1 Apr 2013 16:35
Re: Google Summer of Code - BioPerl / BioSQL proposal?
Fields, Christopher J <cjfields <at> illinois.edu>
2013-04-01 14:35:25 GMT
2013-04-01 14:35:25 GMT
On Apr 1, 2013, at 9:28 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote: > On 18 March 2013 21:26, Christopher Fields <cjfields <at> illinois.edu> 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. ++++1 > So, the core of a BioSQL/BioPerl GSoC project could tackle: > > * Adding SQLite support to the BioSQL scripts for loading taxonomies etc > https://github.com/biosql/biosql > > * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db > https://github.com/bioperl/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? > http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 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. chris