An intermediate language for the stochastic simulation of biological systems

Authors:
Roberto Barbuti;Giulio Caravagna;Andrea Maggiolo-Schettini;Paolo Milazzo
Affiliations:
Dipartimento di Informatica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
Venue:
Theoretical Computer Science
Year:
2009

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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 @p-calculus. We prove soundness and completeness of both the encodings.