A Process Calculus for Molecular Interaction Maps

Details A Process Calculus for Molecular Interaction Maps A Process Calculus for Molecular Interaction Maps

2009-11-25

arxiv.org/abs/0911.4854v1

EPTCS 11, 2009, pp. 33-49

Computer Science

Computational Engineering, Finance, and Science

15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC 2009

Scientific paper

10.4204/EPTCS.11.3

We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.

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