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.
@article{arxiv.0911.4854,
title = {A Process Calculus for Molecular Interaction Maps},
author = {Roberto Barbuti and Andrea Maggiolo-Schettini and Paolo Milazzo and Giovanni Pardini and Aureliano Rama},
journal= {arXiv preprint arXiv:0911.4854},
year = {2009}
}
Comments
15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC 2009