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MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format

2010; Oxford University Press; Volume: 26; Issue: 18 Linguagem: Inglês

10.1093/bioinformatics/btq425

1367-4811

Thomas Forth, Glenn A. McConkey, David R. Westhead,

Bioinformatics and Genomic Networks

Abstract Summary: An application has been developed to help with the creation and editing of Systems Biology Markup Language (SBML) format metabolic networks up to the organism scale. Networks are defined as a collection of Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND reactions with an optional associated Enzyme Classification (EC) number for each reaction. Additional custom reactions can be defined by the user. Reactions within the network can be assigned flux constraints and compartmentalization is supported for each reaction in addition to the support for reactions that occur across compartment boundaries. Exported networks are fully SBML L2V4 compatible with an optional L2V1 export for compatibility with old versions of the COBRA toolbox. Availability and implementation: The software runs in the free Microsoft Access 2007™ Runtime (Microsoft Inc.), which is included with the installer and works on Windows XP SP2 or better. Full source code is viewable in the full version of Access 2007 or 2010. Users must have a license to use the KEGG LIGAND database (free academic licensing is available). Please go to www.bioinformatics.leeds.ac.uk/∼pytf/metnetmaker for software download, help and tutorials. Contact: pytf@leeds.ac.uk