Computation Tree Regular Logic for Genetic Regulatory Networks
ATVA '08 Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis
On algorithmic analysis of transcriptional regulation by LTL model checking
Theoretical Computer Science
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
A Port Graph Calculus for Autonomic Computing and Invariant Verification
Electronic Notes in Theoretical Computer Science (ENTCS)
Query-based verification of qualitative trends and oscillations in biochemical systems
Theoretical Computer Science
A Model and Analysis of the AKAP Scaffold
Electronic Notes in Theoretical Computer Science (ENTCS)
Modular Verification of Interactive Systems with an Application to Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
An integrated approach to P systems formal verification
CMC'10 Proceedings of the 11th international conference on Membrane computing
Dynamically consistent reduction of logical regulatory graphs
Theoretical Computer Science
Theoretical Computer Science
Parameter inference for asynchronous logical networks using discrete time series
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Use of timed automata and model-checking to explore scenarios on ecosystem models
Environmental Modelling & Software
On Parameter Synthesis by Parallel Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Time Series Dependent Analysis of Unparametrized Thomas Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Trend-Based analysis of a population model of the AKAP scaffold protein
Transactions on Computational Systems Biology XIV
Temporal Logics for Phylogenetic Analysis via Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 3.84 |
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 Contact: Hidde.de-Jong@inrialpes.fr