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Bader bosc2010 cytoweb

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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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