title: Web-based metabolic network visualization with a zooming user interface.
abstract: BACKGROUND
  Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.
  
  
  METHODS
  We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.
  
  
  CONCLUSIONS
  This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.
authors: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA. latendre@ai.sri.com
authors: Mario
authors: M
authors: Latendresse
authors: Peter D
authors: PD
authors: Karp
references: Nucleic Acids Res. 2006 Aug 07;34(13):3771-8
references: 16893960
references: Plant Physiol. 2005 Jul;138(3):1195-204
references: 16009995
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D428-32
references: 15608231
references: Plant Physiol. 2010 Aug;153(4):1479-91
references: 20522724
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9
references: 19850718
references: Trends Biochem Sci. 2008 Mar;33(3):101-3
references: 18276143
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references: 19880382
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W625-32
references: 17586824
references: Genome Res. 2003 Nov;13(11):2498-504
references: 14597658
references: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W423-6
references: 18477636
references: Bioinformatics. 2007 Feb 1;23(3):344-50
references: 17142815
references: Bioinformatics. 2010 Dec 1;26(23):2997-9
references: 20947526
references: BMC Bioinformatics. 2007 Apr 26;8:139
references: 17462086
references: PLoS One. 2009 Nov 11;4(11):e7710
references: 19907644
references: Curr Protoc Bioinformatics. 2007 Mar;Chapter 9:Unit 9.9
references: 18428797
references: BMC Bioinformatics. 2010 Jan 08;11:15
references: 20064214
references: Brief Bioinform. 2010 Jan;11(1):40-79
references: 19955237
references: Genome Biol. 2009;10(8):R84
references: 19682380