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
  • Bader bosc2010 cytoweb

    1. 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. 2. Cytoscape Web <ul><li>Web-based component </li></ul><ul><li>Interactive </li></ul><ul><li>Pared down version of Cytoscape </li></ul><ul><ul><li>http://www.cytoscape.org </li></ul></ul><ul><li>Reusable </li></ul><ul><li>Customizable </li></ul><ul><li>Open source (LGPL) </li></ul>
    3. 3.
    4. 4. <ul><li>Most of the visual styles of Cytoscape </li></ul><ul><li>Visual mappings ( VizMapper ) </li></ul><ul><li>Node/edge attributes </li></ul><ul><li>SIF and XGMML file support </li></ul><ul><li>Automatic layout </li></ul>Cytoscape Concepts
    5. 5. Web Component Network View (Flash/ActionScript) API (JavaScript) Client-side only. No server-side technology required
    6. 6. Customization JavaScript only!
    7. 7. <ul><li>Select nodes and edges </li></ul><ul><li>Drag nodes </li></ul><ul><li>Pan the network </li></ul><ul><li>Zoom </li></ul><ul><li>Customization using JS can add more features (e.g. double-click node to highlight neighbors) </li></ul>Interactivity
    8. 8. <ul><li>Export image: </li></ul><ul><ul><li>PDF, PNG </li></ul></ul><ul><li>Import/Export data: </li></ul><ul><ul><li>GraphML, XGMML, SIF </li></ul></ul><ul><li>Add and remove nodes and edges </li></ul><ul><li>Filter nodes and edges </li></ul>Other Features
    9. 9. <ul><li>Depends on: </li></ul><ul><ul><li>Number of elements and attributes </li></ul></ul><ul><ul><li>Layout (force-directed is the slowest) </li></ul></ul><ul><ul><li>Visual Styles and visual mappings </li></ul></ul><ul><ul><li>End user configuration (e.g. browser, machine, OS, Flash version) </li></ul></ul><ul><ul><li>Website implementation </li></ul></ul><ul><li>Better with small to medium sized networks </li></ul><ul><li>Usually sluggish over 2000 elements (e.g. 800 nodes + 1200 edges) </li></ul>Performance
    10. 10. <ul><li>Time to load and render a network with 2400 elements </li></ul>Performance Tested on an Apple laptop computer with 2 GHz dual core CPU and 4 GB RAM
    11. 11. Some Clients
    12. 12. http://www.genemania.org
    13. 13. http://wodaklab.org/iRefWeb/
    14. 14. http://www.pathguide.org
    15. 15. <ul><li>Download </li></ul><ul><ul><li>Distribution </li></ul></ul><ul><ul><li>Source code (SVN) </li></ul></ul><ul><li>Tutorials </li></ul><ul><li>Demos </li></ul><ul><li>API documentation </li></ul><ul><li>Discussion group </li></ul>How to Start cytoscapeweb-discuss @googlegroups.com
    16. 16.
    17. 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

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