[Bioperl-l] Google Summer of Code: Call for Bio* Volunteers

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Fri Feb 13 12:57:31 EST 2009

The past december I have posted an idea[1] on the open-bio list that
could be interesting.

It is about creating a common repository of tests and use cases for
all the bio.* projects, to make it easier the development of all of
them and make them more compatible, easier to compare.
For example, if we store all the possible use cases on sequence
handling (e.g. which format to parse, which tests, which are the most
common things that people need to do with sequences), then it would be
easier to coordinate all the bio.* projects and see which are the
better way to implement them.

What do you think? Is it a good idea? Is it feasible?
I don't have much experience in writing use cases, so we will need a
good mentor.
Moreover, how much time of the day does it take to partecipate to a
summer of code program?
Is it a full-time work, or I can do it only on the evenings and on my free time?

cheers! :-)

[1] http://lists.open-bio.org/pipermail/open-bio-l/2008-December/000502.html

On Fri, Feb 13, 2009 at 5:53 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
> Google is committed to run the Summer of Code program [1] again this year.
> It will be for the 5th time.
> In broad strokes, the program funds what you might call remote summer
> internships for students to contribute to an open-source software project.
> Participating projects (or umbrella organizations) provide project ideas and
> supply mentors that guide the work on those. Students apply to a project
> within the program with specific project ideas, based on those suggested or
> based on their own idea, get ranked by the mentors of the project, and those
> accepted into the program get paired up with mentors. Projects are chiefly
> about programming, the coding period is 3 months (Jun-Aug), and there is no
> travel required by either student or mentor. The program is global; other
> than the US trade restrictions that Google is under, there are no
> restrictions as to where student or mentor reside. The main motivations
> behind the program are to recruit new contributors to open-source projects,
> and to produce more open-source code. See the program FAQs [2] for more
> information.
> I've had the honor of being part of the program for the last two years,
> administering NESCent's participation as an organization [3] and in 2007
> mentoring a student. I have to say I find it the most awesome open-source
> program since sliced bread (or the invention of BLAST if that means more to
> you). Despite that and sadly enough, there has been a dearth of
> participating bioinformatics projects (though some notable ones, such as
> CytoScape have participated).
> There have been two Bio* Summer of Code projects under the NESCent umbrella,
> one in 2007 [4] and one in 2008 [5]. I would be willing to volunteer to take
> the lead on and administer a full-blown participation of O|B|F as a Bio*
> umbrella organization, provided 1) at least one Bio* person volunteers to
> serve as backup administrator, and 2) enough Bio* contributors volunteer to
> serve as prospective mentors.
> Mentoring involves participating in creating the page of project ideas (I'd
> provide template and guidance), corresponding with applicants who have
> questions, participating in student application ranking, and for primary
> mentors (those directly assigned to a student) based on empirical evidence
> at least 5hrs/week of time spent with the student to help him/her get over
> obstacles or avoid wrong paths.
> I think almost all mentors would concur that the experience was very
> gratifying, but as a mentor you will be spending a non-negligible amount of
> time with the student. I think it is the student-mentor pairing and
> interaction, not the stipend, that in the end makes the participation for
> students uniquely productive in terms of learning, and different from simply
> contributing to the project of choice (which they could always do).
> For a personal impression for how the program is from a mentor perspective,
> I'll let Chris Fields speak who was the mentor for the 2008 phyloXML in
> BioPerl project. From a student's perspective, I'll leave it to the 2007
> Biojava student Bohyun Lee (blee34-at-mail.gatech.edu) and the 2008 BioPerl
> student Mira Han (mirhan-at-indiana.edu) to comment (if they are still on
> the list).
> So if you think this is a good idea for Bio* to be part of, if you would
> like to help in some way, if you can see yourself as a mentor, or if you are
> a lurking would-be student, please let yourself be heard. Email either to
> the list or to me.
> Cheers,
>        -hilmar
> [1] http://code.google.com/soc/2008
> [2] http://code.google.com/opensource/gsoc/2009/faqs.html
> [3] http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2007
> http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2008
> [4] http://biojava.org/wiki/BioJava:PhyloSOC07
> [5] http://bioperl.org/wiki/PhyloXML_support_in_BioPerl
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
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My blog on bioinformatics (now in English): http://bioinfoblog.it

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