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

Gilbert, D. and Heiner, M. (2006) From petri nets to differential equations - an integrative approach for biochemical network analysis. Lecture Notes in Computer Science, 4024, pp. 181-200. (doi: 10.1007/11767589)

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.

• Item Type: Articles
• Additional Information: PDF attached is encrypted so the coversheet cannot be added. Unencrypted version requested 13/8/07.
• Keywords: Systems Biology, modelling, ODE ordinary differential equations, petri nets, biochemical networks, signalling pathways
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Gilbert, Prof David
• Authors: Gilbert, D., and Heiner, M.
• Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science; Q Science > QA Mathematics > QA76 Computer software; Q Science > QH Natural history > QH345 Biochemistry
• College/School: College of Science and Engineering > School of Computing Science
• Journal Name: Lecture Notes in Computer Science
• Publisher: Springer
• ISSN: 1611-3349
• Copyright Holders: Copyright © 2006 Springer
• First Published: First published in Lecture Notes in Computer Science 4024:181-200
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher.

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
40996	1	The Glasgow computing science research festival 2005	Muffy Calder	Engineering & Physical Sciences Research Council (EPSRC)	EP/D030110/1	Computing Science