Qualitative reasoning: modeling and simulation with incomplete knowledge
Qualitative reasoning: modeling and simulation with incomplete knowledge
Proving properties of continuous systems: qualitative simulation and temporal logic
Artificial Intelligence
Patterns in property specifications for finite-state verification
Proceedings of the 21st international conference on Software engineering
Model checking
An automata-theoretic approach to branching-time model checking
Journal of the ACM (JACM)
Computers and Biomedical Research
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
Automatica (Journal of IFAC)
IJCAI'05 Proceedings of the 19th international joint conference on Artificial intelligence
CADP 2006: a toolbox for the construction and analysis of distributed processes
CAV'07 Proceedings of the 19th international conference on Computer aided verification
On approximative reachability analysis of biochemical dynamical systems
Transactions on Computational Systems Biology XIV
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Formal verification based on model checking provides a powerful technology to query qualitative models of dynamical systems. 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 capturing recurring questions which can be automatically translated to temporal logic. We develop a set of patterns for the analysis of qualitative models of genetic regulatory networks, which are sufficiently generic though to be useful in other application domains. The applicability of the patterns has been investigated by the analysis of a model of the network of global regulators controlling the carbon starvation response in Escherichia coli.