Abstract
We investigate the modeling of biological systems with static compartments through Beta-binders, a recently developed process calculus. Biological entities are represented as bio-processes and the calculus is extended with the notion of compartment. Entities can either be internal to compartments or reside on compartment borders. Movement in and out of compartments is requested by internal objects and mediated by border objects. The extended calculus is equipped with the notion of locality, and various kinds of relations between actions are defined. Moreover, we compare our proposal with similar formalisms and we show how to use the proposed calculus for modeling and analyzing the cAMP-signaling pathway in OSNs.
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References
Cardelli, L.: Brane Calculi - Interactions of Biological Membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.Y.: BioAmbients: an Abstraction for Biological Compartments. Theoretical Computer Science 325(1), 141–167 (2004)
Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20–33. Springer, Heidelberg (2005)
Priami, C., Quaglia, P.: Operational patterns in Beta-binders. Transactions on Computational Systems Biology 1, 50–65 (2005)
Milner, R.: Communicating and mobile systems: the π-calculus. Cambridge Universtity Press, Cambridge (1999)
Degano, P., Priami, C.: Non-interleaving semantics for mobile processes. Theoretical Computer Science 216(1–2), 237–270 (1999)
Degano, P., Gadducci, F., Priami, C.: Causality and Replication in Concurrent Processes. In: Broy, M., Zamulin, A.V. (eds.) PSI 2003. LNCS, vol. 2890, pp. 307–318. Springer, Heidelberg (2004)
Curti, M., Degano, P., Priami, C., Baldari, C.T.: Modelling biochemical pathways through enhanced π-calculus. Theoretical Computer Science 325(1), 111–140 (2004)
Romanel, A., Dematté, L., Priami, C.: The Beta Workbench. Technical report TR-03-2007, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (2007)
Bergstra, J.A., Ponse, A., Smolka, S.A. (eds.): Handbook of Process Algebra. Elsevier, Amsterdam (2001)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Proceedings of Pacific Symposium on Biocomputing (PSB 2001), vol. 6, pp. 459–470 (2001)
Cardelli, L., Gordon, A.D.: Mobile Ambients. In: Nivat, M. (ed.) ETAPS 1998 and FOSSACS 1998. LNCS, vol. 1378, pp. 140–155. Springer, Heidelberg (1998)
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular biology of the cell. Garland Science (2002)
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Guerriero, M.L., Priami, C., Romanel, A. (2007). Modeling Static Biological Compartments with Beta-binders. In: Anai, H., Horimoto, K., Kutsia, T. (eds) Algebraic Biology. AB 2007. Lecture Notes in Computer Science, vol 4545. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73433-8_18
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DOI: https://doi.org/10.1007/978-3-540-73433-8_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73432-1
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