[Biopython] GSoC Ortholog Module Proposal

[Brad Chapman]

Matthew;

> > Thanks for the introduction and pointers to your work. Your
> > http://ortholog.us interface looks like a useful resource; it's
> > really nice to see web interfaces being developed with programmable
> > JSON APIs. Out of curiousity, is the code available for what you've
> > done so far?
> 
> Thanks, we have found it useful for finding unindexed orthologs. Fetching
> results from the pre-compiled databases is faster but of course requires
> writing wrappers that are time consuming to develop. The plan is to release
> all code as an open source Django app with a paper that is in the works.
> However, I'd be happy to share any code with mentors/organizers for
> evaluation purposes off-list in the meantime.

Cool; definitely let us know on the mailing lists when the paper and
code are out. It would be fun to see.

> > For the practical GSoC things, project proposals are due this
> > Friday, April 9th so time is running short. I'm unfortunately a bit
> > over-committed as this point to mentor but hopefully someone will
> > be available to step in that role. I'm happy to make suggestions on
> > the proposal as it comes together.
> 
> Thanks, I hope so too. I will post a full proposal in the near future.
> Feedback would of course be greatly appreciated. I'm a little unclear, do I
> need a mentor to submit a proposal? Is writing a proposal a mute point
> without a mentor?

You will need a mentor and this is always the tough part of GSoC: there
are more good students and ideas than mentors and funded spots. I would
never discourage anyone from getting together a proposal; it is a good
exercise and helps you think through the work you are planning to do.
In terms of acceptance rates, it is lower when coming in later in the
process with your own ideas since mentors will have already settled on
a few ideas and begun feeling committed to students working on those.
However, nothing is locked down or decided until the deadline hits,
proposals are ranked by all of the mentors, and we see how many spots
we'll get from Google.

GSoC is kind of like interviewing job candidates without being sure how
many positions you'll have at the end. In summary, if you feel like the
proposal writing process would be interesting and useful to you, I'd
definitely encourage you to go for it and see where it takes you.

Brad