bader bosc2010 cytoweb
TRANSCRIPT
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