[Bioperl-l] Fwd: [Bioperl-guts-l] AffyDB a module to handle Affymetrix annotation tables and more...

Jason Stajich jason.stajich at duke.edu
Tue Apr 26 11:03:34 EDT 2005

I think Allen is the main developer for the microarray stuff so I guess 
it is up to him to figure out how to incorporate the code.
I'm sure we'd like to have more people contributing to that project so 
hopefully he can point you in the right direction for bringing your 
work into it.

Jason Stajich
jason.stajich at duke.edu

Begin forwarded message:

> From: rambaldi <davide.rambaldi at ifom-ieo-campus.it>
> Date: April 12, 2005 11:12:56 AM EDT
> To: bioperl-guts-l at bioperl.org
> Cc: Subject: [Bioperl-guts-l] AffyDB a module to handle Affymetrix 
> annotation tables and more...
> Hi, I am a young researcher and Perl developer of the IFOM-FIRC
> Institute of Cancer Research (Milan)
> In the last month i have worked on a Perl module to handle Affymetrix
> Probesets Informations and store it in a Relational Database
> Actually I have an account at PAUSE as RAMBALDI but i would like to add
> my modules to the BioPerl Bundle
> Under CPAN search i FIND actualy only 2 packages
> bioperl-microarray-0.1
> Bio-Affymetrix-0.3
> that work with Affymetrix Mass Fille.
> My Package handle information about probesets design, alignments oligos
> ecc... and generate new data about single probes position over RefSeq
> and Genome.
> Actually a web-interface to my modules are avaible at
> http://bio.ifom-firc.it/AffyDB/
> Just type 'random' into the INPUT BOX to get a random list of 10
> probesets
> I would like to integrate my modules in the BioPerl distribution
> I have used OOPerl and the template of 'Mastering Perl for
> Bioinformatics (Gene.pm)'
> Actualy i have 2 modules called:
> AffyDB.pm
> parse annotation tables, insert tables into a Entity Relationship mySQL
> database, retrive informations
> Probeset.pm
> Really similar to Gene.pm, is an OOPerl module to create an object
> (Probeset) and handle informations about design, alignments, ecc...
> And some perl CGI scripts to generate the web interface.
> Perl DOCs about the 2 modules are available (html version) at
> http://bio.ifom-firc.it/AffyDB/src/AffyDB.html
> http://bio.ifom-firc.it/AffyDB/src/Probeset.html
> I post IT one month AGO at the bioperl-macroarray list and one person 
> ask to reuse my module,
> i would like to include mu modules into the BioPerl distribution...
> Is It possible?
> What I have to do?
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