Parameter Identification and Model Ranking of Thomas Networks

  • Hannes Klarner
  • Adam Streck
  • David Šafránek
  • Juraj Kolčák
  • Heike Siebert
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7605)

Abstract

We propose a new methodology for identification and analysis of discrete gene networks as defined by René Thomas, supported by a tool chain: (i) given a Thomas network with partially known kinetic parameters, we reduce the number of acceptable parametrizations to those that fit time-series measurements and reflect other known constraints by an improved technique of coloured LTL model checking performing efficiently on Thomas networks in distributed environment; (ii) we introduce classification of acceptable parametrizations to identify most optimal ones; (iii) we propose two ways of visualising parametrizations dynamics wrt time-series data. Finally, computational efficiency is evaluated and the methodology is validated on bacteriophage λ case study.

Keywords

Thomas network parameter identification model checking 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Hannes Klarner
    • 1
  • Adam Streck
    • 2
  • David Šafránek
    • 2
  • Juraj Kolčák
    • 2
  • Heike Siebert
    • 1
  1. 1.Freie Universität BerlinBerlinGermany
  2. 2.Masaryk UniversityBrnoCzech Republic

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