code from NRNB Academy Summer Session 2015 by Matthias Koenig (Andreas Dräger)
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README.md

cy3sbml - SBML for Cytoscape

cy3sbml is a Cytoscape app for the Systems Biology Markup Language SBML.

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cy3sbml 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.

Status : beta
Support & Forum : https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
Bug Tracker : https://github.com/matthiaskoenig/cy3sbml/issues

Features (beta release)

  • Java based SBML parser for Cytoscape based on JSBML (http://sourceforge.net/projects/jsbml/)
  • access to models and annotations via BioModel (http://www.biomodels.org/) and MIRIAM WebServices (http://www.ebi.ac.uk/miriam/main/)
  • supports all versions of SBML
  • SBML validation (SBML warnings and errors accessible)
  • Network graph based on the species/reaction model
  • Network graph of full SBML information
  • Support of qual, comp and fbc extensions
  • Provides access to RDF based annotation information within the network context
  • Annotation information
  • succesfully tested against all SBML.org and Biomodels.org test cases (BioModels_Database-r29)

We are currently porting missing features from the Cytoscape 2 plugin to Cytoscape 3. Release information and changelogs are provided below.

License

Installation

  • cy3sbml is available via the Cytoscape App Store. Download and install the latest version of Cytoscape (>=3.2). Within Cytoscape open Apps → App Manager → Install Apps and search for cy3sbml. Select cy3sbml click install. After installation cy3sbml will be listed in the Currently Installed apps tab.
    To uninstall or disable cy3sbml, go to the menu bar and choose Apps → App Manager → Currently Installed. Select cy3sbml and click Uninstall or Disable.

Build from source

For working with the latest stable development release follow the [build instructions] (https://docs.google.com/document/d/1EILRjGBPi1dmVaI8xXNE7Uk9RY-nmlVB8mkMzsDqgVo/edit?usp=sharing). This includes recently developed features not yet released.

Funding

We are funded by the NRNB (National Resource for Network Biology) within the NRNB Academy Summer Session based on the following cy3sbml proposal.

Changelog

v0.1.6 [2015/08/27]

  • Testing, bug fixes and documentation
  • sbml-test-cases models successfully parsed
  • BIGG models successfully parsed
  • cobrapy test models parsed
  • full SBML FBC v2 support
  • basic SBML distrib support

v0.1.5 [2015/07/04]

  • SBO Name and definitions for information
  • Parsing of rateRules, InitialAssignments and kineticLaws
  • Display of NamedSBase attributes in information
  • Example loader (menu) & examples added
  • FBC support
  • NetworkReader tests (passed all BioModels r29 curated models)
  • master SBML graph (compartments, kinetics, parameters, ...)
  • File selection & multiple file import ported
  • SBML validator ported

v0.1.4 [2015/06/24]

  • support of multiple networks, views and subnetworks
  • qualitative model support
  • biomodel webservice search & retrieval
  • redesign & bug fixes

v0.1.3 [2015/06/14]

  • cy3sbml VisualStyles
  • Support of multiple networks and views (subnetworks)
  • Model information is now displayed
  • RDF annotations displayed (MIRIAM)
  • proxy support
  • first unit tests created and integrated with maven
  • logging with log4j and slf4j implemented (cy3sbml.log)
  • support of cy3sbml properties for general settings like preferred VisualStyle
  • node EventListener for updating annotation information
  • application of layout after generating views

v0.1.2 [2015/06/01]

  • documentation update (build instructions, installation instructions)

v0.1 [2015/05]

  • first app release (OSGI build with JSBML integration)

© 2015 Matthias König. Developed and maintained by Matthias König, Andreas Dräger and Nicolas Rodriguez.