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Bioinformatics Advance Access originally published online on November 16, 2004
Bioinformatics 2005 21(7):1219-1226; doi:10.1093/bioinformatics/bti145
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber

Ina Koch 1,*, Björn H. Junker 2 and Monika Heiner 3

1Department of Bioinformatics, Technical University of Applied Sciences Berlin Seestrasse 64, Berlin, 13347, Germany
2Institute of Plant Genetics and Crop Plant Research Corrensstrasse 3, Gatersleben, 06466, Germany
3Computer Science Department, Brandenburg University of Technology at Cottbus PO 10 13 44, Cottbus, 03013, Germany

*To whom correspondence should be addressed.

Motivation: Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and analysis in order to validate the model. The metabolism between sucrose and starch in the potato tuber is of great research interest. Even if the metabolism is one of the best studied in sink organs, it is not yet fully understood.

Results: We provide an approach for model validation of metabolic networks using Petri net theory, which we demonstrate for the sucrose breakdown pathway in the potato tuber. We start with hierarchical modelling of the metabolic network as a Petri net and continue with the analysis of qualitative properties of the network. The results characterize the net structure and give insights into the complex net behaviour.

Availability: Free availability of the Petri net editor PED, the animator PedVisor via http://www-dssz.informatik.tu-cottbus.de/~wwwdssz, and the analysis tool Integrated Net Analyser (INA) via http://www.informatik.hu-berlin.de/~starke/ina.html

Contact: Ina.Koch{at}tfh-berlin.de


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