Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks

Pedro T. Monteiro (1) , Delphine Ropers (1) , Radu Mateescu (2) , Ana T. Freitas (3) , Hidde de Jong (1)

1 HELIX - Computer science and genomics
2 VASY - System validation - Research and applications
3 KDBIO - Knowledge Discovery and Bioinformatics

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 modelchecking 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. Availability: GNA and the model of the carbon starvation response network are available at http://www-helix.inrialpes.fr/gna

Mots clés: Formal verification; Genetic regulatory networks; Systems biology; Qualitative simulation; Temporal logic

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong. Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks. Bioinformatics, 2008, ECCB 2008 CONFERENCE PROCEEDINGS 22-26 SEPTEMBER 2008, CAGLIARI, ITALY, 24 (16), pp.i227-i233. ⟨10.1093/bioinformatics/btn275⟩. ⟨inria-00357805⟩