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

Abstract : 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 stoch-astic 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.
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Submitted on : Tuesday, January 10, 2017 - 5:17:03 PM
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Laurence Calzone, François Fages, Sylvain Soliman. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, Oxford University Press (OUP), 2006, 22 (14), pp.1805--1807. ⟨10.1093/bioinformatics/btl172⟩. ⟨hal-01431364⟩

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