[Bioperl-l] medperl, something kinda like bioperl

[pablo marin-garcia]

Hello Spiros,

I have been writing a set of modules and scripts called pmGWAS (perl
modules for genome wide association) and PMG (Perl for Medical
Genetics). They are based in bioperl and ensembl and I was going to
release in github and later in CPAN. They are modules for
visualization and creating report analysis for medical sequencing and
genotyping. Also I have been writing parsers for the common genotype
and SNPs file formats that at some point I would like to 'bioperlize'
following the SeqIO factory style.

Would be nice to use the bioperl wiki for organize and coordinate
these kind of modules. The current view on bioperl development,  I
think, today is more like the unix motto: do one thing, do it well and
interact well with others. As Rob said the trick is to keep things
simple and modular following the bioperl interfaces or defining new
ones and try to convince people to adhere.

Nice to see more people wanting to increase the perl contribution in this area.

  -Pablo

> >
> Hello Rob,
>
> thanks for the feedback. It will be definitely a learning experience for me
> as well. I'm planing on setting up some sort of public resource for people
> to have a look at and discuss / make a plan before actual coding gets done.
> Will keep you posted.
>
> thanks
> Spiros
>
>
> > Spiros Denaxas wrote:
> >
> >> Hello,
> >>
> >> I am sending this email here since I consider all people that contribute
> >> and/or follow the bioperl project as the best starting point for advice on
> >> a
> >> new project I am currently planning ; my apologies if its considered
> >> off-topic.
> >>
> >> While the bioinformatics community has greatly benefitted from the Perl
> >> community, with the shining example of bioperl, the medical community is
> >> sadly a bit behind. I am currently employed in a public health /
> >> epidemiology environment and have under numerous occasions discovered
> >> opportunities to contribute code to CPAN that has made my life easier. I
> >> know I am not alone, but a very quick search on CPAN for related modules
> >> form the medical / biomedical domain does not return much for now.
> >>
> >> I recently gave a presentation at the London Perl Workshop [1] and while
> >> creating it, I thought, would it be useful to have something similar to
> >> bioperl for modules which largely contribute to the medical /
> >> epidemiological domain? I was thinking of creating something like medperl,
> >> alas similar to bioperl, but in a very very simple form. It would serve as
> >> a
> >> reference point to the (albeit small) numbers of modules that are
> >> currently
> >> on CPAN and will also hopefully urge people to contribute some of their
> >> code
> >> along the way.
> >>
> >> So I would like to request your advice on:
> >>
> >> a) Can you think of any reasons for not doing this?
> >> b) Does anybody know of something similar?
> >> c) Does anybody feel like they could contribute?
> >>
> >> Regards,
> >> Spiros Denaxas


-- 
   - Pablo Marin-Garcia