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QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style A visualization tool for high level relationship and clustering analysis in large scale networks Georgios Pavlopoulos Data integration & knowledge management group Structural and Computational Biology unit Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL visualization tools style ClickKnown to edit Master title Pajek NetDraw Ondex MultiNet HyperGraph Cytoscape Medusa Negopy GraphViz Plankton SocNetV Osprey Tulip Otter Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Large networks Click to editscale Master title style What if the network is a bit bigger with many connections? Is there any way to visualize some clusters out of this mess? Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL – Generaltitle goalstyle ClickMotivation to edit Master 1.Interactive 2.Visualize everything in 3D 3.Combine different kinds of data under the same Network 4.Provide and Visualize some clustering algorithms Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL – Generaltitle goalstyle ClickMotivation to edit Master 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 A C B A Direct connection C Indirect connection Between A-C B A Georgios Pavlopoulos TAC-2, 15 Nov 2007 C European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to editArena3D Master title style Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Arena3D Click to…about edit Master title style Tree based clustering algorithms: UPGMA NJ HCL Non-Tree based clustering algorithms: MCL (not yet) Affinity Propagation K-Means Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany example Click toInput editfile Master title style QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Input file example: node_i:layer _x node_j:layer_y weight A:pathways B:pathways 5.61 A:pathways A:chemicals 1.2 B:chemicals A:diseases 4.3 A:diseases 2.7 C:proteins … Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL – Mytitle part style Click to Overview edit Master Visualization Text Mining Databases EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 public data European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL with SRS Click Connectivity to edit Master title style Evangelos Pafilis Web Servises Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL data Master integration system ClickSRS: to edit title style • > 80 databases in EMBL Heidelberg Venkata Satagopam • queries against multiple databases • cross-linking between the records http://srs.embl.de Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL with Bioalma Click Connectivity to edit Master title style Visualization Evangelos Pafilis Text Mining Databases EMBL Georgios Pavlopoulos TAC-2, 15 Nov 2007 public data European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style bioalma: query Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click bioalma: to edit Master title style analysis creation Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click edit Master title style entityto recognition & co-occurrences Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style bioalma:analysis report, cooccurrences Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style bioalma:analysis report, cooccurrences Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Overview Master title style Visualization USER Text Mining Databases EMBL public data Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL DEMO title style Click to edit Master VIDEO - DEMONSTRATION Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to editSnapshots Master title style Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to editSnapshots Master title style Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL last year Click toWhat editI did Master title style 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 Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL WhatMaster is next? title style Click to edit 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 Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Groupto Members - Acknowledgements Click edit Master title style Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany QuickTime™ and a TIFF (U ncompressed) decompressor are needed to see this picture. EMBL Click to edit Master title style Thank you ! Georgios Pavlopoulos TAC-2, 15 Nov 2007 European Molecular Biology Laboratory, Heidelberg, Germany