The biochemical abstract machine BIOCHAM

Abstract

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. 1 Introduction In networks biology, the complexity of the systems at hand (metabolic net-works, extracellular and intracellular networks, networks of gene regulation) clearly shows the necessity of software tools for reasoning globally about bio-logical systems [1]. Several formalisms have been proposed in recent years for modeling biochemical processes either qualitatively [2-4] or quantitatively [5-9].State-of-the-art tools integrate a graphical user interface and a simulator, yet few formal tools are available for reasoning about these processes and provingproperties about them. Our focus in Biocham has been on the design of a biochemical rule language and a query language of the model in temporal logic,that are intended to be used by biologists. Biocham has been designed in the framework of the ARC CPBIO on "ProcessCalculi and Biology of Molecular Networks " [10] which aims at pushing forward a declarative and compositional approach to modeling languages in SystemsBiology. Biocham is a language and a programming environment for modeling biochemical systems, making simulations, and checking temporal properties. Itis composed of