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Volume 3

Special Issue:
Petri Nets for
Metabolic
Networks



Full article

In Silico Biology 3, 0029 (2003); ©2003, Bioinformation Systems e.V.  



Topological analysis of metabolic networks based on Petri net theory

Ionela Zevedei-Oancea and Stefan Schuster*

Max Delbrück Center for Molecular Medicine, Department of Bioinformatics Robert-Rössle-Str 10, 13092 Berlin-Buch, Germany
Email: stschust@mdc-berlin.de

* corresponding author


Edited by E. Wingender; received April 28, 2003; revised and accepted May 21, 2003; published June 07, 2003


Abstract

Petri net concepts provide additional tools for the modelling of metabolic networks. Here, the similarities between the counterparts in traditional biochemical modelling and Petri net theory are discussed. For example the stoichiometry matrix of a metabolic network corresponds to the incidence matrix of the Petri net. The flux modes and conservation relations have the T-invariants, respectively, P-invariants as counterparts. We reveal the biological meaning of some notions specific to the Petri net framework (traps, siphons, deadlocks, liveness). We focus on the topological analysis rather than on the analysis of the dynamic behaviour. The treatment of external metabolites is discussed. Some simple theoretical examples are presented for illustration. Also the Petri nets corresponding to some biochemical networks are built to support our results. For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps. All Petri net properties treated in this contribution are exemplified on a system extracted from nucleotide metabolism.

Key words: Petri nets, elementary flux mode, metabolic networks, P-invariant, T-invariant, incidence matrix