[BioRuby] Making Contributions

[Angel Pizarro]

Looks like it is sold out, so no ;)

I made a small bioinf web application, you can take a look at the unfinished
(but close!) product here

http://wasabi.itmat.upenn.edu/zebrafish

The schema behind the app is a stripped down biosql that has been railed (
e.g. plural names)

The originating schema was populated using bioperl and the SQL scripts to
ETL into the rails schema and augment with data types missing from biosql.

Keyword searching is basic MySQL on the full text records and some
additional annotations (GO, Ingenuity, etc)

Source code will be avail upon request or publication. Whichever comes
first!

Other Ruby RoR projects I amworking on:

- pure ruby mzXML/mzData reader (finished, but slow 221 seconds to read
peaks from mzXML file)
- fast (e.g. C ext wrapper on RAMP) read libs for mzXML/mzData  format
(working but unpolished, adds minimal overhead to straight RAMP access (21
seconds vs. 31 seconds for equiv readmzXML performance test)
- MS1 signal processing and quantification (based on C++ code from OpenMS
group)

If anyone is is interested in these drop a line.

-angel


On 3/8/07, Sohel Merchant <s-merchant at northwestern.edu> wrote:
>
> Hey Guys,
>   It is very exciting to see a number of people using Ruby/Rails in the
> Bioinformatics community. Although, I have been primarily developing in
> Perl, I have started and am working on some new projects in Rails. I was
> wondering if any of you guys are planning to attend the Rails conference
> coming up in May 2007, we could have a BOF session.
>
> Cheers,
> Sohel Merchant.
> dictyBase
>
> -----Original Message-----
> From: bioruby-bounces at lists.open-bio.org
> [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Joel Dudley
> Sent: Wednesday, March 07, 2007 11:23 AM
> To: george
> Cc: bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Making Contributions
>
> Ditto for me as well. I'm using BioRuby and Ruby on Rails in
> translational genomics research.
>
> - Joel
>
> On Mar 6, 2007, at 11:50 PM, george wrote:
>
> > Hello Guys!
> > I have been using ruby for 2 months now and i have loved its elegance.
> > Previous i have been much of a perl guy and what i miss in ruby is the
> > extensive bioinformatics library available in perl. However am
> > grateful
> > that ruby also has some bioinformatics library though the last release
> > is over an year ago.
> >
> > Please is there any news of a major expected release for bioruby? How
> > can i make some contributions? Am excited about rails and am
> > developing
> > on rails.
> > i would be happy to contribute in a small way to the development of
> > bioruby API on RoR framework.
> >
> > Thanks
> >
> > george
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
> _______________________________________________
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>
>
> _______________________________________________
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>



-- 
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004