Simulation of kohn's molecular interaction maps through translation into stochastic CLS+

Authors:
Roberto Barbuti;Daniela Lepri;Andrea Maggiolo-Schettini;Paolo Milazzo;Giovanni Pardini;Aureliano Rama
Affiliations:
Dipartimento di Informatica, Università di Pisa;Institutt for Informatikk, Universitetet i Oslo;Dipartimento di Informatica, Università di Pisa;Dipartimento di Informatica, Università di Pisa;Dipartimento di Informatica, Università di Pisa;Dipartimento di Informatica, Università di Pisa
Venue:
PSI'09 Proceedings of the 7th international Andrei Ershov Memorial conference on Perspectives of Systems Informatics
Year:
2009

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Abstract

Kohn's Molecular Interaction Maps (MIMs) are a graphical notation for describing bioregulatory networks at the molecular level. Even if the meaning of Kohn's diagrams can be often easily understood, in many cases, due to the lack of a precise mathematical semantics, the notation can be ambiguous. By this paper we achieve two goals. Firstly, we give a precise meaning to MIMs by their translation into a formalism, the Stochastic Calculus of Looping Sequences (SCLS+), with a mathematical semantics. Further, by this translation we provide MIMs with all the tools developed for SCLS+, namely analysers and simulators. The ability of SCLS+ to specify compartments allows us to easily translate MIMs descriptions also when membranes are involved in the interactions.