Simulation of Kohn's Molecular Interaction Maps through Translation into Stochastic CLS+

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.