Cytoscape

FluxViz - Cytoscape Plug-In for the flux distributions in networks. Platforms: Windows, Mac, Linux

3DScape is designed as an accessible and handy 3D visualization plugin for Cytoscape. 3DScape is an Open Source Java application. The extra dimension in 3DScape offers more flexibility for hierarchical or layered representation in Cytoscape. Because its visualization and layout functions are... Platforms: Windows

CytoSEED was built as a Cytoscape plugin that can help you view, manipulate and analyze metabolic models created using the Model SEED. The CytoSEED plugin was designed in order to enable users of the Model SEED to create informative visualizations of the reaction networks generated for their... Platforms: Windows, Windows Vista, 7

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues. Platforms: Mac

CySBGN adds support to Cytoscape to import, visualize and analyse System Biology Graphical Notation (SBGN) maps. Platforms: Windows, Mac, Linux

This is currently in *alpha* development. You'll need one of these metabolism reaction files as input to the program: * Red Blood Cell * Peroxisome * Red Blood cell with vmax data * Perox test (Internal Only) CHECK THAT THE BUILD NUMBER (top right corner) IS 0.8.16 I have created a Mac... Platforms: Mac

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues. Platforms: *nix

Homepage: www.cellnopt.org Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge... Platforms: Windows, Mac, Linux

The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations. Platforms: Windows, Mac

GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms and pathways to describe a particular set of input identifiers. This tool calculates over-representation statistics similiar to the program MAPPFinder and subsequently produces... Platforms: Mac