Abstract
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.
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References
ARC CPBIO: Process calculi and biology of molecular networks (2002–2003), http://contraintes.inria.fr/cpbio/
Cimatti, A., Clarke, E., Enrico Giunchiglia, F.G., Pistore, M., Roveri, M., Sebastiani, R., Tacchella, A.: Nusmv 2: An opensource tool for symbolic model checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, p. 359. Springer, Heidelberg (2002)
Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. MIT Press, Cambridge (1999)
Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sönmez, M.K.: Pathway logic: Symbolic analysis of biological signaling. In: Proceedings of the seventh Pacific Symposium on Biocomputing, pp. 400–412 (2002)
Chabrier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and querying biochemical networks. Theoretical Computer Science (2004) (to appear)
Chabrier, N., Fages, F.: Symbolic model cheking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 149–162. Springer, Heidelberg (2003)
Chiaverini, M., Danos, V.: A core modeling language for the working molecular biologist. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, p. 166. Springer, Heidelberg (2003)
Kohn, K.W.: Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Molecular Biology of Cell 10, 703–2734 (1999)
Bockmayr, A., Courtois, A.: Using hybrid concurrent constraint programming to model dynamic biological systems. In: Stuckey, P.J. (ed.) ICLP 2002. LNCS, vol. 2401, pp. 85–99. Springer, Heidelberg (2002)
Chabrier-Rivier, N., Fages, F., Soliman, S.: The biochemical abstract machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 172–191. Springer, Heidelberg (2005)
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Fages, F. (2004). Automated Reasoning Tools for Molecular Biology. In: Biundo, S., Frühwirth, T., Palm, G. (eds) KI 2004: Advances in Artificial Intelligence. KI 2004. Lecture Notes in Computer Science(), vol 3238. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30221-6_1
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DOI: https://doi.org/10.1007/978-3-540-30221-6_1
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