Peter Cock | 1 Apr 16:28 2013

Google Summer of Code - BioPerl / BioSQL proposal?

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?


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