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. |