Antimony2SBML and SBML2Antimony

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Conversion between Antimony and SBML

Introduction

About Antimony
Antimony is a text-based model definition language originally based on Jarnac, and extended to be fully modular. Antimony models can be converted to and from SBML, flattening the modularity in the process. For more information, please visit the Antimony website.


Download

You can download the converters Antimony2SBML and SBML2Antimony 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. The user must install the package antimony and 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. Antimony2SBML and SBML2Antimony should be printed.
    ./sbfConverterList.sh
    # Print the list of available models. AntimonyModel 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 Antimony to SBML
    ./sbfConverter.sh AntimonyModel Antimony2SBML [file.txt | folder]
    # Convert a model from SBML to Antimony
    ./sbfConverter.sh SBMLModel SBML2Antimony [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