Data integration & knowledge management group Structural and Computational Biology unit

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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

Known visualization toolsPajek

Medusa

Cytoscape

MultiNet

Plankton

Osprey

NetDraw

Negopy

SocNetV

HyperGraph

GraphViz

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?

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

Motivation – General goal

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

Arena3D

…about Arena3D

Tree based clustering algorithms:

Non-Tree based clustering algorithms:

MCL (not yet)

Affinity Propagation

K-Means

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

Overview – My part

EMBL public data

Visualization

Databases Text Mining

Connectivity with SRS

Evangelos PafilisWeb Servises

SRS: data integration system

• > 80 databases in EMBL Heidelberg

• queries against multiple databases

• cross-linking between the records

http://srs.embl.de

Venkata Satagopam

Connectivity with Bioalma

EMBL public data

Visualization

Databases Text MiningEvangelos Pafilis

bioalma: query

bioalma: analysis creation

entity recognition & co-occurrences

bioalma:analysis report, cooccurrences

Overview

EMBL public data

Visualization

Databases Text Mining

VIDEO - DEMONSTRATION

Snapshots

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

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

Group Members - Acknowledgements

Thank you !

Data integration & knowledge management group Structural and Computational Biology unit

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