cy3sbml: SBML for Cytoscape 3
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README.md

cy3sbml logo cy3sbml - SBML for Cytoscape 3

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cy3sbml is a Cytoscape 3 app for the Systems Biology Markup Language SBML.
Our mission is the visualization of SBML information within the network context. Our vision is a visualization tool for computational models and simulations which seamlessly integrates with computational modeling frameworks and workflows.

App store: http://apps.cytoscape.org/apps/cy3sbml
Latest release: https://github.com/matthiaskoenig/cy3sbml/releases/latest
Support & Forum: https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
Bug Tracker: https://github.com/matthiaskoenig/cy3sbml/issues

Features

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.

  • Java based SBML parser for Cytoscape based on JSBML
  • access to models and annotations via BioModels, MIRIAM, and Ontology Lookup Service
  • supports all versions of SBML
  • SBML validation (SBML warnings and errors accessible)
  • Network graph based on the species/reaction model
  • Graph of SBML objects (Kinetics, FunctionDefinitions, Parameters, ...)
  • Support of qual, comp and fbc extensions
  • Provides access to RDF based annotation information within the network context (and non-RDF annotations)
  • Tested with all models from sbml-test-suite (3.2.0), Biomodels (release 30) and BiGG models (v1.3)

For Cytoscape 2 use cy2sbml with documentation available from http://matthiaskoenig.github.io/cy2sbml/

Screenshots

cy3sbml screenshot

License

Citation

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

Funding

Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and Virtual Liver Network (VLN, grant number 0315756), and by the National Resource for Network Biology NRNB within the NRNB Academy Summer Session 2015.

Installation

Install

cy3sbml is available via the Cytoscape App Store.

  • install the latest version of Cytoscape (>=3.5.1)

  • In Cytoscape open Apps → App Manager → Install Apps and search for cy3sbml.

  • Select cy3sbml and click install.

After installation cy3sbml is listed in the Currently Installed apps tab.

Alternatively the latests release jars are available from https://github.com/matthiaskoenig/cy3sbml/releases/latest to install manually.

Uninstall

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 instructions

The develop release contains all features implemented since the latest release. To work with the latest develop release clone the repository and build with maven

git clone https://github.com/matthiaskoenig/cy3sbml.git cy3sbml
cd cy3sbml
mvn install -DskipTests

The test suite takes some minutes to finish. If you want to build with tests use

mvn install

The cy3sbml-vx.x.x.jar if available in the target folder.

More detailed build instructions are available from https://goo.gl/4xMgff.

Changelog

v0.2.8 [?]

v0.2.7 [2017/11/12]

Bugfix and dependency release

  • bugfixes
  • updated dependencies

v0.2.6 [2017/10/03]

Major bugfix release to handle EBI https and Uniprot https.

  • bugfixes
  • updated dependencies
  • cleanup of unused functionality and dependencies

v0.2.5 [2017/06/19]

  • Bug fixes
  • Updated UniProt Information
  • Updated HTML display
  • Updated VisualStyles
  • Tested with latest bigg models (v1.3)

v0.2.2 [2016/08/10]

  • Complete redesign of information pane (JavaFx instead of Swing with CSS, JS and HTML)
  • HTML export of information
  • Ontology information retrieved via Ontology Lookup Service
  • Proper formating and display of raw xml in annotations
  • Support of KineticLaws
  • Offline MIRIAM with latest MIRIAM registry (faster access & reduced webservice calls)
  • Improved visual styles (distinguish reversible & irreversible reactions)
  • Fixed name attributes
  • Improved compatibility to SBMLCore reader (identical attributes)
  • Updated icons
  • UniProt secondary information for RDF
  • Caching of webservice information from OLS and UniProt
  • Support of *.sbml files
  • Multitude of bug fixes
  • Improved session saving & loading (now with layout information)
  • Unittest coverage increased to 37%
  • Simplified maven dependencies
  • Testing of serialization & deserialization
  • Updated and tested sbml-test-suite 3.2.0
  • Licence update to LGPL v3.0
  • Dependencies updated
  • Improved logging

v0.2.1 [2016/07/11]

  • bug fixes (autofocus)

v0.2.0 [2016/07/01]

  • bug fixes

v0.1.9 [2016/06/28]

  • updated test models to BiGG v1.2
  • updated test BioModels to release 30
  • improved unit tests against test models
  • bug fixes related to new test models, SBOTerms, LocalParameters & annotations
  • additional support for cy3sabiork
  • updated JSBML dependencies and pom files

v0.1.8 [2016/06/07]

  • visualStyles for new and reopened sessions
  • display of RDF & non-RDF annotation information
  • kineticLaws as first class objects (with annotation display)
  • FunctionDefinitions are now parsed correctly
  • refactoring of CyNode to SBase mapping (performance increase)
  • multitude of smaller bugfixes

v0.1.7 [2016/03/24]

  • position saving and restoring ported from cy2sbml (saving & restoring layouts)
  • dark VisualStyle implemented (cy3sbml-dark)
  • improved visual styles & dynamic compartment colors
  • saving and restoring of full session with SBML files
  • COBRA information parsed into attributes
  • multiple bugfixes
  • first version of cofactor nodes
  • tested with Cy3.3 and Cy3.4-milestone-2

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)

Third-party software

cy3sbml uses the following third-party software libraries; these are distributed along with the bundled cy3sbml app. The license statements for these third-party software libraries can be found at the web addresses noted below.

JSBML License (LGPL 2.1) [checked 2016-08-03]

Cytoscape License (LGPL 2.1) [checked 2016-08-03]

org.osgi.core License (Apache 2) [checked 2016-08-03]

Ehcache License (Apache 2) [checked 2016-08-03]

Apache Commons Lang License (Apache 2) [checked 2016-08-03]

Apache Commons IO License (Apache 2) [checked 2016-08-03]

Apache Velocity License (Apache 2) [checked 2016-08-03]

Unirest Java License (MIT) [checked 2016-08-03]

Apache HttpClient License (Apache 2) [checked 2016-08-03]

Apache HttpAsyncClient License (Apache 2.0) [checked 2016-08-03]

Apache HttpClient Mime License (Apache 2) [checked 2016-08-03]

JSON in Java License (JSON) [checked 2016-08-03]

LibFX License (LGPL 3.0) [checked 2016-08-03]

uk.ac.ebi.miriam.registry-lib License (LGPL 2.1) [checked 2016-08-03]

uk.ac.ebi.miriam.mirian-lib License (LGPL 2.1) [checked 2016-08-03]

OLS client License (Apache 2.0) [checked 2016-08-03]

Jackson Databind License (Apache 2.0) [checked 2016-08-03]

Uniprot Japi License (Apache 2.0) [checked 2016-08-03]

chebiWS-client License (Apache 2.0) [checked 2016-08-03]

SLF4J API Module License (MIT) [checked 2016-08-03]

SLF4J LOG4J 12 Binding License (MIT) [checked 2016-08-03]

Junit License (EPL-1.0) [checked 2016-08-03]

Mockito License (MIT) [checked 2016-08-03]

Apache Taverna Language License (Apache 2.0) [checked 2016-08-16]


© 2017 Matthias König. Developed and maintained by Matthias König, Andreas Dräger and Nicolas Rodriguez.