Administering GBrowse Sites with WebGBrowse

Ram Podicheti1, Qunfeng Dong2

1 Indiana University, Bloomington, Indiana, 2 University of North Texas, Denton, Texas
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.14
DOI:  10.1002/0471250953.bi0914s33
Online Posting Date:  March, 2011
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

GBrowse is widely used by biologists to visualize genome annotation. We have developed WebGBrowse to facilitate hosting multiple GBrowse instances specific for different users on the same Web server. WebGBrowse automatically sets up each user‐specific GBrowse instance by extracting information from user‐supplied data to produce the appropriate configuration. This unit describes installation and administration of WebGBrowse for bioinformaticians who plan to manage local WebGBrowse servers in their institutions.Curr. Protoc. Bioinform. 33:9.14.1‐9.14.9. © 2011 by John Wiley & Sons, Inc.

Keywords: Genome Browser; WebGBrowse; GBrowse; GMOD; visualization; genome; annotation

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: Installing WebGBrowse
  • Basic Protocol 2: Testing the WebGBrowse Server
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Podicheti, R. and Dong, Q. 2010. Using WebGBrowse to Visualize Genome Annotation on GBrowse. Cold Spring Harb. Protoc. doi:10.1101/pdb.prot5392.
   Podicheti, R., Gollapudi, R., and Dong, Q. 2009. WebGBrowse: A web server for GBrowse. Bioinformatics 25:1550‐1551.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library