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Bioinformatics Advance Access published online on November 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti145
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 7, 2004
Revised November 9, 2004
Accepted November 9, 2004

Article

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

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

* To whom correspondence should be addressed.
Ina Koch, E-mail: Ina.Koch{at}tfh-berlin.de


  Abstract

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 characterise 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 INA via http://www.informatik.hu-berlin.de/~starke/ina.html.


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