1. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Data integration & knowledge management group Structural and Computational Biology unit A visualization tool for high level relationship and clustering analysis in large scale networks Georgios Pavlopoulos

2. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Known visualization tools Pajek Medusa Ondex Cytoscape MultiNet Otter Plankton Osprey NetDraw Negopy SocNetV Tulip HyperGraph GraphViz

3. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 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. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 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. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Motivation – General goal AC A B C C B A 5.Keep it generic so that it can be used in any case study 6.Keep it compatible with already existing tools 8.Extract indirect connections – Find hidden information 7.Maintain it read a very simple input file format Direct connection Indirect connection Between A-C

6. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Arena3D

7. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 …about Arena3D Tree based clustering algorithms:  UPGMA  NJ  HCL Non-Tree based clustering algorithms:  MCL (not yet)  Affinity Propagation  K-Means

8. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Input file example Input file example: node_i:layer _x node_j:layer_y weight A:pathwaysB:pathways5.61 A:pathwaysA:chemicals1.2 B:chemicalsA:diseases4.3 A:diseases C:proteins2.7 …

9. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Overview – My part EMBL public data Visualization Databases Text Mining

10. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Connectivity with SRS Evangelos Pafilis Web Servises

11. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 SRS: data integration system > 80 databases in EMBL Heidelberg queries against multiple databases cross-linking between the records http://srs.embl.de Venkata Satagopam

12. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Connectivity with Bioalma EMBL public data Visualization Databases Text Mining Evangelos Pafilis

13. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 bioalma: query

14. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 bioalma: analysis creation

15. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 entity recognition & co-occurrences

16. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 bioalma:analysis report, cooccurrences

17. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 bioalma:analysis report, cooccurrences

18. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Overview EMBL public data Visualization Databases Text Mining USER

19. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 DEMO VIDEO - DEMONSTRATION

20. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Snapshots

21. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Snapshots

22. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 What I did last year  Better graphics  More interactive  Increase memory and speed performance  Simpler GUI  Directed graphs support  Moving layers in 3D space  Clustering Algorithms – individual layers  Clustering algorithms – layer combination  PREDEFINED clustering  Indirect Connections  Integration with SRS  Integration with Bioalma Text Mining

23. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 What is next? Data analysis  Mitocheck  Anne Claude  Tamahud project  Bioquant project Functionality  SBML support  Even more interactivity – make everything clickable  Minimization of crossovers  Apply the same functionality to Medusa-2D  Sub-Network selection Future plan  Publication  EMBLEM license – invention record form

24. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007

25. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Group Members - Acknowledgements

26. Click to edit Master title style European Molecular Biology Laboratory, Heidelberg, Germany EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 Thank you !