The Biochemical Abstract Machine BIOCHAM


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 to ols for querying the temporal properties of the system under all its possible behavi ors. 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 model s w.r.t. their temporal properties.

In Vincent Danos, Vincent Schächter, editor, CMSB'04: Proceedings of the second Workshop on Computational Methods in Systems Biology, pages 172–191, Springer-Verlag