A Process Calculus for Molecular Interaction Maps

Roberto Barbuti
Andrea Maggiolo-Schettini
Paolo Milazzo
Giovanni Pardini
Aureliano Rama

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.

In Gabriel Ciobanu: Proceedings Third Workshop on Membrane Computing and Biologically Inspired Process Calculi 2009 (MeCBIC 2009), Bologna, Italy, 5th September 2009, Electronic Proceedings in Theoretical Computer Science 11, pp. 35–49.
Published: 30th November 2009.

ArXived at: http://dx.doi.org/10.4204/EPTCS.11.3 bibtex PDF

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