Convert2Sbml / Convert2Matlab
Java tool to convert various metabolic network source files into SBML / MATLAB files.
License
Redistribution and use in source and binary forms, with or without
modification, are permitted provided agreeing to the Simplified BSD Style License.
- DownloadLicense (TXT, 2 KB)vertical_align_bottom
- Read about Simplified BSD Style License at external pagehttp://www.opensource.orgcall_made
Installation
- Java version 1.5 (SDK or JRE 5.0) or newer must be installed on your computer, see external pagehttp://java.sun.comcall_made
- 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
containing
- reaction definition column
- reaction name column
Flux Analyzer / CellNetAnalyzer
Flux Analyzer / CellNetAnalyzer source files
Stoichiometry
Tab (or comma, ...) separated text files:
- stoichiometric matrix
- reaction names
- metabolite names
- reaction reversibilities vector
SBML files
Files in the external pageSBMLcall_made (XML) file format
Supported Output Formats
SBML
An sbml file level 2/version 1, see external pagehttp://sbml.orgcall_made
MATLAB
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