Software
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
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* Corresponding author: Aristotelis Chatziioannou achatzi@eie.gr
1 Department of Informatics with Applications in Biomedicine, University of Central Greece. Papasiopoulou 2-4, 35100, Lamia, Greece
2 Department of Information and Communication Systems Engineering, University of the Aegean, 83200, Karlovasi, Samos, Greece
3 Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Vassileos Konstantinou 48, 11635, Athens, Greece
BMC Bioinformatics 2009, 10:324 doi:10.1186/1471-2105-10-324
Published: 8 October 2009Additional files
Additional file 1:
Command line options. File containing the description of the commands of the command line version of KEGGConverter.
Format: DOC Size: 27KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 2:
Case study files. Input: 6 KGML Pathway files: Glycolysis/Gluconeogenesis - hsa00010.xml, Citrate cycle (TCA cycle) - hsa00020.xml, Pentose phosphate pathway - hsa00030.xml, Fatty acid biosynthesis - hsa00061.xml, Fatty acid metabolism - hsa00071.xml, Urea cycle and metabolism of amino groups - hsa00220.xml. Output from KEGGconverter: the initial merged KGML file: mergedKEGG.xml, SBML converted model: sbml_mergedKEGGconverter.xml, SBML converted model with default kinetics: sbml_mergedKEGGconverterKinetics.xml, a circular layout diagram of the resulted model from CellDesigner: CaseStudyFinalDiagram.pdf.
Format: ZIP Size: 1.1MB Download file
Additional file 3:
Case study files with alternative procedures. • FeaturesComparisonTable.doc: a comparison of features table regarding the applications mentioned in the case study. • hsa_paths.zip: The 6 case study pathways produced by KEGG2SBML. • RamanAllMerged.xml: The intergrated SBML model using [22] alternative procedure and having as input the 6 SBML files produced by KEGG2SBML. • semanticAll.xml: The intergrated SBML model using semanticSBML and having as input the 6 SBML files produced by KEGG2SBML.
Format: ZIP Size: 21KB Download file
Additional file 4:
KEGGconverter tool. This is the version (1.0) of the KEGGconverter tool which runs as a command line utility. It searches in the '/in' subdirectory for KGML models and performs the conversion depending on the specific command arguments.
Format: ZIP Size: 6.2MB Download file