Computation Tree Regular Logic for Genetic Regulatory Networks

  • Authors:
  • Radu Mateescu;Pedro T. Monteiro;Estelle Dumas;Hidde Jong

  • Affiliations:
  • Inria Rhône-Alpes, Montbonnot St Martin, France F-38330;Inria Rhône-Alpes, Montbonnot St Martin, France F-38330 and Inesc-Id/Ist, Lisboa, Portugal 1000-029;Inria Rhône-Alpes, Montbonnot St Martin, France F-38330;Inria Rhône-Alpes, Montbonnot St Martin, France F-38330

  • Venue:
  • ATVA '08 Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis
  • Year:
  • 2008

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Abstract

Model checking has proven to be a useful analysis technique not only for concurrent systems, but also for the genetic regulatory networks (Grns) that govern the functioning of living cells. The applications of model checking in systems biology have revealed that temporal logics should be able to capture both branching-time and fairness properties. At the same time, they should have a user-friendly syntax easy to employ by non-experts. In this paper, we define Ctrl(Computation Tree Regular Logic), an extension of Ctlwith regular expressions and fairness operators that attempts to match these criteria. Ctrlsubsumes both Ctland Ltl, and has a reduced set of temporal operators indexed by regular expressions, inspired from the modalities of Pdl(Propositional Dynamic Logic). We also develop a translation of Ctrlinto HmlR(Hennessy-Milner Logic with Recursion), an equational variant of the modal μ-calculus. This has allowed us to obtain an on-the-fly model checker with diagnostic for Ctrlby directly reusing the verification technology available in the Cadptoolbox. We illustrate the application of the Ctrlmodel checker by analyzing the Grncontrolling the carbon starvation response of Escherichia coli.