Table 2

Examples of tools useful for the visualisation of networks and PPIs.

Tool

URL

Features

Refs.

BioLayout Express 3D

http://www.biolayout.org/ webcite

Facilitates microarray data analysis

[89]

Cytoscape

http://www.cytoscape.org/ webcite

Versatile; implements many visualisation algorithms; many plug-ins available

[55]

Large Graph Layout (LGL)

http://sourceforge.net/projects/lgl webcite

Especially useful for dynamic visualisation of large graphs (10⁵ nodes, 10⁶ edges); force-directed layout algorithm

[90]

Osprey

http://biodata.mshri.on.ca/osprey/servlet/Index webcite

Provides network filters, connectivity filters, many layouts and facilitates dataset superimposing

[91]

Pajek

http://vlado.fmf.uni-lj.si/pub/networks/pajek/ webcite

Especially useful for the analysis of very large networks

[92]

Visant

http://visant.bu.edu/ webcite

Especially facilitates analysis of gene ontologies

[53]

Yed

http://www.yworks.com/products/yed/ webcite

General purpose graph editor

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Raman Automated Experimentation 2010 2:2   doi:10.1186/1759-4499-2-2