Computational Methods in Systems Biology

Volume 3082 of the series Lecture Notes in Computer Science pp 225-230

Black Box Checking for Biochemical Networks

  • Dragan BošnačkiAffiliated withDept. of Biomedical Engineering, Eindhoven University of Technology

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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.