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EMBL
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A visualization tool for high level
relationship and clustering analysis in
networks
Georgios Pavlopoulos
Data integration & knowledge management group
Structural and Computational Biology unit
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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visualization
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Master title
 Pajek (V. Batagelj 1998)
 Medusa (Sean D. Hooper 2005)
 Ondex (Kohler J 2006)
Other programs:
Osprey (Breitkreutz 2003)
Cytoscape (Shannon 2003)
MAPMAN (Thimm 2004)
Shark (Pinney 2005)
CNPlot (Batada 2004)
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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Large
networks
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editscale
Master
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What if the network is a bit bigger with many
connections ???????????????????????????
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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General
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Master
•Flexible 3D interactive visualization tool
for heterogeneous data types
•Clustering Analysis
•Simple and generic way for data input
Example of input file
•Extraction of connections
Direct Connection
A
C
Indirect Connection
B
A
C
B
A
18th September 2006
C
European Molecular Biology Laboratory, Heidelberg, Germany
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Let’s see how it works
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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Snapshots-1
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18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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(Clustering)
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18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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wasMaster
done last year
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Rewriting big part of the code
5 clustering algorithms were added
Detection of indirect connetions
Allowing rotations of the layers around themselves
Integrated tree viewers like ATV
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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wasMaster
done last year
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Performance improvement (faster – lower memory)
Much better graphics
VRML compatibility
Crossovers was solved by
Allowing specific rotations to
each layer
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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Future
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Master
Biology oriented
Project
context
AKS
proceeds as a regular search
engine that looks for desired query
SRS
is a platform for life-science
database and application integration,
?
providing rapid, easy and user-friendly
access to the large volumes of diverse
data stored in over 1000 internal and
public domain databases.
terms into existing scientific
knowledge; it also performs a
conceptual search, meaning that
whether the terms found possess a
relevant biological meaning, the system
will retrieve all documents where that
term is present in any of its conceptual
definitions
SRS
EMBL
18th September 2006
public data
European Molecular Biology Laboratory, Heidelberg, Germany
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Future
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Master
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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Click to Acknowledgements
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Reinhard Schneider (Group Leader)
Venkata Satagopam (SRS administrator)
Theodoros Soldatos (Text mining)
Evangelos Pafilis (Web Services)
Seán O'Donoghue
18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany
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18th September 2006
European Molecular Biology Laboratory, Heidelberg, Germany