An intermediate language for the stochastic simulation of biological systems

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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 ππ-calculus. We prove soundness and completeness of both the encodings.
Original languageEnglish
Pages (from-to)3085 - 3109
Number of pages25
JournalTheoretical Computer Science
Volume410
Issue number33–34
DOIs
Publication statusPublished - 2009

Keywords / Materials (for Non-textual outputs)

  • Stochastic π -calculus

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