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From: Hilmar Lapp <hlapp <at> drycafe.net>
Subject: Re: Google Summer of Code - BioPerl / BioSQL proposal?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 1st April 2013 16:38:46 UTC (over 5 years ago)
Just to add another possibility for a summer project here, Bioperl-db (the
BioPerl bindings to BioSQL) in essence constitute a self-made ORM, invented
at a time when DBIx::Class didn't exist yet. As such, it has some
advantages (if you are willing to count overly clever features to be
counted in this category), but arguably many more disadvantages, chief
among them being the unsustainably small (you could also say non-existent)
developer community supporting it, and the fact that DBIx::Class now has
existed for years, and is fairly mature.

So, rewriting Bioperl-db with a DBIx::Class (or another well-supported
generic ORM) would, I think, stand to make a considerable impact on our
ability to further develop Bioperl's relational storage capabilities, as
well as BioSQL itself.

And I'd be willing to help out with such a project in a at least a
co-mentoring capacity. (If primary mentor, I'd need a committed co-mentor
to make it viable.)


On Apr 1, 2013, at 10:35 AM, Fields, Christopher J wrote:

> On Apr 1, 2013, at 9:28 AM, Peter Cock  wrote:
>> On 18 March 2013 21:26, Christopher Fields 
>>> Just a heads-up, if there are any students interested in the Google
Summer of
>>> Code, the Open Bioinformatics Foundation is planning on participating
>>> 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
>> 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
> chris
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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