Introduction

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

SBMLReader2 is an open source Cytoscape Plugin which enables the import of networks in SBML format. The importer is backward compatibel to the SBMLReader of the Cytoscape core plugins and supports all level and versions of SBML.

SBMLReader2 is based on the libSBML library.

Features SBMLReader2 v0.1

SBMLReader2 is developed and maintained by Matthias Koenig at the Computational Systems Biochemistry group of the Charite Berlin.

Project homepage:
http://www.charite.de/sysbio/people/koenig/software/sbmlreader2/help/.
Project hosted at:
http://sourceforge.net/projects/sbmlreader2/.

Installation

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Cytoscape has to be installed prior to the plugin installation. The plugin works with the current Cytoscape 2.6 version.

A working libSBML installation with java bindings is necessary. The CLASSPATH to the libSBML library and the LD_LIBRARY_PATH have to be set.
libSBML installation
http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-installation.html
Setting the pathes:
http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-accessing.html
Without working libSBML installation only the classic SBMLReader functionality is available.

The path to the libsbmlj.jar has to be specified as startup option for Cytoscape in the following manner:
-P libSBMLPath=/usr/local/lib/libsbml.jar

The simplest way to set the pathes in the cytoscape.sh or cytoscape.bat respectively:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
java -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar cytoscape.CyMain -p plugins "$@" -P libSBMLPath=/usr/local/lib/libsbmlj.jar

Manual Installation

SBMLReader2 is avaiblable for download at http://sourceforge.net/projects/sbmlreader2/.

[1] Download the latest version and move sbmlreader2-vx.x.jar and SBML2.jar into the Cytoscape plugin directory, which is located in the Cytoscape installation directory under plugins
$CYTO_INSTALL/plugins/.

[2] Remove the core SBMLReader SBMLReader.jar from the plugin directory.

The plugin is loaded automatically during the next start of Cytoscape.

Manual Uninstall

[1] Remove sbmlreader2-vx.x.jar and SBML2.jar from the Cytoscape plugin directory $CYTO_INSTALL/plugins/.

[2] Move the core SBMLReader SBMLReader.jar back in the plugin directory.

Test Installation

The successful installation of SBMLReader2 and libSBML can be tested in the Cytoscape plugin menu (Plugins -> Test SBMLReader2).

Usage guide

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After installation the SBMLReader2 plugin is integrated into Cytoscape at startup. SBML networks can be loaded via
File -> Import -> Network (multiple file types).

Additional Resources

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Links

SBMLReader2
http://www.charite.de/sysbio/people/koenig/software/sbmlreader2/help/index.html
http://sourceforge.net/projects/sbmlreader2/
http://www.charite.de/sysbio/people/koenig/

Cytoscape
http://www.cytoscape.org/

Cytoscape plugins
http://chianti.ucsd.edu/cyto_web/plugins/index.php

SBML.org
http://sbml.org/

libSBML
http://sbml.org/Software/libSBML
http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-installation.html

Development

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Subversion Access

The project is open source. Everybody can participate.

This project's SourceForge.net Subversion repository can be checked out through SVN with the following instruction set:
svn co https://sbmlreader2.svn.sourceforge.net/svnroot/sbmlreader2 sbmlreader2

Bugs in SBMLReader-v0.1

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Comming Features in SBMLReader2

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