The Biochemical Abstract Machine BIOCHAM

  • Nathalie Chabrier-Rivier
  • François Fages
  • Sylvain Soliman
Conference paper

DOI: 10.1007/978-3-540-25974-9_14

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)
Cite this paper as:
Chabrier-Rivier N., Fages F., Soliman S. (2005) The Biochemical Abstract Machine BIOCHAM. In: Danos V., Schachter V. (eds) Computational Methods in Systems Biology. CMSB 2004. Lecture Notes in Computer Science, vol 3082. Springer, Berlin, Heidelberg

Abstract

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Nathalie Chabrier-Rivier
    • 1
  • François Fages
    • 1
  • Sylvain Soliman
    • 1
  1. 1.Projet Contraintes, INRIA RocquencourtLe ChesnayFrance

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