data integration & knowledge management group structural and computational biology unit
DESCRIPTION
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. Known visualization tools. Pajek. NetDraw. HyperGraph. Ondex. MultiNet. - PowerPoint PPT PresentationTRANSCRIPT
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Known visualization toolsPajek
Medusa
Ondex
Cytoscape
MultiNet
Otter
Plankton
Osprey
NetDraw
Negopy
SocNetV
Tulip
HyperGraph
GraphViz
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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?
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Motivation – General goal
A C
AB
C
CB
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 connectionBetween A-C
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Arena3D
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Input file example
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 C:proteins 2.7
…
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Overview – My part
EMBL public data
Visualization
Databases Text Mining
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Connectivity with SRS
Evangelos PafilisWeb Servises
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Connectivity with Bioalma
EMBL public data
Visualization
Databases Text MiningEvangelos Pafilis
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
bioalma: query
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
bioalma: analysis creation
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
entity recognition & co-occurrences
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
bioalma:analysis report, cooccurrences
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
bioalma:analysis report, cooccurrences
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Overview
EMBL public data
Visualization
Databases Text Mining
USER
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
DEMO
VIDEO - DEMONSTRATION
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Snapshots
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Snapshots
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
What I did last year
Better graphicsMore interactiveIncrease memory and speed performanceSimpler GUIDirected graphs supportMoving layers in 3D space
Clustering Algorithms – individual layersClustering algorithms – layer combinationPREDEFINED clustering
Indirect ConnectionsIntegration with SRSIntegration with Bioalma Text Mining
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
What is next?
Data analysisMitocheckAnne ClaudeTamahud project Bioquant project
Functionality
SBML supportEven more interactivity – make everything clickableMinimization of crossoversApply the same functionality to Medusa-2DSub-Network selection
Future planPublicationEMBLEM license – invention record form
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Group Members - Acknowledgements
Click to edit Master title style
European Molecular Biology Laboratory, Heidelberg, Germany
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
Thank you !