Bader bosc2010 cytoweb

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  • Created as a result of the need for a visualization interface for the GeneMANIA project at the University of Toronto. The idea was to create a simple version of Cytoscape for the Web, not as a complete user application, but as an independent component that could be reused by other developers.
  • Despite using different technologies, Cytoscape Web follows most of the Cytoscape concepts.
  • Client-side only! No server-side technology required or enforced.
  • 800 nodes and 1600 edges
  • GeneMANIA
  • iRefWeb
  • Pathguide

Transcript

  • 1. Cytoscape Web Gary Bader http://www.baderlab.org July 10 2010 – ISMB, BOSC An interactive, customizable web-based network browser http://cytoscapeweb.cytoscape.org
  • 2. Cytoscape Web
    • Web-based component
    • Interactive
    • Pared down version of Cytoscape
      • http://www.cytoscape.org
    • Reusable
    • Customizable
    • Open source (LGPL)
  • 3.
  • 4.
    • Most of the visual styles of Cytoscape
    • Visual mappings ( VizMapper )
    • Node/edge attributes
    • SIF and XGMML file support
    • Automatic layout
    Cytoscape Concepts
  • 5. Web Component Network View (Flash/ActionScript) API (JavaScript) Client-side only. No server-side technology required
  • 6. Customization JavaScript only!
  • 7.
    • 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
  • 8.
    • Export image:
      • PDF, PNG
    • Import/Export data:
      • GraphML, XGMML, SIF
    • Add and remove nodes and edges
    • Filter nodes and edges
    Other Features
  • 9.
    • 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
  • 10.
    • 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
  • 11. Some Clients
  • 12. http://www.genemania.org
  • 13. http://wodaklab.org/iRefWeb/
  • 14. http://www.pathguide.org
  • 15.
    • Download
      • Distribution
      • Source code (SVN)
    • Tutorials
    • Demos
    • API documentation
    • Discussion group
    How to Start cytoscapeweb-discuss @googlegroups.com
  • 16.
  • 17. Acknowledgements Cytoscape Consortium Funding Lead developers: Christian Tannus Lopes, Max Franz www.GeneMANIA.org Quaid Morris, Rashad Badrawi, Ovi Comes, Sylva Donaldson, Farzana Kazi, Jason Montojo, Harold Rodriguez, Khalid Zuberi