate in past GSoCs? If so, please summarize your involvement and the successes and challenges of your participation. (required)

The OBF has applied for GSoC in past years, but has not been accepted so far. The past two years, some of the GSoC students working under NESCent's aegis have made some contributions to our projects, but those have necessarily been related to our toolkits' support for comparative genomics, evolution, phylogeny, and so forth, since those are in NESCent's domain. However, we have a lot of opportunities for student contributions in areas outside of NESCent's purview, for example, in more technical areas of project build systems and refactoring, or other more fundamental areas of bioinformatics such as sequence alignment, assembly, annotation, and so forth.

The main reason that OBF is applying as a separate organization (apart from TPF and NESCent) is to get some GSoC students to work in these areas.

If your organization participated in past GSoCs, please let us know the ratio of students passing to students allocated, e.g. 2006 3/6 for 3 out of 6 students passed in 2006. (required) 

OBF has not directly participated.

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If your organization has not previously participated in GSoC, have you applied in the past? If so, for what year(s)? (required)

We applied once previously, last year in 2009.

What is the URL for your ideas page? (required)


What is the main development mailing list for your organization? This question will be shown to students who would like to get more information about applying to your organization for GSoC 2010. If your organization uses more than one list, please make sure to include a description of the list so students know which to use. (required)
Each sub-project has their own mailing list(s), they are linked and described on the OBF GSoC page above. Lists:
What is the main IRC channel for your organization? (required)

BioPerl has an IRC channel, #bioperl on freenode. The other subprojects do not maintain IRC channels. Depending on the number of GSoC students we end up with and their working habits, we will most likely create an #obf-soc or similar channel to coordinate student and mentor work, if OBF is accepted as a mentoring organization.

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Does your organization have an application template you would like to see students use? If so, please provide it now. Please note that it is a very good idea to ask students to provide you with their contact information as part of your template. Their contact details will not be shared with you automatically via the GSoC 2010 site. (required)

We have a list of information that every student must include with their application. Pasted from http://www.open-bio.org/wiki/Google_Summer_of_Code#When_you_apply:

What criteria did you use to select the individuals who will act as mentors for your organization? Please be as specific as possible (required) 

The list of mentors was assembled by asking for volunteers and project ideas on the public mailing lists of the projects. Every volunteer this time around was an experienced developer on their project, so there was no problem there.

What is your plan for dealing with disappearing students? (required)

The first line of defense for dealing with this situation is of course to make sure it doesn't happen in the first place, by keeping the student engaged (see question below). That said, if a student disappears for a long period without prior arrangement with us, and/or a very good reason and explanation, it's not fair to us or to the program. We will give them a (short) window of opportunity to catch up and make amends, but any further problems with them after that will most likely force us to fail them and move on.

What is your plan for dealing with disappearing mentors? (required)

Our mentors are drawn from a relatively small and tightly knit academic community, so this very unlikely to happen, but in that event, a backup mentor would simply have to be found and substituted. If another active project developer can't take over, chances are very good that one of the inactive ones could be persuaded to serve in that kind of scenario. Failing that, the organization administrator (Rob Buels) or backup organization administrator (Hilmar Lapp) would have to take over the orphan student(s).

What steps will you take to encourage students to interact with your project's community before, during and after the program? (required)

All students will be subscribed to the developer mailing list of the relevant project. Before the coding period, students and mentors will conduct the bulk of their development plans publicly on the mailing list. During the coding period, the students will post their progress reports on their project's wiki page on the relevant project wiki (pages which will be watched by the mentors and organization administrators), and will announce major milestones to the relevant mailing list. If a student is hesitant to communicate, it is their mentor's primary responsibility to get them out of their shell and working with the rest of the team.

For mentors, they will of course be referred to the excellent materials developed by previous GSoC mentors. In particular, within 2 weeks of OBF getting accepted as a mentoring organization, each mentor will be required to read through the new mentoring guide (http://en.flossmanuals.net/GSoCMentoringGuide), and the organization administrator will follow up with each of them to make sure that they have read and absorbed the wisdom therein. A number of the OBF mentor volunteers have previous experience mentoring students for GSoC as well.

What will you do to ensure that your accepted students stick with the project after GSoC concludes? (required)

The two most important indicators for a student's continued participation are 1.) the student's career path continuing in biology and bioinformatics, and 2.) the quality and success of the student's GSoC experience.

Let's face it, it's unlikely that someone would continue as a regular contributor to open-source bioinformatics toolkits without it being related to their career in biology or bioinformatics in some way. That aspect is mostly out of our control, but we can influence that somewhat by which students we pick to fill whatever GSoC slots would be allocated to our organization.

With respect to the quality of the experience, responsibility for that lies primarily with the mentors, guided by the organization administrator. If they have a good, realistic project (preferably one that they thought up themselves), and we keep them engaged and on track for the summer, and bring it to a successful conclusion, that's about as much as one can ask for.

Is there anything else you would like to tell the Google Summer of Code program administration team? (required)

No, I think we've made our case.

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