Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks

TL;DR

This paper introduces a set of high-level temporal logic query patterns to simplify the process of querying large cellular interaction network models, demonstrated on E. coli regulatory networks.

Contribution

It proposes a pattern-based approach to make temporal logic model checking accessible for non-experts in systems biology.

Findings

Patterns effectively capture common biological questions.

Automated translation of patterns into temporal logic is feasible.

Application to E. coli model validates approach.

Abstract

Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The application of model-checking approaches is hampered, however, by the difficulty for non-expert users to formulate appropriate questions in temporal logic. In order to deal with this problem, we propose the use of patterns, that is, high-level query templates that capture recurring biological questions and that can be automatically translated into temporal logic. The applicability of the developed set of patterns has been investigated by the analysis of an extended model of the network of global regulators controlling the carbon starvation response in Escherichia coli.