An Intermediate Language for the 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:
Electronic Notes in Theoretical Computer Science (ENTCS)
Year:
2008

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Abstract

We propose String MultiSet Rewriting (SMSR) as an intermediate language for simulation of biomolecular systems. Higher level formalisms for biological systems description can be translated into SMSR and SMSR descriptions can be simulated by adapting an existing simulator. In this paper we show the translation of one of these formalisms, CLS+, into SMSR, and we prove correctness and completeness of the translation.