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)
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.
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