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Bioinformatics Advance Access originally published online on August 25, 2007
Bioinformatics 2007 23(20):2651-2659; doi:10.1093/bioinformatics/btm401
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Tools for visually exploring biological networks

Matthew Suderman * and Michael Hallett

McGill Centre for Bioinformatics, 3775 University Street, Montreal, QCH3A 2B4, Canada

*To whom correspondence should be addressed.


  Abstract

Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond ‘static’ representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features.

Contact: msuder{at}mcb.mcgill.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Jonathan Wren

Received on February 27, 2007; revised on June 4, 2007; accepted on August 3, 2007

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