Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks

Pedro T. Monteiro; Delphine Ropers; Radu Mateescu; Ana T. Freitas; Hidde De Jong

inria-00260980, version 3

Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks

Pedro T. Monteiro ( Author to contact preferably )^a^, 1, Delphine Ropers ()^a^, 1, Radu Mateescu ()^a^, 2, Ana T. Freitas ()^b^, 3, Hidde De Jong ()^a^, 1

N° RR-6470 (2008)

Abstract: 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 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 that capture recurring biological questions and that 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.

a – INRIA
b – INESC-ID
1: HELIX (INRIA Rhône-Alpes)
INRIA – CNRS : UMR5558 – Université Claude Bernard - Lyon I
2: VASY (Dijon) (INRIA Grenoble Rhône-Alpes)
INRIA
3: Knowledge Discovery and Bioinformatics (KDBIO)
INESC-ID

inria-00260980, version 3
http://hal.inria.fr/inria-00260980
oai:hal.inria.fr:inria-00260980
From: Rapport De Recherche Inria <>
Submitted on: Tuesday, 11 March 2008 11:52:46
Updated on: Thursday, 20 March 2008 15:55:31

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arXiv: 0803.0802

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