Black Box Checking for Biochemical Networks

  • Dragan Bošnački
Conference paper

DOI: 10.1007/978-3-540-25974-9_18

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)
Cite this paper as:
Bošnački D. (2005) Black Box Checking for Biochemical Networks. In: Danos V., Schachter V. (eds) Computational Methods in Systems Biology. CMSB 2004. Lecture Notes in Computer Science, vol 3082. Springer, Berlin, Heidelberg

Abstract

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Dragan Bošnački
    • 1
  1. 1.Dept. of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands

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