Data integration & knowledge management group Structural and Computational Biology unit

1. Data integration & knowledge management group Structural and Computational Biology unit Georgios Pavlopoulos A visualization tool for high level relationship and clustering analysis in large scale networks

2. Known visualization tools Pajek NetDraw HyperGraph Ondex MultiNet Cytoscape Medusa Negopy GraphViz SocNetV Plankton Otter Tulip Osprey

3. Large scale networks What if the network is a bit bigger with many connections? Is there any way to visualize some clusters out of this mess?

4. Motivation – General goal 1.Interactive 2.Visualize everything in 3D 3.Combine different kinds of data under the same Network 4.Provide and Visualize some clustering algorithms

5. Motivation – General goal A C 5.Keep it generic so that it can be used in any case study 6.Keep it compatible with already existing tools 7.Maintain it read a very simple input file format 8.Extract indirect connections – Find hidden information Direct connection B C Indirect connection Between A-C A B A C

6. Arena3D

7. …about Arena3D • Tree based clustering algorithms: • UPGMA • NJ • HCL • Non-Tree based clustering algorithms: • MCL • Affinity Propagation • K-Means

8. Input file example Input file example: node_i:layer _x node_j:layer_y weight A:pathways B:pathways 5.61 A:pathwaysA:chemicals 1.2 B:chemicals A:diseases 4.3 A:diseases C:proteins 2.7 …

9. Overview Visualization Text Mining Databases public data EMBL

21. Snapshots

22. Snapshots

24. Group Members - Acknowledgements

25. Thank you !