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In Silico Biology 3, 0031 (2003); ©2003, Bioinformation Systems e.V.  

Steady state analysis of metabolic pathways using Petri nets

Klaus Voss1, Monika Heiner2 and Ina Koch3,*

1 Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) [GMD], D-53754 Sankt Augustin
2 Computer Science Department, Brandenburg University of Technology at Cottbus, D-03013 Cottbus
3 Department of Bioinformatics, Technical University of Applied Sciences Berlin, D-13347 Berlin; Email:

* corresponding author

Edited by E. Wingender; received April 28, 2003; revised and accepted May 20, 2003; published September 13, 2003


Computer assisted analysis and simulation of biochemical pathways can improve the understanding of the structure and the dynamics of cell processes considerably. The construction and quantitative analysis of kinetic models is often impeded by the lack of reliable data. However, as the topological structure of biochemical systems can be regarded to remain constant in time, a qualitative analysis of a pathway model was shown to be quite promising as it can render a lot of useful knowledge, e. g., about its structural invariants. The topic of this paper are pathways whose substances have reached a dynamic concentration equilibrium (steady state). It is argued that appreciated tools from biochemistry and also low-level Petri nets can yield only part of the desired results, whereas executable high-level net models lead to a number of valuable additional insights by combining symbolic analysis and simulation.

Key words: metabolic pathway, steady state, elementary mode, high-level Petri net, S-invariant, T-invariant