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Petri nets in systems biology

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Abstract

Petri nets are used in many areas. This article discusses the application of Petri nets in systems biology. Using an example from biochemistry, concepts for the automatic decomposition of biochemical systems are introduced. The article focuses on those concepts that fulfill steady-state conditions. Interestingly, all the concepts are based on minimal, semi-positive transition invariants. The article describes, which new definitions for network decomposition can be derived and how they can be interpreted in the context of biology. This is illustrated with the example of the citric acid cycle, for which a new metabolic pathway could be predicted with the help of such an analysis.

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Acknowledgments

In particular, I would like to thank the initiators of this special edition, Wolfgang Reisig and Jörg Desel, for their invitation to this contribution. My special thanks goes to Stefan Schuster for introducing me to the works of Reddy in 1997 and for many inspiring discussions. I also would like to thank Jörg Ackermann, Falk Schreiber, Björn Junker, Andrea Sackmann, Eva Grafahrend-Belau, Astrid Speer and Stefanie Grunwald for fruitful collaboration. Additionally, many thanks to Michael Rücker for the professional translation and careful reading of this article.

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  1. Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main Robert-Mayer-Straße, 11-15, 60325,  Frankfurt am Main, Germany

    Ina Koch

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Correspondence to Ina Koch.

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Communicated by Dr. Wolfgang Reisig.

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Koch, I. Petri nets in systems biology. Softw Syst Model 14, 703–710 (2015). https://doi.org/10.1007/s10270-014-0421-5

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