cy3sbml

cy3sbml visualizes SBML models (Systems Biology Markup Language)
# cy3sbml - SBML for Cytoscape ![alt tag](https://github.com/matthiaskoenig/cy3sbml/raw/master/docs/images/logo100.png) **cy3sbml** is a [Cytoscape](http://www.cytoscape.org) app for the Systems Biology Markup Language [SBML](http://www.sbml.org). **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](http://www.biomodels.org) and one-click access to annotation resources and SBML model information. SBML validation information about the imported files is available. **App store** : http://apps.cytoscape.org/apps/cy3sbml **Support & Forum** : https://groups.google.com/forum/#!forum/cysbml-cyfluxviz **Bug Tracker** : https://github.com/matthiaskoenig/cy3sbml/issues ## Features * Java based SBML parser for Cytoscape based on [JSBML](https://github.com/sbmlteam/jsbml) * access to models and annotations via [BioModel](http://www.biomodels.org/), [MIRIAM](http://www.ebi.ac.uk/miriam/main/), and [Ontology Lookup Service](http://www.ebi.ac.uk/ols/index) * 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 (v1.2) ## License * Source Code: [LGPLv3.0](http://opensource.org/licenses/LGPL-3.0) * Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/) ## Installation cy3sbml is available via the [Cytoscape App Store](http://apps.cytoscape.org/apps/cy3sbml). * install the latest version of [Cytoscape](http://www.cytoscape.org/) (>=3.4) * 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. ## Funding * [NRNB](http://nrnb.org) (National Resource for Network Biology) within the [NRNB Academy Summer Session 2015](http://nrnb.org/gsoc.html) * Virtual Liver Network (VLN) * Systems Medicine of the Liver (LiSyM) ## Citation Matthias König, Andreas Dräger and Hermann-Georg Holzhütter *CySBML: a Cytoscape plugin for SBML* Bioinformatics. 2012 Jul 5. [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/22772946) ## Changelog **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) ---- © 2016 Matthias König. Developed and maintained by Matthias König, Andreas Dräger and Nicolas Rodriguez.

0.2.2

Works with Cytoscape 3.4

Release Notes

**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

0.2.1

Works with Cytoscape 3.4

Apps that depend on this release


0.2.0

Works with Cytoscape 3.4

Apps that depend on this release


0.1.9

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* 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

0.1.8

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* 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

0.1.7

Works with Cytoscape 3.2

Release Notes

* 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

0.1.6

Works with Cytoscape 3.2

Release Notes

* 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

0.1.5

Works with Cytoscape 3.2

Release Notes

* 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

0.1.4

Works with Cytoscape 3.2

Release Notes

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

0.1.3

Works with Cytoscape 3.2

Release Notes

* 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

CYTOSCAPE 3

Version 0.2.2

License Click here

Released 10 Aug 2016

Works with Cytoscape 3.4

Download Stats Click here