[Biococoa-dev] some BioCocoa news

Scott Christley schristley at mac.com
Tue Mar 1 17:31:29 EST 2011

Hello All,

Here is some news about BioCocoa.

* BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2].

* There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models.  The classes for metabolic models are being designed to interface with Argonne's SEED system [3].

* The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework.

* The BioCocoa wiki [4] has undergone some re-organization, check it out!


[1] http://www.debian.org/devel/debian-med
[2] http://packages.debian.org/search?keywords=libbiococoa
[3] http://www.theseed.org/wiki/Main_Page
[4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php

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