http://cytoscapeweb.cytoscape.org/

Cytoscape Web

Gary Bader http://www.baderlab.orgJuly 10 2010 – ISMB, BOSC

An interactive, customizable web-based network browser

http://cytoscapeweb.cytoscape.org

http://cytoscapeweb.cytoscape.org/

Cytoscape Web

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• Web-based component

• Interactive

• Pared down version of Cytoscape

– http://www.cytoscape.org

• Reusable

• Customizable

• Open source (LGPL)

http://cytoscapeweb.cytoscape.org/ 3

http://cytoscapeweb.cytoscape.org/

• Most of the visual styles of Cytoscape

• Visual mappings (VizMapper)

• Node/edge attributes

• SIF and XGMML file support

• Automatic layout

Cytoscape Concepts

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http://cytoscapeweb.cytoscape.org/

Web Component

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Network View(Flash/ActionScript)

API(JavaScript)

Client-side only. No server-side technology required

http://cytoscapeweb.cytoscape.org/

Customization

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JavaScript only!

http://cytoscapeweb.cytoscape.org/

• Select nodes and edges

• Drag nodes

• Pan the network

• Zoom

• Customization using JS can add more features (e.g. double-click node to highlight neighbors)

Interactivity

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http://cytoscapeweb.cytoscape.org/

• Export image:

– PDF, PNG

• Import/Export data:

– GraphML, XGMML, SIF

• Add and remove nodes and edges

• Filter nodes and edges

Other Features

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http://cytoscapeweb.cytoscape.org/

• Depends on:

– Number of elements and attributes

– Layout (force-directed is the slowest)

– Visual Styles and visual mappings

– End user configuration (e.g. browser, machine, OS, Flash version)

– Website implementation

• Better with small to medium sized networks

• Usually sluggish over 2000 elements (e.g. 800 nodes + 1200 edges)

Performance

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http://cytoscapeweb.cytoscape.org/

Time to load and render a network with 2400 elements

Performance

Tested on an Apple laptop computer with 2 GHz dual core CPU and 4 GB RAM

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http://cytoscapeweb.cytoscape.org/

Some Clients

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http://cytoscapeweb.cytoscape.org/

http://www.genemania.org

http://cytoscapeweb.cytoscape.org/

http://wodaklab.org/iRefWeb/

http://cytoscapeweb.cytoscape.org/

http://www.pathguide.org

http://cytoscapeweb.cytoscape.org/

• Download

– Distribution

– Source code (SVN)

• Tutorials

• Demos

• API documentation

• Discussion group

How to Start

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cytoscapeweb-discuss @googlegroups.com

http://cytoscapeweb.cytoscape.org/ 16

http://cytoscapeweb.cytoscape.org/

Acknowledgements

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Cytoscape Consortium

Funding

Lead developers: Christian Tannus Lopes, Max Franz

www.GeneMANIA.orgQuaid Morris, Rashad Badrawi, Ovi Comes, Sylva Donaldson, Farzana Kazi, Jason Montojo, Harold Rodriguez, Khalid Zuberi