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Bioinformatics Advance Access originally published online on February 19, 2007
Bioinformatics 2007 23(8):1040-1042; doi:10.1093/bioinformatics/btm057
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation

Aaron Barsky 1, Jennifer L. Gardy 2, Robert E. W. Hancock 2 and Tamara Munzner 1,*

1Department of Computer Science and 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada

*To whom correspondence should be addressed.


  Abstract

Summary: Cerebral (Cell Region-Based Rendering And Layout) is an open-source Java plugin for the Cytoscape biomolecular interaction viewer. Given an interaction network and subcellular localization annotation, Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system. The molecules are separated into layers according to their subcellular localization. Potential products or outcomes of the pathway can be shown at the bottom of the view, clustered according to any molecular attribute data—protein function—for example. Cerebral scales well to networks containing thousands of nodes.

Availability: http://www.pathogenomics.ca/cerebral

Contact: tmm{at}cs.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on December 21, 2006; revised on February 10, 2007; accepted on February 10, 2007

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