Learning regular sets from queries and counterexamples
Information and Computation
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Journal of Automata, Languages and Combinatorics - Selected papers of the workshop on logic and algebra for concurrency
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Testing Software Design Modeled by Finite-State Machines
IEEE Transactions on Software Engineering
Spin model checker, the: primer and reference manual
Spin model checker, the: primer and reference manual
Model checking and testing combined
ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
Model checking genetic regulatory networks with parameter uncertainty
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
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We propose black box checking as a framework for analyzing biochemical networks. Black box checking was originally introduced by Peled, Yannakakis and Vardi in the context of formal verification of concurrent systems as a strategy that combines model checking and testing, as two main techniques in that area. Based on the natural analogy between biochemical networks and concurrent systems we argue that black box checking can be used to design and perform experiments in a systematic manner, and also to learn about the network underlying mechanisms. We also discuss potential applications with emphasis on forward engineering of biochemical networks.