A Process Calculus for Molecular Interaction Maps

• Main Authors: Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini, Aureliano Rama
• Format: Article
• Language: English
• Published: Open Publishing Association 2009-11-01
• Series: Electronic Proceedings in Theoretical Computer Science
• Online Access: http://arxiv.org/pdf/0911.4854v1

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.