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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 Presentation
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European Molecular Biology Laboratory, Heidelberg, Germany
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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
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European Molecular Biology Laboratory, Heidelberg, Germany
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
Known visualization toolsPajek
Medusa
Ondex
Cytoscape
MultiNet
Otter
Plankton
Osprey
NetDraw
Negopy
SocNetV
Tulip
HyperGraph
GraphViz
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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?
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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
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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
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
Arena3D
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…about Arena3D
Tree based clustering algorithms:
UPGMA
NJ
HCL
Non-Tree based clustering algorithms:
MCL (not yet)
Affinity Propagation
K-Means
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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
…
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
Overview – My part
EMBL public data
Visualization
Databases Text Mining
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Connectivity with SRS
Evangelos PafilisWeb Servises
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SRS: data integration system
• > 80 databases in EMBL Heidelberg
• queries against multiple databases
• cross-linking between the records
http://srs.embl.de
Venkata Satagopam
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Connectivity with Bioalma
EMBL public data
Visualization
Databases Text MiningEvangelos Pafilis
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bioalma: query
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bioalma: analysis creation
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entity recognition & co-occurrences
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bioalma:analysis report, cooccurrences
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bioalma:analysis report, cooccurrences
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Overview
EMBL public data
Visualization
Databases Text Mining
USER
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DEMO
VIDEO - DEMONSTRATION
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Snapshots
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Snapshots
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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
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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
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
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Group Members - Acknowledgements
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
Thank you !
