Portal:Cytoscape3

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Welcome to Cytoscape 3 at Open Tutorials

The purpose of this portal is to distribute tutorial materials for Cytoscape 3 and Cytoscape Apps.

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. Many apps 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

Cytoscape 3 User Tutorials

These tutorials are for users getting started with Cytoscape.

Image:bullet.png Introduction to Cytoscape 3: Welcome Screen
Image:bullet.png Introduction to Cytoscape 3: User Interface
Image:bullet.png Introduction to Cytoscape 3: Networks, Data, Styles, Layouts and App Manager
Image:bullet.png Filtering and Editing in Cytoscape 3

Cytoscape 3 App Tutorials

These tutorials show how to use popular Cytoscape apps to analyze and visualize data.

Image:bullet.png WikiPathways App
Image:bullet.png Extend Biological Process with regulatory interactions

Cytoscape 3 App Developer Tutorials

These tutorials are for developers either a) porting 2.x plugins to 3.x apps, or b) writing a new 3.x app from scratch. We hope they give developers an easy way to get started, with information up to date and all in one place. We assume that app developers have a working knowledge of Java programming, ant, Maven, Git, and optionally Eclipse.

Image:bullet.png Setup App Development Environment
Image:bullet.png Two types of App -- Simple App and Bundle App
Image:bullet.png Debug: Work with OSGi Console
Image:bullet.png Debug: Remote Execution for Debugging

External Links

Image:bullet.png Cytoscape Plugin Porting Guide (for porting 2.x plugins to 3.x apps)
Image:bullet.png Cytoscape 3 App Cookbook
Image:bullet.png Cytoscape App Store

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Other Resources

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