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Bioinformatics. 2010 Jun 15;26(12):1542-7. doi: 10.1093/bioinformatics/btq169. Epub 2010 May 6.

Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

Author information

1
Sysdiag CNRS Bio-Rad UMR 3145, Cap delta/Parc euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France. sabine.peres@sysdiag.cnrs.fr

Abstract

MOTIVATION:

In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes.

RESULTS:

We present a formalism that uses the BioPsi concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure-function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation.

AVAILABILITY:

www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
20448138
PMCID:
PMC2881354
DOI:
10.1093/bioinformatics/btq169
[Indexed for MEDLINE]
Free PMC Article

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