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『繋がり』を見る: Cytoscapeと周辺ツールを使ったグラフデータ可視化入門

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第10回 データマイニング+WEB 勉強会@東京 ( #TokyoWebmining 10th)-1st Week-広告ネットワーク・グラフ解析・並列機械学習 祭り- でのTwitter ID c_z による発表資料

Publié dans : Technologie
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『繋がり』を見る: Cytoscapeと周辺ツールを使ったグラフデータ可視化入門

  1. 1. CYTOSCAPE TOKYO WEB MINING #10 Keiichiro OnoUniversity of California, San Diego Dept. of Medicine
  2. 2. Keiichiro Ono (Twitter ID: c_z) Cytoscape Core Developer
  3. 3. ••• http://nrnb.org/
  4. 4. BioGRID Human Interactome Visualization Cytoscape
  5. 5. ••• Cytoscape•
  6. 6. • ‣ ‣•
  7. 7. 10K+ NODES• 500k Nodes • • ••••• Facebook Visualization
  8. 8. Network generated by igraphs Watts-Strogatz small-world model (50k nodes / 250k edges) visualized by Cytoscape
  9. 9. 1K 10K NODES 2k nodes network generated by BA model•• • •
  10. 10. Twitter Visualization Example
  11. 11. ~1K NODES•• •• • •
  12. 12. •• • •
  13. 13. • Graphviz -• pajek - Windows• Gephi - OpenGL• Cytoscape -
  14. 14. CYTOSCAPE•• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003 Nov; 13(11):2498-504
  15. 15. WEB Protovis JavaScript InfoVis Toolkit• • JavaScr ipt • We b
  16. 16. CYTOSCAPE WEB
  17. 17. <?xml version="1.0" encoding="UTF-8"?><graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"><!-- Created by igraph --> <key id="degree" for="node" attr.name="degree" attr.type="double"/> <key id="betweenness" for="node" attr.name="betweenness" attr.type="double"/> <graph id="G" edgedefault="directed"> <node id="n0"> <data key="degree">79</data> <data key="betweenness">0</data> </node> <node id="n1"> <data key="degree">9</data> <data key="betweenness">167</data> </node> <node id="n2"> <data key="degree">18</data> <data key="betweenness">75</data> </node> <node id="n3"> <data key="degree">8</data> <data key="betweenness">12</data> </node> <node id="n4"> <data key="degree">26</data> <data key="betweenness">210</data> </node> <node id="n5"> <data key="degree">29</data> <data key="betweenness">320</data> </node>
  18. 18. • -•••
  19. 19. • ••
  20. 20. ••• API• • “Protein A interacts with protein B.” • A B
  21. 21. • -• • • - • ←
  22. 22. • • • GML • • dot (graphviz) • GraphML • • XGMML • • Edge List (
  23. 23. CYTOSCAPE• LGPL• (GML, XGMML, GraphML, Excel, CSV )•• • •
  24. 24. IGRAPH•• (shortest path, minimum spanning tree, etc)•R
  25. 25. • • Cytoscape - • igraph -R• -
  26. 26. DEMO
  27. 27. • igraph•• •• • • Cytoscape
  28. 28. • • • • • •••
  29. 29. Sample image created by Processing Visualizer + CytoscapeMISSING LINK
  30. 30. •••• ‣ ‣
  31. 31. • •• ~60 + •
  32. 32. • Data Miner • • (Neo4j )•
  33. 33. http://www.cytoscape.org/
  34. 34. http://www.cytoscape.org/ Thank You!

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