cy2sbml: SBML for Cytoscape 2

cy2sbml is a Cytoscape 2 plugin for the Systems Biology Markup Language SBML.
For Cytoscape 3 use cy3sbml.

Download
Documentation : http://matthiaskoenig.github.io/cy2sbml/
Support & Forum : https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
Bug Tracker : https://github.com/matthiaskoenig/cy2sbml/issues

Features

cy2sbml provides advanced functionality for the import and work with models encoded in SBML, amongst others the visualization of SBML network annotations within the network context, direct import of models from repositories like biomodels and one-click access to annotation resources and SBML model information and SBML validation.

• Java based SBML parser for Cytoscape based on JSBML
• access to models and annotations via BioModel and MIRIAM WebServices
• supports all versions of SBML
• support of SBML Layout Package
• support of SBML Qualitative Models Package
• SBML validation (SBML warnings and errors accessible)
• Standard network layout based on the species/reaction model
• Provides access to RDF based annotation information within the network context
• Navigation menu based on the SBML structure linked to layout and annotation information
• succesfully tested with all SBML.org and Biomodels.org testcases (sbml-test-cases-2.0.2, BioModels_Database-r21-sbml_files)

The cy2sbml tutorial covers the following topics

• Installation
• CySBML interface
• Import of SBML models
• Access to annotation information
• SBML validation in CySBML
• Programmatic Interaction with CySBML

License

• Source Code: GPLv3
• Documentation: CC BY-SA 4.0

Citation

Matthias König, Andreas Dräger and Hermann-Georg Holzhütter
CySBML: a Cytoscape plugin for SBML
Bioinformatics. 2012 Jul 5. PubMed

Installation

Install

• install Cytoscape v2.8.3
  http://www.cytoscape.org/download.html
  http://chianti.ucsd.edu/Cyto-2_8_3/
• download latest release jar
  https://github.com/matthiaskoenig/cy2sbml/releases
• move downloaded cy2sbml-vx.x.x.jar in the Cytoscape plugin folder under Cytoscape_v2.8.3/plugins/.
• remove sbml-reader-2.8.3-jar-with-dependencies.jar from the plugin folder.

cy2sbml is installed and available in the plugins menu after restarting Cytoscape.

Uninstall

Remove the cy2sbml-vx.x.x.jar from the plugin folder.

Build instructions

Clone the repository and build with ant

git clone https://github.com/matthiaskoenig/cy2sbml.git cy2sbml
cd cy2sbml
ant cy2sbml

Development is done in develop branch, documentation in gh-pages

git checkout -b develop --track origin/develop
git checkout -b gh-pages --track origin/gh-pages

Changelog

v1.4.2 [?]

v1.4.1 [2015-11-03]

• major bugfix release (AttributeBrowser)

v1.4.0 [2015-10-26]

• github migrate release

v1.30 [2014-01-24]

• java 1.6 compatibility (bug fix)

v1.29 [2013-11-05]

• Source code with ANT build files from sourceforge available
• Implemented: Gene Regulatory Network support (GRN2SBML with ExTILAR & NetGenerator)
• Speed Improvements: Caching of Miriram resource loading
• Speed Improvements: Deactivation of CySBML results in hybernating of all lookups
• Fixed: offline not starting problems -> offline mode implemented
• Fixed: working offline mode without Miriram connection
• Implemented: Improved display of loading networks with layout
• Fixed: bug with fast selection of nodes (wrong information was displayed, due to different Thread runtime
• Implemented: reading of model attributes in networkAttributes

v1.27 [2013-10-29]

• Update of libraries: biomodels-1.21; MiriamJavaLib-1.1.5; jsbml-1.0-a1; jsbml-layout-1.0-b1; jsbml-qual-2.1-b1.jar
• Fixed: direction of modifier-reaction edges & naming of the edge interaction (also in qual)
• Fixed: additional information from the SpeciesGlyphs & ReactionGlyphs is parsed in layout, namely SBOId, MetaId, Name
• Fixed: layout:role is now handled correctly to set edge interaction type for layout (multiple edges in layout with different layout:role correctly handled).

v1.25

• Layout bug fixes (width & height)
• Parsing of kinetic information to node attributes

v1.23

• full compatibility with CyFluxViz
• smaller bug fixes

v1.2

• Dialoques, Tutorial, Usage examples
• Reversibility Bug fixed

v1.1

• BioModel Search Interface renewed
• BioModel Search via arbitrary Text with IDs
• Compability with NetMatch, NetworkAnalyzer and FluxViz