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SBML Kinetics Help

SBML Kinetics Help - Bioinformatics

SBML Kinetics Help - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 07-14-2010, 11:44 AM
Pipette Filler
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Lightbulb SBML Kinetics Help



I tried to convert KGML (KEGG XML) files to SBML format with KeggConverter.
In normal mode (java -jar keggconvert.jar JustConvert) it works without problems, but when I try to create additional kinetics information to the SBML file (java -jar keggconver.jar makekinetics) I get a java NullPointer Exception.
I wonder a bit how this kinetics information are generated. Within KeggConverter there is a kinetics libary, but in the XML Files from KEGG seems to be no link information in the reaction parameters to the KEGG LIGAND database reaction.lst files where the stochiometric Information for the kinetics are stored. Unfortunatly the package classes where the kinetics functions are stored are in binary code so I can't see the source code. Don't know how to get rid of the NullPointer problem. Could it be that I have to copy any libSBML jar file (got Version 2.8) anywhere ? Maybe someone could help??
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