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Bioinformatics Advance Access originally published online on May 3, 2006
Bioinformatics 2006 22(14):1805-1807; 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

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

Laurence Calzone , François Fages and Sylvain Soliman *

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

*To whom correspondence should be addressed.

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 with respect to 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/

Contact: Sylvain.Soliman{at}inria.fr

Received on March 1, 2006; revised on April 28, 2006
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