Browsing Multidimensional Molecular Networks with the Generic Network Browser (N‐Browse)

Huey‐Ling Kao1, Kristin C. Gunsalus1

1 New York University, New York, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.11
DOI:  10.1002/0471250953.bi0911s23
Online Posting Date:  September, 2008
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Abstract

N‐Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. N‐Browse runs as a Java applet in a Web browser, providing highly dynamic and interactive on‐demand access to network data available from a remote server. The N‐Browse interface is easy to use and accommodates multiple types of functional linkages with associated information, allowing the exploration of many layers of functional information simultaneously. Although created for applications in biology, N‐Browse uses a generic database schema that can be adapted to network representations in any knowledge domain. The N‐Browse client‐server package is freely available for distribution, providing a convenient way for data producers and providers to distribute and offer interactive visualization of network‐based data. Curr. Protoc. Bioinform. 23:9.11.1‐9.11.21. © 2008 by John Wiley & Sons, Inc.

Keywords: network; molecular; interaction; graph; browser; Web‐based; client‐server system; JAVA; functional genomics; GUI; visualization; database; MySQL

     
 
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Table of Contents

  • Introduction
  • Navigating the N‐Browse GUI
  • Basic Protocol 1: Basics of the N‐Browse GUI
  • Basic Protocol 2: Working with Datasets and User‐Defined Uploads
  • Basic Protocol 3: Installing and Configuring the N‐Browse Client‐Server Package
  • Basic Protocol 4: Installing and Populating the N‐Browse Generic Database
  • Commentary
  • Acknowledgements
  • Key Reference
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y.L., Dewey, C.N., Sood, P., Colombo, T., Bray, N., MacMenamin, P., Kao, H.L., Gunsalus, K.C., Pachter, L., Piano, F., and Rajewsky, N. 2006. A genome‐wide map of conserved microRNA targets in C. elegans. Curr. Biol. 16: 460‐471.
  This is the first article in the literature to describe the use of N‐Browse for integrating a new genome‐scale dataset with other available molecular interaction data. N‐Browse was used to integrate microRNA‐target predictions with multiple types of functional links in C. elegans gathered from a variety of sources (these datasets are described on the gnetbrowse.org Web site).
Internet Resources
   http://gnetbrowse.org
  The main N‐Browse Web site, currently providing access to heterogeneous functional data in E. coli, C. elegans, D. melanogaster, and H. sapiens (see the Web site for details on available datasets). Provides a link to the downloadable N‐Browse client‐server distribution package.
   http://sourceforge.net/projects/nbrowse
  The N‐Browse client‐server distribution package can be downloaded from here.
   http://www.gmod.org/wiki/index.php/nbrowse
  Provides a description of the N‐Browse project with news and links to other N‐Browse resources.
   http://www.wormbase.org
  The first example of an independent N‐Browse client‐server installation. WormBase currently uses N‐Browse as a graphical interface to server molecular interaction data curated there. Links to the N‐Browse GUI at WormBase are available on the Gene Summary pages. Also see UNIT .
  http://interactome.dfci.harvard.edu/C_elegans/host.php
  An N‐Browse portal is provided by the CCSB Interactome Database to visualize C. elegans protein‐protein interaction data in the context of other functional genomic data.
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