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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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  • Transcript

    • 1. CYTOSCAPE TOKYO WEB MINING #10 Keiichiro OnoUniversity of California, San Diego Dept. of Medicine
    • 2. Keiichiro Ono (Twitter ID: c_z) Cytoscape Core Developer
    • 3. ••• http://nrnb.org/
    • 4. BioGRID Human Interactome Visualization Cytoscape
    • 5. ••• Cytoscape•
    • 6. • ‣ ‣•
    • 7. 10K+ NODES• 500k Nodes • • ••••• Facebook Visualization
    • 8. Network generated by igraphs Watts-Strogatz small-world model (50k nodes / 250k edges) visualized by Cytoscape
    • 9. 1K 10K NODES 2k nodes network generated by BA model•• • •
    • 10. Twitter Visualization Example
    • 11. ~1K NODES•• •• • •
    • 12. •• • •
    • 13. • Graphviz -• pajek - Windows• Gephi - OpenGL• Cytoscape -
    • 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. WEB Protovis JavaScript InfoVis Toolkit• • JavaScr ipt • We b
    • 16. CYTOSCAPE WEB
    • 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. • -•••
    • 19. • ••
    • 20. ••• API• • “Protein A interacts with protein B.” • A B
    • 21. • -• • • - • ←
    • 22. • • • GML • • dot (graphviz) • GraphML • • XGMML • • Edge List (
    • 23. CYTOSCAPE• LGPL• (GML, XGMML, GraphML, Excel, CSV )•• • •
    • 24. IGRAPH•• (shortest path, minimum spanning tree, etc)•R
    • 25. • • Cytoscape - • igraph -R• -
    • 26. DEMO
    • 27. • igraph•• •• • • Cytoscape
    • 28. • • • • • •••
    • 29. Sample image created by Processing Visualizer + CytoscapeMISSING LINK
    • 30. •••• ‣ ‣
    • 31. • •• ~60 + •
    • 32. • Data Miner • • (Neo4j )•
    • 33. http://www.cytoscape.org/
    • 34. http://www.cytoscape.org/ Thank You!