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SBML Support Tools

SBML Support Tools (Importer and Exporter). SBML tools can convert EML (E-Cell Model description language) and SBML(System Biology Modeling language) bi-directionally. SBML tools are the Importer and the Exporter. SBML Importer can convert a SBML file into an EML file. To the contrary, SBML Exporter can convet a EML file into SBML file.

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To use SBML tools, you must install the folloing library.

libsbml :
LIBSBML is a C application programming interface (API) library for reading, writing and manipulating the Systems Biology Markup Language (SBML). Currently, the library supports all of SBML Level 1 Version 1 and Version 2, and nearly all of SBML Level 2 Version 1. (The still-unimplemented parts of Level 2 are support for RDF and support for MathML's semantics, annotation and annotation-xml elements. These will be implemented in the near future.)
LIBSBML HP

libsbml-2.1.0-1.i386.rpm [ DOWNLOAD ]
libsbml-python-2.1.0-1.i386.rpm [ DOWNLOAD ]

xerces :
Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents.
APACHE XML Project

xerces-c-2.3.0-3.i386.rpm[ DOWNLOAD ]

Installation


To install the Xerces, you command as follows : 

    % rpm -ivh xerces-c-2.3.0-3.i386.rpm

To install the libsbml, you command as follows : 

    % rpm -ivh libsbml-2.1.0-1.i386.rpm
    % rpm -ivh libsbml-python-2.1.0-1.i386.rpm

If you get the following error: 

    Error: Failed dependencies:
    libsbml.so is needed by libsbml-python-2.1.0-1.i386.rpm

Please ignore these dependencies as follows: 

    % rpm -ivh --nodeps libsbml-python-2.1.0-1.i386.rpm

Usage (in environment that E-Cell3 is installed)

SBML Importer

To convert an SBML file into a EML file, you command as follows: 

    % ecell3-sbml2eml sample.xml

"sample.xml" is a SBML format file. After this command, "sample.eml" is generated in current directory.

SBML Exporter

To convert a EML file into an SBML file, you command as follows: 

    % ecell3-eml2sbml sample.eml

"sample.eml" is an EML format file. After this command, "sample.xml" is generated in current directory.

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