UNIVERSITY of GLASGOW

Computing at Glasgow University
 
Paper ID: 8099
DCS Tech Report Number: TR-2005-208

From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis
Gilbert,D. Heiner,M.

Publication Type: Tech Report (internal)
Appeared in: DCS Technical Report Series
Page Numbers : 23
Publisher: Dept of Computing Science, University of Glasgow
Year: 2005
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.

Keywords: Petri-nets, Ordinary Differential Equations, biochemical networks, signalling pathways, modelling


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