Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
Pedro Tiago Monteiro, Delphine Ropers, Radu Mateescu, Ana Teresa Freitas, and Hidde de Jong
Bioinformatics 24(16):i227-i233, 2008
A conference version of this paper is available here.
Motivation: 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 nonexpert users to formulate appropriate
questions in temporal logic.
Results: 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 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.