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

Aaron Barsky, Jennifer L. Gardy, Robert E.W. Hancock, Tamara Munzner

Research output: Contribution to journalArticlepeer-review

132 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1040-1042
Number of pages3
JournalBioinformatics
Volume23
Issue number8
DOIs
Publication statusPublished or Issued - 15 Apr 2007

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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