SBML2SBGNML

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Conversion from SBML to SBGN ML

Introduction

About SBML
SBML is a machine-readable format for representing models. It is oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML framework is suitable for representing models commonly found in research on a number of topics, including cell signalling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML.
About SBGN ML
SBGN ML offers a standard graphical language for representing biological processes and interactions. To know more, you can read the SBGN-About page.


Documentation

The converter is based on JSBML, so support all the levels and versions of SBML until SBML level 3 version 1 core.

Most of the mathematical parts of the SBML model are ignored, only the reaction network is exported.

When present the RDF annotations or the SBO terms are used to determine which SBGN glyph to use in the graph. At the moment, no layout is applied to the graph so you would need to use a third party software to generate the layout..

Download

You can download SBML2SBGNML by downloading sbfc-1.3.7.zip on sourceforge.

End users

To run SBML2SBGNML you need java 1.6 or higher.

After unpacking the zipped file, move to the folder that have been created and run:

    # Convert SBML (any *.xml files if you put a folder) to SBGN-ML
    # The output file(s) will be in the same folder as the SBML file(s) with an extension .xml
    ./sbml2sbgnml.sh [file.xml | folder]

Developers

To compile SBML2SBGNML from source, you also need Apache Ant 1.6.5 or higher.

After editing the source code you can build the jar file by just typing in the SBML2SBGNML folder:

    # Generate the jar file
    ant jar

    # Generate the java documentation
    ant javadoc

Getting Help and Support

In case you discover a bug within SBFC or request new features, please let us know. There are two dedicated trackers:

For general discussions about SBFC, please use the forum:

sbfc-forum [at] googlegroups.com.

If you need further support or you wish to develop new modules in SBFC you can contact the team using the following e-mail address:

sbfc-devel [at] googlegroups.com.