title: Tools for visually exploring biological networks.
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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: McGill Centre for Bioinformatics, 3775 University Street, Montreal, QCH3A 2B4, Canada. msuder@mcb.mcgill.ca
authors.forename: Matthew
authors.initials: M
authors.lastname: Suderman
authors.forename: Michael
authors.initials: M
authors.lastname: Hallett
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome