[Biopython] GSoC Ortholog Module Proposal

[Matthew Strand]

> 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.


>
> This is a good project idea and nicely spec'ed out. One additional
> direction that might also be worth exploring is using BioMart to
> retrieve orthologs from the Ensembl Compara work. Here's a recent
> thread on BioStar with the queries to use:
>
>
> http://biostar.stackexchange.com/questions/569/how-do-i-match-orthologues-in-one-species-to-another-genome-scale
>
> I don't know of Python programming interfaces to BioMart, but there
> is a nice R bioconductor library that can be leveraged with Rpy2:
>

I agree, this would be a good addition. I have some messy Python wrappers to
BioMart but the Rpy route would probably provide a more reliable solution
with less effort.


> http://www.bioconductor.org/packages/bioc/html/biomaRt.html
> http://rpy.sourceforge.net/rpy2.html
>
> 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?

Best,
-Matt Strand