Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM

Recent progress in high-throughput data-production technologies pushes research toward systems biology, focusing on the global interaction between the components of biomolecular processes. In this article we present a formal modelling environment for network biology, called the Biochemical Abstract Machine (BIOCHAM). Biocham delivers 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 behaviours. We present the main features of Biocham and report on our modelling experience with this language. Keywords: computational biology, model checking, protein interaction, systems biology