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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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『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

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

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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 Ono University 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 igraph's 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 + Cytoscape MISSING 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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