A framework for modelling Molecular Interaction Maps

TL;DR

This paper introduces a method to model complex metabolic networks as Molecular Interaction Maps using Linear Temporal Logic, enabling automated reasoning about their properties with SAT solvers.

Contribution

It presents a novel logical framework for representing and analyzing metabolic networks, facilitating property verification and network modification strategies.

Findings

Implemented a tool for logical reasoning on metabolic networks.

Demonstrated the approach with case studies.

Enabled automatic verification of network properties.

Abstract

Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of these reactions. Most of these pathways are formed by an intricate and complex network of chain reactions, and can be represented in a human readable form using graphs which describe the cell cycle checkpoint pathways. This paper proposes a method to represent Molecular Interaction Maps (graphical representations of complex metabolic networks) in Linear Temporal Logic. The logical representation of such networks allows one to reason about them, in order to check, for instance, whether a graph satisfies a given property $\phi$, as well as to find out which initial conditons would guarantee $\phi$, or else how can the the graph be updated in order to satisfy $\phi$. Both the translation and resolution methods have been implemented in a tool capable of addressing such questions thanks to a reduction to propositional logic which allows exploiting classical SAT solvers.