Hilmar Lapp | 1 Apr 18:38 2013

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

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 <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
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :