Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
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A graphical representation for biological processes in the stochastic pi-calculus
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Probabilistic model checking of complex biological pathways
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Using probabilistic model checking in systems biology
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Synapses as stochastic concurrent systems
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Electronic Notes in Theoretical Computer Science (ENTCS)
External Control in Process Algebra for Systems Biology
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Electronic Notes in Theoretical Computer Science (ENTCS)
Modeling of Genetic Regulatory Network in Stochastic π-Calculus
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A flexible architecture for performance experiments with the pi-Calculus and its extensions
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A generic abstract machine for stochastic process calculi
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Refining dynamics of gene regulatory networks in a stochastic π-calculus framework
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The attributed pi-calculus with priorities
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Transactions on Computational Systems Biology XII
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
Stochastic simulation of multiple process calculi for biology
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Maximally Parallel Probabilistic Semantics for Multiset Rewriting
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Electronic Notes in Theoretical Computer Science (ENTCS)
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Electronic Notes in Theoretical Computer Science (ENTCS)
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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.