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An Intermediate Language for Stochastic Simulation of Biological Systems

Barbuti, Roberto and Caravagna, Giulio and Maggiolo-Schettini, Andrea and Milazzo, Paolo (2008) An Intermediate Language for Stochastic Simulation of Biological Systems. Theoretical Computer Science . ISSN 0304-3975 (In Press)

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    Abstract

    We introduce Stochastic String MultiSet Rewriting (sSMSR), and propose this formalism as an intermediate language for the simulation of biomolecular systems. Higher level formalisms for biological systems description can be translated into sSMSR, and the features of sSMSR allow the development of efficient simulators. In this paper, we show the encoding into sSMSR of two formalisms for the description of biological systems, namely Stochastic CLS and the Stochastic π-calculus. We prove soundness and completeness of both the encodings.

    Item Type: Article
    Uncontrolled Keywords: MultiSet rewriting; Stochastic simulation; Stochastic Calculus of Looping Sequences; Stochastic π-calculus
    Subjects: Area01 - Scienze matematiche e informatiche > INF/01 - Informatica
    Divisions: Dipartimenti (until 2012) > DIPARTIMENTO DI INFORMATICA
    Depositing User: Dr Paolo Milazzo
    Date Deposited: 08 Nov 2008
    Last Modified: 20 Dec 2010 11:54
    URI: http://eprints.adm.unipi.it/id/eprint/534

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