Stochastic simulation of multiple process calculi for biology
نویسندگان
چکیده
منابع مشابه
Stochastic simulation of multiple process calculi for biology
Numerous programming languages based on process calculi have been developed for biological modelling, many of which can generate potentially unbounded numbers of molecular species and reactions. As a result, such languages cannot rely on standard reaction-based simulation methods, and are generally implemented using custom stochastic simulation algorithms. As an alternative, this paper proposes...
متن کاملStochastic Simulation of Process Calculi for Biology
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot...
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A syntactic framework called SGSOS, for defining well-behaved Markovian stochastic transition systems, is introduced by analogy to the GSOS congruence format for nondeterministic processes. Stochastic bisimilarity is guaranteed a congruence for systems defined by SGSOS rules. Associativity of parallel composition in stochastic process algebras is also studied within the framework.
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A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a measure indicating their rates. We show how RTS can be used for providing the operational semantics of...
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A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a measure indicating their rates. We show how RTS can be used for providing the operational semantics of...
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ژورنال
عنوان ژورنال: Theoretical Computer Science
سال: 2012
ISSN: 0304-3975
DOI: 10.1016/j.tcs.2011.12.057