From petri nets to differential equations – an integrative approach for biochemical network analysis

  • Authors:

  • David Gilbert;Monika Heiner

  • Affiliations:

  • Bioinformatics Research Centre, University of Glasgow, Glasgow, Scotland, UK;Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany

  • Venue:
  • ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
  • Year:
  • 2006

Quantified Score

Hi-index 0.00

Visualization

Abstract

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.