1. CYTOSCAPE
TOKYO WEB MINING #10
Keiichiro Ono
University of California, San Diego
Dept. of Medicine

2. Keiichiro Ono (Twitter ID: c_z)
Cytoscape Core Developer

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• http://nrnb.org/

4. BioGRID Human Interactome Visualization
Cytoscape

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• Cytoscape
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14. 10K+ NODES
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500k Nodes
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• Facebook Visualization

15. Network generated by igraph's Watts-Strogatz small-world model
(50k nodes / 250k edges) visualized by Cytoscape

16. 1K 10K NODES
2k nodes network generated by BA model
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17. Twitter Visualization
Example

18. ~1K NODES
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21. • Graphviz -
• pajek -
Windows
• Gephi - OpenGL
• Cytoscape -

22. CYTOSCAPE
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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

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

24. CYTOSCAPE WEB

25. <?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>

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

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• ←

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

35. CYTOSCAPE
• LGPL
• (GML, XGMML, GraphML, Excel, CSV )
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36. IGRAPH
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(shortest path, minimum
spanning tree, etc)
•R

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• Cytoscape -
• igraph -R
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38. DEMO

39. • igraph
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• Cytoscape

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43. Sample image created by Processing
Visualizer + Cytoscape
MISSING LINK

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• ~60 +
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46. • Data Miner
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• (Neo4j )
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48. http://www.cytoscape.org/

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