『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

CYTOSCAPE TOKYO WEB MINING #10 Keiichiro OnoUniversity of California, San Diego Dept. of Medicine

Keiichiro Ono (Twitter ID: c_z) Cytoscape Core Developer

••• http://nrnb.org/

BioGRID Human Interactome Visualization Cytoscape

••• Cytoscape•

• ‣ ‣•

10K+ NODES• 500k Nodes • • ••••• Facebook Visualization

Network generated by igraphs Watts-Strogatz small-world model (50k nodes / 250k edges) visualized by Cytoscape

1K 10K NODES 2k nodes network generated by BA model•• • •

Twitter Visualization Example

~1K NODES•• •• • •

•• • •

• Graphviz -• pajek - Windows• Gephi - OpenGL• Cytoscape -

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

WEB Protovis JavaScript InfoVis Toolkit• • JavaScr ipt • We b

CYTOSCAPE WEB

<?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"> <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>

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• ••

••• API• • “Protein A interacts with protein B.” • A B

• -• • • - • ←

• • • GML • • dot (graphviz) • GraphML • • XGMML • • Edge List (

CYTOSCAPE• LGPL• (GML, XGMML, GraphML, Excel, CSV )•• • •

IGRAPH•• (shortest path, minimum spanning tree, etc)•R

• • Cytoscape - • igraph -R• -

• igraph•• •• • • Cytoscape

• • • • • •••

Sample image created by Processing Visualizer + CytoscapeMISSING LINK

•••• ‣ ‣

• •• ~60 + •

• Data Miner • • (Neo4j )•

http://www.cytoscape.org/

http://www.cytoscape.org/ Thank You!

http://d.hatena.ne.jp	710
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http://wiki.onakasuita.org	21
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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

by Keiichiro Ono on Feb 27, 2011

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