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Volume 3

Special Issue:
Petri Nets for
Metabolic
Networks



Full article

In Silico Biology 3, 0030 (2003); ©2003, Bioinformation Systems e.V.  



Quantitative Petri net model of gene regulated metabolic networks in the cell

Ming Chen* and Ralf Hofestaedt

Bioinformatics / Medical Informatics, Technische Fakultät, Universität Bielefeld, Postfach 10 01 31, D-33501 Bielefeld
Email: mchen@techfak.uni-bielefeld.de

* corresponding author


Edited by E. Wingender; received April 28, 2003; revised and accepted April 29, 2003; published June 07, 2003


Abstract

A method to exploit hybrid Petri nets (HPN) for quantitatively modeling and simulating gene regulated metabolic networks is demonstrated. A global kinetic modeling strategy and Petri net modeling algorithm are applied to perform the bioprocess functioning and model analysis. With the model, the interrelations between pathway analysis and metabolic control mechanism are outlined. Diagrammatical results of the dynamics of metabolites are simulated and observed by implementing a HPN tool, Visual Object Net ++. An explanation of the observed behavior of the urea cycle is proposed to indicate possibilities for metabolic engineering and medical care. Finally, the perspective of Petri nets on modeling and simulation of metabolic networks is discussed.

Key words: metabolic network, gene regulation, Petri nets, quantitative model, urea cycle, modeling and simulation