Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
BACKGROUND
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.
Koch
Ina
I
Department of Bioinformatics, Technical University of Applied Sciences Berlin, Seestrasse 64, Berlin, 13347, Germany. Ina.Koch@tfh-berlin.de
Junker
Björn H
BH
Heiner
Monika
M
D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D004734:Energy Metabolism / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical; D009097:Multienzyme Complexes / Q000378:metabolism; D016571:Neural Networks, Computer; D010940:Plant Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D011198:Solanum tuberosum / Q000378:metabolism*; D013395:Sucrose / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
D009097:Multienzyme Complexes; D010940:Plant Proteins; D014157:Transcription Factors; D013395:Sucrose