Transcript Data integration & knowledge management group Structural

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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
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visualization
tools style
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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
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Large
networks
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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
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– Generaltitle
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ClickMotivation
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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
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– Generaltitle
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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
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Click to editArena3D
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Arena3D
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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
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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
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– Mytitle
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Visualization
Text Mining
Databases
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
public data
European Molecular Biology Laboratory, Heidelberg, Germany
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with SRS
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Evangelos Pafilis
Web Servises
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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data Master
integration
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• > 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
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with Bioalma
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Visualization
Evangelos Pafilis
Text Mining
Databases
EMBL
Georgios Pavlopoulos TAC-2, 15 Nov 2007
public data
European Molecular Biology Laboratory, Heidelberg, Germany
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bioalma:
query
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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analysis creation
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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entityto
recognition
& co-occurrences
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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bioalma:analysis
report, cooccurrences
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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bioalma:analysis
report, cooccurrences
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Visualization
USER
Text Mining
Databases
EMBL
public data
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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VIDEO - DEMONSTRATION
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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last year
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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
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WhatMaster
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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
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Groupto
Members
- Acknowledgements
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Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany
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Thank you !
Georgios Pavlopoulos TAC-2, 15 Nov 2007
European Molecular Biology Laboratory, Heidelberg, Germany