Convert2Sbml / Convert2Matlab

Main content

Java tool to convert various metabolic network source files into SBML / MATLAB files.


Redistribution and use in source and binary forms, with or without
modification, are permitted provided agreeing to the Simplified BSD Style License.


  • Java version 1.5 (SDK or JRE 5.0) or newer must be installed on your computer, see
  • Unzip the downloaded file, a mapping directory will be extracted
  • To run, simply run
    java -jar convert2sbml.jar
    java -jar convert2matlab.jar
  • Help:
    java -jar convert2sbml.jar --help
    java -jar convert2matlab.jar --help

Supported Input Files

Currently supported input types (run tool with --help option for details):

Reaction List

Tab separated text file with quoted columns:

  • reaction definition column
  • reaction name column

Excel file


  • reaction definition column
  • reaction name column

Flux Analyzer / CellNetAnalyzer

Flux Analyzer / CellNetAnalyzer source files


Tab (or comma, ...) separated text files:

  • stoichiometric matrix
  • reaction names
  • metabolite names
  • reaction reversibilities vector

SBML files

Files in the SBML (XML) file format

Supported Output Formats


An sbml file level 2/version 1, see


A matlab .m file generating a structure (struct). The matlab structure defines the following fields

  • N: stoichiometric matrix
  • metaNames: metabolite names
  • reacNames: reaction names
  • lower, upper: lower and upper bounds for reaction fluxes
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