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On Approximative Reachability Analysis of Biochemical Dynamical Systems

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Transactions on Computational Systems Biology XIV

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 7625))

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Abstract

This is an extended version of the workshop paper [1], in which a new computational technique called quantitative discrete approximation has been introduced. The technique provides finite discrete approximation of continuous dynamical systems which is suitable especially for a significant class of biochemical dynamical systems. With decreasing granularity the approximation of behaviour between a discrete state and its successor converges to the behaviour of the original continuous system in the respective part of the phase space.

This paper provides a detailed description of the method and algorithms solving the reachability problem in biochemical dynamical systems. The method is supplemented with heuristics for reducing the cardinality of the reachable state space. The algorithms are evaluated on six models (with numbers of variables ranging from 2 to 12).

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Authors and Affiliations

  1. Faculty of Informatics, Masaryk University, Botanická 68a, Brno, Czech Republic

    L. Brim, J. Fabriková, S. Dražan & D. Šafránek

Authors
  1. L. Brim
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  2. J. Fabriková
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  3. S. Dražan
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  4. D. Šafránek
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Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo, TN, Italy

    Corrado Priami

  2. Department of Information Technologies, Akademi University, Joukohaisenkatu 3-5, 20520, Turku, Finland

    Ion Petre

  3. Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, The Netherlands

    Erik de Vink

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Brim, L., Fabriková, J., Dražan, S., Šafránek, D. (2012). On Approximative Reachability Analysis of Biochemical Dynamical Systems. In: Priami, C., Petre, I., de Vink, E. (eds) Transactions on Computational Systems Biology XIV. Lecture Notes in Computer Science(), vol 7625. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35524-0_4

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  • DOI: https://doi.org/10.1007/978-3-642-35524-0_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-35523-3

  • Online ISBN: 978-3-642-35524-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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