Automated Reasoning Tools for Molecular Biology

In recent years, molecular biology has engaged in a large-scale effort to elucidate high-level cellular processes in terms of their biochemical basis at the molecular level. The mass production of post genomic data, such as ARN expression, protein production and protein-protein interaction, raises the need of a strong parallel effort on the formal representation of biological processes.In this talk, we shall 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 shall review the main features of Biocham and report on our modeling experience with this language. In particular we shall report on a model of the mammalian cell cycle’s control developped after Kohn’s map.