[Bioperl-l] protein identification program for proteomics
Peter J Ulintz
Thu, 14 Sep 2000 10:27:58 -0400 (EDT)
> Ewan, I think that bioperl should jump into proteomics. Could you
> comment more on your ideas about this.
I'd be curious to know what folks would find useful in this area-- seems
as if much of the work being done using BioPerl is pretty DNA-focused.
I've started writing a set of objects that might possibly be useful as a
starting point for discussion. These form a core layer for a project I've
recently resurrected for tracking and managing data generated in proteome
research projects, particularly peptide mapping projects. Outside of
inheriting from Bio::Root::Object, however, there isn't much of an
interaction with other BioPerl objects, except occasionally Bio::Seq. The
object core is trivially EnsEMBL-like in the sense that Bio::(name)
objects have related Bio::DB::(name)_ObjI and Bio::DBSQL::(name)_Obj
adaptors for interfacing with a MySQL database. Anyway, the objects
represent 2D Gels, spots identified on those gels, peaks generated by mass
spec analysis of the spots, protein IDs, things like that.
I'm not sure how useful these would be to a global community, being
somewhat grounded in experimental data and perhaps specific to the needs
of this project, but I'd love to discuss this. Based on feedback from last
week's Sienna conference, the time is right for Open Source software in
the context of proteomics.
(BTW, an initial site for the project mentioned above is up at
http://prime.proteome.med.umich.edu. Its meant mostly for internal use,
but it might serve to provide some context.)
On Thu, 14 Sep 2000, Leonardo Marino-Ramirez wrote:
> Ewan, I think that bioperl should jump into proteomics. Could you comment
> more on your ideas about this.