Click to edit Master title style

coilcruelΔιαχείριση

6 Νοε 2013 (πριν από 4 χρόνια και 1 μήνα)

59 εμφανίσεις

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

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

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Known visualization tools

Pajek

Medusa

Ondex

Cytoscape

MultiNet

Otter

Plankton

Osprey

NetDraw

Negopy

SocNetV

Tulip

HyperGraph

GraphViz

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

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?

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

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

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Motivation


General goal


A


C

A

B

C

C

B

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 connection

Between A
-
C

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Arena3D

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

…about Arena3D



Tree based clustering algorithms:





UPGMA




NJ




HCL





Non
-
Tree based clustering algorithms:





MCL (not yet)




Affinity Propagation




K
-
Means




Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

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







Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Overview


My part


EMBL


public data

Visualization

Databases

Text Mining

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Connectivity with SRS

Evangelos Pafilis

Web Servises

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

SRS: data integration system




> 80 databases in EMBL Heidelberg



queries against multiple databases



cross
-
linking between the records

http://srs.embl.de





Venkata Satagopam

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Connectivity with Bioalma


EMBL


public data

Visualization

Databases

Text Mining

Evangelos Pafilis

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

bioalma: query

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

bioalma: analysis creation

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

entity recognition & co
-
occurrences

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

bioalma:analysis report, cooccurrences

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

bioalma:analysis report, cooccurrences

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Overview


EMBL


public data

Visualization

Databases

Text Mining

USER

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

DEMO

VIDEO
-

DEMONSTRATION

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Snapshots

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Snapshots

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

What I did last year


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

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

What is next?

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








Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Group
Members

-

Acknowledgements

Click to edit Master title style

European Molecular Biology Laboratory, Heidelberg, Germany

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
EMBL

Georgios Pavlopoulos TAC
-
2, 15 Nov 2007

Thank you !