CellML2SBML and SBML2CellML

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Conversion between CellML and SBML

Introduction

About CellML
The purpose of CellML is to store and exchange computer-based mathematical models. For more information, please visit the http://antimony.sourceforge.net/ website. For more information, please visit the Antimony and CellML website.


Download

You can download the converters CellML2SBML and SBML2CellML and their jar dependencies here.


End users

These converters require java 1.6+. To run these converters, you have to copy all the jar files from the folder:

https://sourceforge.net/p/sbfc/code/HEAD/tree/converters/sbfc-antimony/lib/

to the folder SBFC_core/lib.

These converters are based on the external program sbtranslate provided in the Antimony website. In order to use the program sbtranslate to convert between CellML and SBML, the option WITH_CELLML must be turned on (see antimony-installation). This may involve the additional installation of CellML API and re-compilation of the source code. Once sbtranslate is ready for supporting the conversion between CellML and SBML, the user must configure the path to the sbtranslate command in the sbfc script sbfConverter.sh located in the folder SBFC_core. This can be done in two ways:

    # FILE: sbfConverter.sh
    # Add the path to the program sbtranslate 
    # by configuring the Java system property SBTRANSLATE_PATH:
    #PROPERTIES="$PROPERTIES -DSBTRANSLATE_PATH=/path/to/sbtranslate"
    # Configure the environment variable SBTRANSLATE_PATH
    #export SBTRANSLATE_PATH=/path/to/sbtranslate

To test the correct installation, you can type the scripts:

    # Print the list of available converters. CellML2SBML and SBML2CellML should be printed.
    ./sbfConverterList.sh
    # Print the list of available models. CellMLModel and SBMLModel should be printed.
    ./sbfModelList.sh

To run the converter, you can use the script sbfConverter.sh with the usual syntax:

    # Convert a model from CellML to SBML
    ./sbfConverter.sh CellMLModel CellML2SBML [file.cellml | folder]
    # Convert a model from SBML to CellML
    ./sbfConverter.sh SBMLModel SBML2CellML [file.xml | folder]

To compile the package sbfc-antimony 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 sbfc-antimony folder:

    # Generate the jar file
    ant jar
    # Generate the java documentation
    ant javadoc