Research article
Modularization of biochemical networks based on classification of Petri net t-invariants
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* Corresponding authors: Eva Grafahrend-Belau grafahr@ipk-gatersleben.de - Ina Koch ina.koch@molgen.mpg.de
1 Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347 Berlin, Germany
2 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Dept. of Molecular Genetics, Corrensstrasse 3, 06466 Gatersleben, Germany
3 Brandendenburg University of Technology at Cottbus, Dept. of Computer Science, Postbox 10 13 44, 03013 Cottbus, Germany
4 Poznań University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965 Poznań, Poland
5 Max Planck Institute for Molecular Genetics, Dept. Computational Molecular Biology, Ihnestr. 73, 14195 Berlin, Germany
BMC Bioinformatics 2008, 9:90 doi:10.1186/1471-2105-9-90
Published: 8 February 2008Additional files
Additional File 1:
Distance measures. In the PDF file, DistanceMeasures.pdf, a mathematical definition and evaluation of the distance measures tested in preliminary investigations is given.
Format: PDF Size: 54KB Download file
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Additional File 2:
Cluster validity measures. In the PDF file, ClusterValidityMeasures.pdf, a mathematical definition and evaluation of the cluster validity measures tested in preliminary investigations is given.
Format: PDF Size: 65KB Download file
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Additional File 3:
Petri net models. In the ZIP file, PetriNetModels.zip, the Petri net models of the two case studies are provided. In addition, tables, listing the transitions and places of the models by their name and biological meaning, are given.
Format: ZIP Size: 144KB Download file
Additional File 4:
T-invariants of the Petri net model of DMD. Description: In the PDF file, DMDTinvariants.pdf, a table, depicting the composition of the t-invariants of the Petri net model of DMD based on the transitions, is provided.
Format: PDF Size: 30KB Download file
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Additional File 5:
Clustering results of the Petri net model of DMD. In the ZIP file, DMDClusteringResults.zip, the clustering results of the Petri net model of DMD, using Single Linkage, Complete Linkage, and Neighbor Joining, are provided. For each method, the constructed dendrogram as well as a detailed description of the clustering result is given.
Format: ZIP Size: 126KB Download file