Temporal logic patterns for querying dynamic models of cellular interaction networks

• DOI: 10.1093/bioinformatics/btn275
• Publication Date: 2008-08-09T13:08:02Z
• Authors: Pedro T. Monteiro; Delphine Ropers; Radu Mateescu; Ana T. Freitas; Hidde de Jong
• Keywords: 0301 basic medicine; [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; Proteome; Software Validation; 006; Temporal logic; [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; Quantitative Biology - Quantitative Methods; Models, Biological; Qualitative simulation; Formal verification; 03 medical and health sciences; Logistic Models; FOS: Biological sciences; Protein Interaction Mapping; Computer Simulation; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; Systems biology; Genetic regulatory networks; Algorithms; Software; Quantitative Methods (q-bio.QM); [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]; Signal Transduction

Abstract Motivation: Models of the dynamics 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 scale and complexity. The application modelchecking approaches is hampered, however, by difficulty for nonexpert users formulate appropriate questions temporal logic. Results: In order deal problem, we propose use patterns, that is, high-level query templates capture recurring biological can be automatically translated into applicability developed set patterns has been investigated analysis an extended network global regulators controlling carbon starvation response Escherichia coli. Availability: GNA are available at http://www-helix.inrialpes.fr/gna Contact: [e-mail]