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

Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks