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Temporal logic patterns for querying qualitative models of genetic regulatory networks

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong

In : M. Ghallab, C.D. Spyropoulos, N. Fakotakis, N. Avouris (eds.), Proceedings of 18th European Conference on Artificial Intelligence (ECAI-08), IOS Press, Amsterdam, 229-233, 2008.

Formal verification based on model checking provides a powerful technology to query qualitative models of dynamical systems. 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 capturing recurring questions which can be automatically translated to temporal logic. We develop a set of patterns for the analysis of qualitative models of genetic regulatory networks, which are sufficiently generic though to be useful in other application domains. The applicability of the patterns has been investigated by the analysis of a model of the network of global regulators controlling the carbon starvation response in Escherichia coli.

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