Conversion from SBML to Octave

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.

The SBML to Octave converter is developed inside the System Biology Format Converter (SBFC) framework that will allow us and contributors to add easily new converter. The framework is developed on sourceforge, see the System Biology Format Converter project pages.

Quick Setup

Download and unpack the sbml2octave-1.0.tar.gz file, move to the folder that have been created and run:

./sbml2octave.sh [file.xml | folder]

Will try to transform SBML (any *.xml files if you put a folder) into Octave
The output file(s) will be in the same folder as the SBML file(s) with an extension .m

Prerequisite

• java 1.5 or higher. You can find it here

• Apache Ant 1.6.5 or higher (only needed to build from source). You can find it here

Build

If you want to modify the sources and build the jar file
just type on the sbml2octave folder:

ant jar
to generate the jar file

ant javadoc
to generate the java documentation

Download

• sbml2octave-1.0.tar.gz

Getting Help and Support

Please send any help requests or bug reports to :