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 networks. Known visualization tools. Pajek (V. Batagelj 1998) Medusa (Sean D. Hooper 2005) - PowerPoint PPT PresentationTRANSCRIPT
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European Molecular Biology Laboratory, Heidelberg, Germany
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EMBL
18th September 2006
Data integration & knowledge management group
Structural and Computational Biology unit
A visualization tool for high level relationship and clustering analysis in
networks
Georgios Pavlopoulos
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European Molecular Biology Laboratory, Heidelberg, Germany
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EMBL
18th September 2006
Known visualization tools
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)
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European Molecular Biology Laboratory, Heidelberg, Germany
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Large scale networks
What if the network is a bit bigger with many connections ???????????????????????????
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European Molecular Biology Laboratory, Heidelberg, Germany
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General goal
•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
Indirect Connection
A C
AB
C
CB
A
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Outline
Let’s see how it works
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Snapshots-1
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Snapshots-2 (Clustering)
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What was done last year
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
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European Molecular Biology Laboratory, Heidelberg, Germany
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What was done last year
Performance improvement (faster – lower memory)
Much better graphics
VRML compatibility
Crossovers was solved byAllowing specific rotations to each layer
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European Molecular Biology Laboratory, Heidelberg, Germany
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Future Work
Project context
EM BL public data
SRS
?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.
AKS proceeds as a regular search engine that looks for desired query 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
Biology oriented
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Future Work
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Acknowledgements
Reinhard Schneider (Group Leader)
Venkata Satagopam (SRS administrator)
Theodoros Soldatos (Text mining)
Evangelos Pafilis (Web Services)
Seán O'Donoghue
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European Molecular Biology Laboratory, Heidelberg, Germany
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Acknowledgements