Abstract
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed.
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References
Alur, R., Henzinger, T.A.: Reactive modules. Formal methods in System Design 15(1), 7–48 (1990)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: A Calculus of Looping Sequences for Modelling Microbiological Systems. Fundamenta Informaticae 72(1-3), 21–35 (2006)
Brim, L., Jacquet, J.-M., Gilbert, D.: A process algebra for synchronous concurrent programming. In: Hanus, M., RodrÃguez-Artalejo, M. (eds.) ALP 1996. LNCS, vol. 1139, pp. 165–178. Springer, Heidelberg (1996)
Bortolussi, L.: Stochastic concurrent constraint programming. In: Proceedings of QAPL 2006: 4th International workshop on quantitative aspects of programming languages, vol. 164, pp. 65–80 (2006)
Bortolussi, L., Policriti, A.: Modelling biological systems in stochastic constraint programming. Constraints 13, 66–90 (2008)
Calder, M., Gilmore, S., Hillston, J.: Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 1–23. Springer, Heidelberg (2006)
Cardelli, L.: Brane Calculus. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Cardelli, L.: On process rate semantics. Theoretical Computer Science 391(1), 190–215 (2008)
Cardelli, L., Panina, E.M., Regev, A., Shapiro, E., Silverman, W.: BioAmbients: An Abstraction for Biological Compartments. Theoretical Computer Science 325(1), 141–167 (2004)
Ciocchetta, F., Guerriero, M.L.: Modelling Biological Compartments in Bio-PEPA. ENTCS 227, 77–95 (2009)
Ciochetta, F., Hillston, J.: Bio-PEPA: a framework for modelling and analysis of biological systems. Theoretical Computer Science (to appear)
Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and querying biomolecular interaction networks. Theoretical Computer Science 325(1), 25–44 (2004)
Calder, M., Vyshemirsky, V., Orton, R., Gilbert, D.: Analysis of signalling pathways using Continuous Time Markov Chains. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 44–67. Springer, Heidelberg (2006)
Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling of cellular signalling. In: Caires, L., Vasconcelos, V.T. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17–41. Springer, Heidelberg (2007)
Degano, P., Prandi, D., Priami, C., Quaglia, P.: Beta-binders for biological quantitative experiments. Electronic Notes in Computer Science 164, 101–117 (2006)
Gillespie, D., Petzold, L.: Numerical Simulation for Biochemical Kinetics. In: System Modelling in Cellular Biology. MIT Press, Cambridge (2006)
Heath, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. In: The Proceedings of 4th International Workshop on Computational Methods in Systems Biology 2006, Trento, Italy, October 18-19 (2006)
Hillston, J.: A Compositional Approach to Performance Modelling. Cambridge University Press, Cambridge (1996)
Hoare, C.A.R.: Communicating Sequential Processes. Prentice-Hall, Englewood Cliffs (1985)
Milner, R.: A Calculus for Communicating Systems. LNCS, vol. 92. Springer, Heidelberg (1980)
Milner, R.: Communicating and Mobile Systems: the π-Calculus. Cambridge University Press, Cambridge (1999)
Priami, C.: Stochastic π-calculus. The Computer Journal 38, 578–589 (1995)
Regev, A., Shapiro, E.: Cellular abstractions: cells as computation. Nature 419, 343 (2001)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using π-calculus process algebra. In: Pacific Symposium on Biocomputing 2001 (PSB 2001), pp. 459–470 (2001)
Tymchyshyn, O., Kwiatkowska, M.: Combining intra- and inter-cellular dynamics to investigate intestinal homeostasis. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol. 5054, pp. 63–76. Springer, Heidelberg (2008)
Tribastone, M., Duguid, A., Gilmore, S.: The PEPA Eclipse Plug-in. Performance Evaluation Review 36(4), 28–33 (2009)
Versari, C.: A Core Calculus for a Comparative Analysis of Bio-inspired Calculi. In: De Nicola, R. (ed.) ESOP 2007. LNCS, vol. 4421, pp. 411–425. Springer, Heidelberg (2007)
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Calder, M., Hillston, J. (2009). Process Algebra Modelling Styles for Biomolecular Processes. In: Priami, C., Back, RJ., Petre, I. (eds) Transactions on Computational Systems Biology XI. Lecture Notes in Computer Science(), vol 5750. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04186-0_1
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DOI: https://doi.org/10.1007/978-3-642-04186-0_1
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