Fields, Christopher J | 1 Apr 16:35 2013

Re: Google Summer of Code - BioPerl / BioSQL proposal?

On Apr 1, 2013, at 9:28 AM, Peter Cock <p.j.a.cock <at>> wrote:

> On 18 March 2013 21:26, Christopher Fields <cjfields <at>> wrote:
>> Just a heads-up, if there are any students interested in the Google Summer of
>> Code, the Open Bioinformatics Foundation is planning on participating again
>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>> looking for prospective projects.
>> We're open for any project ideas this year, so let us know what you would like
>> to do!
> I suggested this last year too, but improving support for BioSQL on
> SQLite would be great - the schema exists and seems to work fine,
> but is currently only handled by the Biopython BioSQL bindings.


> So, the core of a BioSQL/BioPerl GSoC project could tackle:
> * Adding SQLite support to the BioSQL scripts for loading taxonomies etc
> * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db
> There are a number of things that could be added to this basic idea
> to make the project more ambitious and to fill out a full summer. One
> is to extend this to doing BioSQL on SQLite bindings for BioRuby or
> BioJava (assuming suitable co-mentors are available).
> One of the nice things about SQLite compared to MySQL or PostgreSQL
> is the database is just one binary file on disk which is easily portable and
> can even be checked into source code control for unit tests. This means
> we can use it to make cross-binding testing far far easier. Thus another
> part of a GSoC project could be to use the SQlite bindings to establish
> cross-project testing of the BioSQL implementations for consistency.
> At that point I'd be interested from the BioSQL and Biopython side,
> and Biopython may have a few possible co-mentors here.
> Anyway, to be viable this project would need a Perl mentor with a
> good knowledge of BioSQL and BioPerl's bindings for it.
> Is this worth adding to the BioPerl GSoC as a possible idea?

Yes.  Will add this now.

> Regards,
> Peter
> (Who doesn't know enough Perl to qualify as a mentor for this)

There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have
seen.  Not sure where it stands now.