[Bioperl-l] Modware: a BioPerl based API for Chado

Eric Just e-just at northwestern.edu
Wed May 17 11:03:41 EDT 2006

Hi Everyone,

We are announcing a new Sourceforge Project called Modware that may be of 
interest to you.   It is an object-oriented API written in Perl that 
creates BioPerl object representations of biological features stored in a 
Chado database. It basically creates a Bio::Seq object for chromosomes in 
Chado and creates Bio::SeqFeature::Gene objects for protein coding 
transcripts stored in Chado.  Things like contigs are represented as 
Bio::SeqFeature::Generic objects.  We also provide many methods for 
manipulating these objects once they are in memory.

For download please visit our Sourceforge project page:

For API documentation and some short examples of selected use cases visit 
our project home page:

This software is adapted from the production middleware code that dictyBase 
uses.  Modware 0.1 requires the latest stable GMOD release: 0.003 be 
installed.  We are currently calling it a release candidate and if we get 
some feedback will call it an official release if there are no major 
install bugs (we've installed it only on two different machines).  If you 
would like a version that works on the latest CVS version of GMOD, let me 
know and I'll expedite getting that out the door.

Lastly, please use the direct download version, we have not fully recovered 
from the recent Sourceforge CVS issues.

Please try the software out and let us know what you think!

Eric Just and Sohel Merchant

e-just at northwestern.edu
s-merchant at northwestern.edu


Eric Just
e-just at northwestern.edu
dictyBase Programmer
Center for Genetic Medicine
Northwestern University


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