Computational Methods in Systems Biology

Volume 3082 of the series Lecture Notes in Computer Science pp 172-191

The Biochemical Abstract Machine BIOCHAM

  • Nathalie Chabrier-RivierAffiliated withProjet Contraintes, INRIA Rocquencourt
  • , François FagesAffiliated withProjet Contraintes, INRIA Rocquencourt
  • , Sylvain SolimanAffiliated withProjet Contraintes, INRIA Rocquencourt

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In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.