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.
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Barbuti, R., Lepri, D., Maggiolo-Schettini, A., Milazzo, P., Pardini, G., Rama, A. (2010). Simulation of Kohn’s Molecular Interaction Maps through Translation into Stochastic CLS+. In: Pnueli, A., Virbitskaite, I., Voronkov, A. (eds) Perspectives of Systems Informatics. PSI 2009. Lecture Notes in Computer Science, vol 5947. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11486-1_6
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DOI: https://doi.org/10.1007/978-3-642-11486-1_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-11485-4
Online ISBN: 978-3-642-11486-1
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