  Motivation: Network visualizations of complex biological datasets usually
result in 'hairball' images, which do not discriminate network modules.
Results: We present the EntOptLayout Cytoscape plug-in based on a recently
developed network representation theory. The plug-in provides an efficient
visualization of network modules, which represent major protein complexes in
protein-protein interaction and signalling networks. Importantly, the tool
gives a quality score of the network visualization by calculating the
information loss between the input data and the visual representation showing a
3- to 25-fold improvement over conventional methods. Availability and
implementation: The plug-in (running on Windows, Linux, or Mac OS) and its
tutorial (both in written and video forms) can be downloaded freely under the
terms of the MIT license from: http://apps.cytoscape.org/apps/entoptlayout.
Supplementary data are available at Bioinformatics online. Contact:
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