Portal:Cytoscape

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Welcome to Cytoscape 2.x at Open Tutorials

The purpose of this portal is to distribute tutorial materials for Cytoscape 2.x and Cytoscape 2.x plugins.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.

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Available Tutorials

Basic

Image:bullet.png Introduction to Cytoscape, part 1

Image:bullet.png Introduction to Cytoscape, part 2

Image:bullet.png Filtering and Editing

Image:bullet.png Basic Expression Analysis - Yeast

Image:bullet.png Basic Expression Analysis - Human

Image:bullet.png Network Loading and ID Mapping

Advanced

Image:bullet.png Cytoscape Developers Tutorial

Plugins

Image:bullet.png Assorted Cytoscape Plugins

Image:bullet.png Agilent Literature Search

Image:bullet.png MiMiPpi Discovery

Image:bullet.png Structure Visualization and Structure Function Linkage Database

Image:bullet.png Google Charts Plugin - Creating Pie Charts on Nodes

Analysis plugins

Image:bullet.png Cluster Maker

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 1

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 2

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 3

Image:bullet.png DomainGraph

Image:bullet.png MCODE Plugin Demo

Image:bullet.png Network Analyzer

Layout plugins

Image:bullet.png Community Structure Layout

Image:bullet.png Cytoscape Cerebral Plugin

Image:bullet.png Power Graph Analysis with CyOog


3.0 tutorials

Image:bullet.png Cytoscape 3.0 Tutorials

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Other Resources

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Latest News

Cytoscape programming job opening at UCSD
Hi, all -

At the end of June, Peng will be leaving us. We're looking for someone new to fill his shoes.

Here's the job posting . please consider it yourself of consider passing it on to some excellent programmer looking for great work:

[link] [?]

Cytoscape.js 2.0.0 release
*

Cytoscape.js 2.0.0 <[link]> is now available. It has improved performance over Cytoscape Web, built-in support for touch devices, gesture support, core extensions, UI plugins, and an intuitive API modelled after jQuery.

We will continue to support Cytoscape Web for now, but we advise users that [?]

Release of two GPU-accelerated plugins: AllegroMCODE v2.0 & AllegroLayout v1.0
We are pleased to announce the release of two GPU-accelerated plugins for Cytoscape 2.6.x, 2.7.x, 2.8.x. They are available now through the Cytoscape plugin manager and in Cytoscape App Store<[link]> .

Their GPU algorithms can exploits massively parallel GPU computing [?]

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