KEGG2SBML Command-line utility can convert KEGG Pathway database files to SBML
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converter convert conversion convert KEGG KEGG conversion sbml converter

KEGG2SBML Description

Command-line utility can convert KEGG Pathway database files to SBML KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML's capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.KEGG2SBML can convert KEGG Pathway Database Release 46.0 or later. (Past releases of KEGG Pathway Database have not been tested and may not be converted by KEGG2SBML.)KEGG2SBML can generate SBML Level 2 Version 2 and Level 2 Version 3 without annotations used by CellDesigner and Level 1 and Level 2 (Version 1), with or without annotations.NOTE: KEGG2SBML is licensed and distributed under the terms of the GNU Library or Lesser General Public License (LGPL). What's New in This Release: Changes in parsing KEGG Pathway: · KEGG Pathway Databse Release 46.0 or later can be converted. (Past releases of KEGG Pathway Database may not be converted by kegg2sbml version 1.5.0.) · another format file (*.coord) is supported · existing format file (*.conf) is also supported. -o option can be used to explicitly use this format. · *.coord file is parsed instead of *.conf file by default Changes in parsing KEGG LIGAND: · performance improvement by storing a hash table to cache files and reading these cache files instead of parsing LIGNAD database files (about 10 times faster to parse LIGAND database) Changes in writing SBML: · SBML Level 2 Version 2 and Level 2 Version 3 are supported. (Currently, CellDesigner annotation tags are not supported with these SBML level/version.) Added options: · '-r' : Parse ligand database files instead of reading binary cache files located in the same directory. (default : read cache files (*.bin) ) · '-o' : Parse *.conf files instead of *.coord files when a directory name is given as an argument or -a option is set. (default : parse *.coord files) · KGML is no longer used from this release. · Other minor improvements and fixes.

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