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Journal of Mathematical Biology

, Volume 66, Issue 1–2, pp 203–223 | Cite as

Reconstruction of extended Petri nets from time-series data by using logical control functions

  • Markus Durzinsky
  • Wolfgang Marwan
  • Annegret WaglerEmail author
Article

Abstract

The aim of this work is to extend a previously presented algorithm (Durzinsky et al. 2008b in Computational methods in systems biology, LNCS, vol 5307. Springer, Heidelberg, pp 328–346; Marwan et al. 2008 in Math Methods Oper Res 67:117–132) for the reconstruction of standard place/transition Petri nets from time-series of experimental data sets. This previously reported method finds provably all networks capable to reproduce the experimental observations. In this paper we enhance this approach to generate extended Petri nets involving mechanisms formally corresponding to catalytic or inhibitory dependencies that mediate the involved reactions. The new algorithm delivers the set of all extended Petri nets being consistent with the time-series data used for reconstruction. It is illustrated using the phosphate regulatory network of enterobacteria as a case study.

Keywords

Reverse engineering Petri nets Read arcs and inhibitory arcs Phosphate regulatory network 

Mathematics Subject Classification (2000)

68R05 92C42 

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Markus Durzinsky
    • 1
  • Wolfgang Marwan
    • 1
  • Annegret Wagler
    • 2
    Email author
  1. 1.Magdeburg Centre for Systems Biology (MaCS)Otto-von-Guericke Universität MagdeburgMagdeburgGermany
  2. 2.Faculty of Sciences/LIMOSUniversité Blaise Pascal (Clermont-Ferrand II)AubièreFrance

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