A Process Calculus for Molecular Interaction Maps

TL;DR

The paper introduces the MIM calculus, a formal modeling framework inspired by biological reaction symbols, enabling unambiguous, executable representations of molecular interaction maps for biomolecular network analysis.

Contribution

It provides a formal syntax and semantics for the MIM notation, bridging diagrammatic biological models with rigorous computational formalisms.

Findings

Formal definition of MIM calculus syntax and semantics

Unambiguous interpretation of MIM diagrams

Application to biomolecular network modeling

Abstract

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.