cy2fluxviz for Cytoscape 2

cy2fluxviz is an open-source Cytoscape 2 plugin for the visualization of flux distributions in networks.

Download
Documentation : http://matthiaskoenig.github.io/cy2fluxviz/
Support & Forum : https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
Bug Tracker : https://github.com/matthiaskoenig/cy2fluxviz/issues

cy2fluxviz is currently ported to Cytoscape 3, with first versions available at cy3fluxviz.

Features

• import of networks (SBML, GML, XGMML, SIF, BioPAX, PSI-MI)
• import of flux distributions in a variety of formats
• subnetworks based on flux carrying reactions (flux subetwork) or arbitrary network attributes
• flexible mapping architecture for all visual attributes
• export of views in variety of formats (SVG, EPS, PDF, BMP, PNG)
• batch capabilities

License

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

Installation

Requirements

• Java 8
• Cytoscape v2.8.3
  http://www.cytoscape.org/download.html
  http://chianti.ucsd.edu/Cyto-2_8_3/
• cy2sbml

Install

• download latest release jars for cy2fluxviz and cy2sbml
  https://github.com/matthiaskoenig/cy2fluxviz/releases/latest
  https://github.com/matthiaskoenig/cy2sbml/releases/latest
• move cy2sbml-vx.x.x.jar and cy2fluxviz-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

cy2fluxviz and cy2sbml are installed and available in the plugins menu after restarting Cytoscape.

Start cy2fluxviz

The plugin is loaded and installed during the next Cytoscape startup. To start cyfluxviz click the cyfluxviz icon in the Cytoscape toolbar which will load the cyfluxviz panel.

Build instructions

Clone the repository and build with ant

git clone https://github.com/matthiaskoenig/cy2fluxviz.git cy2fluxviz
cd cy2fluxviz
ant cy2fluxviz

Changelog

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Changelog

v1.0.1 [?]

v1.0.0 [2015-11-03]

• fixes empty FluxDistribution bug after loading #1
• updated logging

v0.95 [2015-10-26]

• small bug fix release and rebuild with java 8
• sourceforge to github migration

v0.94 [2014-01-24]

• java 1.6 compatibility (bug fix)

v0.93 [2013-08-07] bugfix release

• attribute subnetwork functionality fixed
• updated CyFluxViz style (SBML localization & irreversibel reactions)

v0.92 [2013-08-01] mayor release

• implemented: changes due to Cytoscape from v2.8.1 -> v2.8.3
• implemented: sortable flux distribution table (id, name, network as keys)
• bug resolved: image export broken (now bitmap export settings are reused for multiple picture)
• implemented: new Mappings and VisualStyles implementation (remove of deprecated methods and adaption to v2.8.3 implementation)
• bug resolved: attribute selection bug (flux related attributes were not made visible)
• bug resolved: initial max-min mapping not properly applied
• implemented: support of multiple VisualStyles & C13 and kinetic style
• bug resolved: flux distribution table was editable with side effects
• bug resolved: selected nodes and edges were lost when FluxDistribution changed.
• bug resolved: global max setting for mapping was not applied properly
• implemented: support of child networks (create additional views for network)
• bug resolved: Network selection changed the focused windows
• implemented: focus CyFluxViz panel via icon click
• implemented: integration with CyFluxViz Toolbox for Matlab for visualization
• bug resolved: NullPointerExceptions during deleting of FluxDistributions
• implemented: importer & exporter rewritten

v0.91

• icon loader NullPointer Exception fixed

v0.88

• smaller bugfixes
• better file import

v0.86 (Mayor Release)

• full support & compatibility to CySBML
• XML import and export of Flux Distributions
• support of multiple networks and subnetworks
• complete redesign of architecture for speed improvement
• new example files (packed in Jar)