Abstract
This paper presents a simulation algorithm for the stochastic π-calculus, designed for the efficient simulation of biological systems with large numbers of molecules. The cost of a simulation depends on the number of species, rather than the number of molecules, resulting in a significant gain in efficiency. The algorithm is proved correct with respect to the calculus, and then used as a basis for implementing the latest version of the SPiM stochastic simulator. The algorithm is also suitable for generating graphical animations of simulations, in order to visualise system dynamics.
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Bloch, A., Haagensen, B., Hoyer, M.K., Knudsen, S.U.: The StoPi-calculus and Simulator, http://www.cs.aau.dk/bh/education.html
Blossey, R., Cardelli, L., Phillips, A.: A compositional approach to the stochastic dynamics of gene networks. Transactions in Computational Systems Biology 3939, 99–122 (2006)
Gansner, E.R., North, S.C.: An open graph visualization system and its applications to software engineering. Software-Practice and Experience, 1–5 (1999)
Gibson, M.A., Bruck, J.: Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. 104, 1876–1889 (2000)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340–2361 (1977)
Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115, 1716–1733 (2001)
Lecca, P., Priami, C.: Cell cycle control in eukaryotes: a biospi model. In: BioConcur 2003. ENTCS (2003)
Milner, R.: Communicating and Mobile Systems: the π-Calculus. Cambridge University Press, Cambridge (1999)
Phillips, A.: The Stochastic Pi-Machine (2006), Available from http://research.microsoft.com/~aphillip/spim/
Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Bioconcur 2004, ENTCS (August 2004)
Phillips, A., Cardelli, L., Castagna, G.: A graphical representation for biological processes in the stochastic pi-calculus. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Nielson, H.R. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 123–152. Springer, Heidelberg (2006)
Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the pi- calculus process algebra. In: Pacific Symposium on Biocomputing, vol. 6, pp. 459–470 (2001)
Romanel, A., Dematte, L., Priami, C.: The Beta Workbench. Available from http://www.cosbi.eu/Rpty_Soft_BetaWB.php
Tian, T., Burrage, K.: Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121, 10356–10364 (2004)
Turner, D.N.: The Polymorphic Pi-Calculus: Theory and Implementation. PhD thesis CST-126-96 (June 1996) (also published as ECS-LFCS-96-345)
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Phillips, A., Cardelli, L. (2007). Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus. In: Calder, M., Gilmore, S. (eds) Computational Methods in Systems Biology. CMSB 2007. Lecture Notes in Computer Science(), vol 4695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75140-3_13
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DOI: https://doi.org/10.1007/978-3-540-75140-3_13
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