Difference between revisions of "JBrowse"

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(Demo)
(JBrowse Configuration Guide)
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* [[JBrowse Configuration Guide|Configuration Guide]]
 
* [[JBrowse Configuration Guide|Configuration Guide]]
 
** [[JBrowse Configuration Guide#Reference Sequences|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database)
 
** [[JBrowse Configuration Guide#Reference Sequences|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database)
** [[JBrowse Configuration Guide#Feature Tracks|Creating feature tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
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** [[JBrowse Configuration Guide#Feature Tracks|Feature Tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
** [[JBrowse Configuration Guide#Image Tracks|Creating image tracks]] (e.g. from WIG files)
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** [[JBrowse Configuration Guide#Image Tracks|Image Tracks]] (e.g. from WIG files)
** [[JBrowse Configuration Guide#Searchable Names|Making features searchable by name]]
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** [[JBrowse Configuration Guide#Wiggle_Tracks|Wiggle/BigWig Tracks]]
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** [[JBrowse Configuration Guide#Name_Searching_and_Autocompletion | Name Search and Autocompletion]]
 
** [[JBrowse Configuration Guide#Removing Tracks|Removing tracks]]
 
** [[JBrowse Configuration Guide#Removing Tracks|Removing tracks]]
** [[JBrowse Configuration Guide#Compressing data stored on the server|Compressing data stored on the server]]
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** [[JBrowse Configuration Guide#Compressing data on the server|Compressing data stored on the server]]
** [[JBrowse Configuration Guide#Using callbacks to customize feature tracks | Using callbacks to customize feature tracks ]]
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** [[JBrowse Configuration Guide#URL Control | URL control ]]
 
** [[JBrowse Configuration Guide#URL Control | URL control ]]
 
** [[JBrowse Configuration Guide#Faceted Track Selection | Faceted track selection ]]
 
** [[JBrowse Configuration Guide#Faceted Track Selection | Faceted track selection ]]
** [[JBrowse Configuration Guide#Name Searching and Autocompletion | Name searching and autocompletion]]
 
 
** [[JBrowse Configuration Guide#Anonymous Usage Statistics | Anonymous usage statistics ]]
 
** [[JBrowse Configuration Guide#Anonymous Usage Statistics | Anonymous usage statistics ]]
  
 
* Additional topics:
 
* Additional topics:
 
** [[JBrowseDev/Using Configuration Files With JBrowse|Using Configuration Files with biodb-to-json.pl]]
 
** [[JBrowseDev/Using Configuration Files With JBrowse|Using Configuration Files with biodb-to-json.pl]]
** [[JBrowseDev/Using a Database With JBrowse|Using a Database]]
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** [[JBrowseDev/Using a Database With JBrowse|Using an Existing Database with JBrowse]]
  
 
= JBrowse Advanced Topics =
 
= JBrowse Advanced Topics =

Revision as of 20:32, 13 August 2012

Status
  • Mature release
  • Active development
  • Active support
Resources
Events

2012 GMOD Summer School

JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse does almost all of its work directly in the user's web browser, with minimal requirements for the server.

Demo

Volvox example data

Quick Start: Tutorial

The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.

Installation

1. Download JBrowse onto your web server.

2. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to /var/www.

   cd /var/www
   tar -xzf jbrowse-*.tar.gz

Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.

3. Run the automated-setup script, ./setup.sh, which will attempt to install all of JBrowse's (modest) prerequisites for you in the jbrowse/ directory itself. setup.sh does not need to be run as root or with sudo. For the installation to completely succeed, including support for WIG and BAM data, your system must have:

  • a working internet connection for downloading Perl modules from CPAN
  • compilers for C and C++
  • make
  • the svn Subversion client (for fetching the samtools code, needed for BAM support)
  • development libraries and header files (not just compiled shared objects) for:
    • libpng
    • Zlib
    • GD

For tips on installing these baseline libraries, see JBrowse Troubleshooting.

4. When you can see the included Volvox example data, you are ready to configure JBrowse to show your own data! Proceed to the JBrowse Configuration Guide.

JBrowse Configuration Guide

JBrowse Advanced Topics

For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.

Status

JBrowse is being actively developed and supported.

Contact

Please direct questions and inquiries regarding JBrowse to the mailing lists below.

In particular, requests for help should be directed to gmod-ajax@lists.sourceforge.net.

Mailing List Link Description Archive(s)
JBrowse gmod-ajax JBrowse help and general questions. Nabble (2010/05+), Sourceforge
jbrowse-dev JBrowse development discussions. Nabble (2011/08+)

JBrowse Development

JBrowse is an open-source project, started and managed by the laboratory of Ian Holmes at the University of California, Berkeley.

The JBrowse source code repository is kept on GitHub. Please feel very free to fork the code on GitHub and make modifications and improvements, submitting pull requests. GitHub has a very nice tutorial on how to get started with this style of development.

As of January 2012, the lead developer of JBrowse is Robert Buels. Most of JBrowse was originally written by Mitch Skinner.

There is a mailing list for developers, and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from Please contact Robert Buels if you would like to listen in or participate.

Presentations

Date Presenter Venue Links
April 2012 Robert Buels GMOD 2012 Community Meeting PDF
January 2012 Robert Buels Plant and Animal Genome (PAG) XX PDF
April 2010 Mitch Skinner UCSC genome browser group ("genecats") meeting PDF
August 2009 Ian Holmes GMOD Community Meeting Talk summary | PDF
January 2009 Mitch Skinner GMOD Community Meeting Talk summary | PDF
July 2008 Ian Holmes GMOD Community Meeting Talk summary | PDF