MDL2SBML

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Conversion from MDL to SBML

Introduction

About MDL
MDL (Model Description Language) is a language for modelling large multi-scale models for the program MCell. MCell (Monte Carlo cell) is a program that uses spatially realistic 3-D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells—cellular microphysiology.
About SBML
SBML (Systems Biology Markup Language) is a machine-readable format for representing models. It's 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's framework is suitable for representing models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML


Documentation

This converter was written by David Tolnay and aims to translate an MDL model into SBML using libsbml-5.8.0 using the spatial package included with this version of libsbml. Due to changes to the spatial package specifications, we cannot guarantee that this works for the latter versions. MCell runs simulations that are specified in model description language (MDL) format. These files typically have the extension .mdl, but are not required to. A MDL file is a text file with commands separated by whitespace. The nature and type of whitespace (space, tab, newline) is unimportant to MCell3. You are thus free to use white space to clarify the contents of the MDL file. For more information about MDL, please visit this page.


Download

You can download MDL2SBML and its jar dependencies here.

You will need as well the core sbfc: sbfc-1.3.7.zip

End users

These converters require java 1.6 or higher. To run this converter, you have to copy all the jar files from the folder:

https://sourceforge.net/p/sbfc/code/HEAD/tree/converters/mdl2sbml/lib/

to the folder SBFC_core/lib.

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

    # Print the list of available converters. MDL2SBML should be printed.
    ./sbfConverterList.sh
    # Print the list of available models. MDLModel and LibSBMLModel should be printed.
    ./sbfModelList.sh

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

    # Convert a model from MDL to SBML
    ./sbfConverter.sh MDLModel MDL2SBML [file.mdl | folder]

Developers

To compile MDL2SBML 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 mdl2sbml 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.