Abstract
Bio-PEPA is a novel stochastic process algebra which has been recently developed for modelling biochemical pathways [5,6]. In Bio-PEPA a reagent-centric style of modelling is adopted, and a variety of analysis techniques can be applied to a single model expression. Such an approach facilitates easy validation of analysis results when the analyses address the same issues [3] and enhanced insight when the analyses are complementary [4]. Currently supported analysis techniques include stochastic simulation at the molecular level, ordinary di..erential equations, probabilistic model checking and numerical analysis of a continuous time Markov chain.
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Bortolussi, L., Policriti, A.: Modeling Biological Systems in Stochastic Concurrent Constraint Programming. Constraints 13(1-2), 55–90 (2006)
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)
Calder, M., Duguid, A., Gilmore, S., Hillston, J.: Stronger computational modelling of signalling pathways using both continuous and discrete-space methods. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 63–77. Springer, Heidelberg (2006)
Ciocchetta, F., Gilmore, S., Guerriero, M.-L., Hillston, J.: Stochastic Simulation and Probabilistic Model-Checking for the Analysis of Biochemical Systems (2008) (submitted for publication)
Ciocchetta, F., Hillston, J.: Bio-PEPA: an extension of the process algebra PEPA for biochemical networks. In: Proc. of FBTC 2007. Electronic Notes in Theoretical Computer Science, vol. 194(3), pp. 103–117 (2008)
Ciocchetta, F., Hillston, J.: Process algebras for Systems Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 265–312. Springer, Heidelberg (2008)
Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Ruled-based modelling of cellular signalling. In: Caires, L., Vasconcelos, V.T. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17–41. Springer, Heidelberg (2007)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81, 2340–2361 (1977)
Hillston, J.: A Compositional Approach to Performance Modelling. Cambridge University Press, Cambridge (1996)
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.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Regev, A.: Representation and simulation of molecular pathways in the stochastic π-calculus. In: Proceedings of the 2nd workshop on Computation of Biochemical Pathways and Genetic Networks (2001)
Regev, A., Shapiro, E.: Cells as computation. Nature 419, 343 (2002)
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Hillston, J., Ciocchetta, F., Duguid, A., Gilmore, S. (2008). Integrated Analysis from Abstract Stochastic Process Algebra Models. In: Heiner, M., Uhrmacher, A.M. (eds) Computational Methods in Systems Biology. CMSB 2008. Lecture Notes in Computer Science(), vol 5307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88562-7_2
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