From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis

  • David Gilbert
  • Monika Heiner
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4024)


We report on the results of an investigation into the integration of Petri nets and ordinary differential equations (ODEs) for the modelling and analysis of biochemical networks, and the application of our approach to the model of the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway. We show that analysis based on a discrete Petri net model of the system can be used to derive the sets of initial concentrations required by the corresponding continuous ordinary differential equation model, and no other initial concentrations produce meaningful steady states. Altogether, this paper represents a tutorial in step-wise modelling and analysis of larger models as well as in structured design of ODEs.


Model Check Metabolic Network Extracellular Signal Regulate Kinase Biochemical Network Reachability Graph 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • David Gilbert
    • 1
  • Monika Heiner
    • 2
  1. 1.Bioinformatics Research CentreUniversity of GlasgowGlasgow, ScotlandUK
  2. 2.Department of Computer ScienceBrandenburg University of TechnologyCottbusGermany

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