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

2. Known visualization tools
Pajek (V. Batagelj 1998)
Medusa (Sean D. Hooper 2005)
Ondex (Kohler J 2006)
Other programs:
Osprey (Breitkreutz 2003)
Cytoscape (Shannon 2003)
MAPMAN (Thimm 2004)
Shark (Pinney 2005)
CNPlot (Batada 2004)

3. Large scale networks
What if the network is a bit bigger with many connections ???????????????????????????

4. General goal
Flexible 3D interactive visualization tool for heterogeneous data types
Clustering Analysis
Simple and generic way for data input
Example of input file
Extraction of connections
Direct Connection
Indirect Connection A C B C A B A C

5. Outline
Let’s see how it works

6. Snapshots-1

7. Snapshots-2 (Clustering)

8. What was done last year Rewriting big part of the code
5 clustering algorithms were added
Detection of indirect connetions
Allowing rotations of the layers around themselves
Integrated tree viewers like ATV

9. What was done last year
Performance improvement (faster – lower memory)
Much better graphics
VRML compatibility
Crossovers was solved by
Allowing specific rotations to
each layer

10. Future Work Biology oriented
AKS proceeds as a regular search engine that looks for desired query terms into existing scientific knowledge; it also performs a conceptual search, meaning that whether the terms found possess a relevant biological meaning, the system will retrieve all documents where that term is present in any of its conceptual definitions
SRS is a platform for life-science database and application integration, providing rapid, easy and user-friendly access to the large volumes of diverse data stored in over 1000 internal and public domain databases.

11. Future Work

12. Acknowledgements Reinhard Schneider (Group Leader)
Venkata Satagopam (SRS administrator)
Theodoros Soldatos (Text mining)
Evangelos Pafilis (Web Services)
Seán O'Donoghue

13. Acknowledgements
Thank you!