The document discusses Cytoscape, a software environment for visualizing biomolecular interaction networks, highlighting its capabilities, tools, and models like the Watts-Strogatz and Barabási-Albert for network generation. It contains technical details about network visualization and examples of node interactions along with a sample GraphML format. Key resources and further information about Cytoscape are also provided.

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

3. •
•
• http://nrnb.org/

4. BioGRID Human Interactome Visualization
Cytoscape

5. •
•
• Cytoscape
•

7. •
‣
‣
•

14. 10K+ NODES
•
500k Nodes
•
•
•
•
•
•
• 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
•
•
•
•

17. Twitter Visualization
Example

18. ~1K NODES
•
•
•
•
•
•

19. •
•
•
•

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

22. 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

23. WEB
Protovis JavaScript InfoVis Toolkit
•
• 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>

27. • -
•
•
•

28. •
•
•

29. •
•
• API
•
• “Protein A interacts with protein B.”
• A B

30. • -
•
•
• -
• ←

31. •
•
• GML •
• dot (graphviz)
• GraphML •
• XGMML •
• Edge List (

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

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

37. •
• Cytoscape -
• igraph -R
• -

38. DEMO

39. • igraph
•
• •
• •
• Cytoscape

40. •
•
•
•
•
•
•
•

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

44. •
•
•
•
‣
‣

45. •
•
• ~60 +
•

46. • Data Miner
•
• (Neo4j )
•

48. http://www.cytoscape.org/

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