cy3sbml - SBML for Cytoscape

Overview

[^] 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

Documentation

Build instructions

License

Source Code: LGPLv3.0
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

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

[^] The following gives an overview how to install, uninstall and build cy3sbml

Install

cy3sbml is available from the Cytoscape App Store.

install Java 11
install the latest version of Cytoscape (>=3.8.0) or
open Cytoscape, open http://apps.cytoscape.org/apps/cy3sbml in a browser, click install

Alternatively one can install via the App Manager

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.

The latest release jars are available from https://github.com/matthiaskoenig/cy3sbml/releases/latest and can also be copied manually in the Cytoscape directory.

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 here.

Changelog

[^]

v0.3.0 [2019-09-19]

major bugfix release
updated dependencies

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 [checked 2016-08-03]