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A Metabolic Pathway converting Tool
 
 

 

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Before downloading the KEGGConverter Tool you need to install the following software :

Java JRE

LibSBML (2.3.4)

CellDesigner

After intalling at least the two out of three required items you may download and unzip the KEGGConverter Tool found in the following link. In order to use it simply unzip it in a folder and run the KeggConverter.jar in a command line environment.

KEGGConverter Tool

If you already have the tool and need to update to the latest annotation tab files follow the links below:

Compounds.tab Created: Wednesday, 06th February, 2013 04:14pm

EnzymeNames.tab Created: Wednesday, 06th February, 2013 04:14pm

Enzyme-Organism.tab Created: Wednesday, 06th February, 2013 04:14pm

OrthologNames.tab Created: Wednesday, 06th February, 2013 04:14pm

Ortholog-Organism.tab Created: Wednesday, 06th February, 2013 04:14pm

GlycanNames.tab Created: Wednesday, 06th February, 2013 04:14pm

Usage:

'java -jar keggconvert.jar justConvert' to process kgml files from .\in directory.

'justConvertCD' to process kgml files from .\in directory to CellDesigner sbml.

'makeKinetics' to convert and introduce kinetics in the produced sbml files.

'makeKineticsCD' to convert and introduce kinetics in the produced CellDesigner SBML files.

'merge' to produce a merged kgml file for all KEGG files in .\in directory.

'keepOrphan' to prevent orphan node elimination during model curation.Use it together with 'justConvert' or 'makeKinetics'.

'STATS' to produce reaction statistics for all sbml files in .\out directory.

'dir=mydir/' to use as subdirectories in in&out directories.

'help' to get these available options.

In case of being behind proxies you must use options before '-jar': '-Dhttp.proxyHost=xxx.xx.xxx.x -Dhttp.proxyPort=8080'

Cite this Tool:

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.

Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN

BMC Bioinformatics 2009, 10:324 (8 October 2009)