『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

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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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