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Bioinformatics Advance Access published online on May 3, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl172
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 1, 2006
Revised April 28, 2006
Accepted April 28, 2006

Applications note

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

Laurence Calzone 1, François Fages 1, and Sylvain Soliman 1 *

1 Projet Contraintes, INRIA Rocquencourt, BP105, 78153 Le Chesnay Cedex, France

* To whom correspondence should be addressed.
Sylvain Soliman, E-mail: Sylvain.Soliman{at}inria.fr


  Abstract

Summary: BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stochastic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model. It then becomes possible to analyze, query, verify, and maintain the model w.r.t. those properties. For kinetic models, BIOCHAM can search for appropriate parameter values in order to reproduce a specific behavior observed in experiments and formalized in temporal logic. Coupled with other methods such as bifurcation diagrams, this search assists the modeler/biologist in the modeling process.

Availability: BIOCHAM (v. 2.5) is a free software available for download, with example models, at http://contraintes.inria.fr/BIOCHAM/.

Associate Editor: Golan Yona
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