Automatic verification of finite-state concurrent systems using temporal logic specifications
ACM Transactions on Programming Languages and Systems (TOPLAS)
Model-Checking: A Tutorial Introduction
SAS '99 Proceedings of the 6th International Symposium on Static Analysis
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Symbolic Model Checking of Logics with Actions
Model Checking and Artificial Intelligence
Automatic verification of knowledge and time with NuSMV
IJCAI'07 Proceedings of the 20th international joint conference on Artifical intelligence
Decision diagrams for the representation and analysis of logical models of genetic networks
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Dynamically consistent reduction of logical regulatory graphs
Theoretical Computer Science
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Considering the logical (Boolean or multi-valued) asynchronous framework, we delineate a reduction strategy for large signalling and regulatory networks. Consequently, focusing on the core network that drives the whole dynamics, we can check which attractors are reachable from given initial conditions, under fixed or varying environmental conditions. More specifically, the dynamics of logical models are represented by (asynchronous) state transition graphs that grow exponentially with the number of model components. We introduce adequate reduction methods (preserving reachability of the attractors) and proceed with model-checking approaches. Input nodes (that generally represent receptors) and output nodes (that constitute readouts of network behaviours) are each specifically processed to reduce the state space. The proposed approach is made available within GINsim, our software dedicated to the definition and analysis of logical models. The new GINsim functionalities consist in a proper reduction of output components, as well as the corresponding symbolic encoding of logical models for the NuSMV model checker. This encoding also includes a reduction over input components (transferring their values from states to transitions labels). Finally, we demonstrate the interest of the proposed methods through their application to a published large scale model of the signalling pathway involved in T cell activation.