Difference between revisions of "JBrowse"
RobertBuels (Talk | contribs) |
RobertBuels (Talk | contribs) (→JBrowse Development) |
||
| Line 56: | Line 56: | ||
JBrowse is an open-source project, started and managed by the laboratory of '''[mailto:ihh@berkeley.edu Ian Holmes]''' at the [http://berkeley.edu University of California, Berkeley]. | JBrowse is an open-source project, started and managed by the laboratory of '''[mailto:ihh@berkeley.edu Ian Holmes]''' at the [http://berkeley.edu University of California, Berkeley]. | ||
| − | |||
| − | |||
The JBrowse source code is kept on '''[http://github.com/GMOD/jbrowse GitHub]'''. Please feel very free to fork the source code on GitHub and make modifications and improvements, submitting GitHub [pull requests | The JBrowse source code is kept on '''[http://github.com/GMOD/jbrowse GitHub]'''. Please feel very free to fork the source code on GitHub and make modifications and improvements, submitting GitHub [pull requests | ||
| − | + | The lead developer of JBrowse is [[User:RobertBuels|Robert Buels]]. Much of the code was originally written by [mailto:mitch_skinner@berkeley.edu Mitch Skinner]. | |
| − | + | ||
| − | + | ||
| − | + | ||
== Developer Communication == | == Developer Communication == | ||
Revision as of 14:53, 16 February 2012
- Mature release
- Active development
- Active support
JBrowse is a genome browser with a fully dynamic AJAX interface. JBrowse renders most tracks using client-side JavaScript, with JSON as its data transfer format. JBrowse is being developed as the official successor to GBrowse.
Contents
Demo
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
See Installing JBrowse on Mac OS X and Linux for step-by-step installation instructions.
Prerequisites
- Perl modules from CPAN:
- BioPerl 1.6
- JSON
- JSON::XS (optional, for speed)
- Heap::Simple
- Heap::Simple::XS
- PerlIO::gzip
- Devel::Size
- libpng
Usage
- General Usage, including information about:
- The JBrowse user interface
- Creating sequence tracks (e.g. from FASTA files, or a Chado database)
- Creating feature tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
- Creating image tracks (e.g. from WIG files)
- Making features searchable by name
- Removing tracks
- Additional topics:
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 is kept on GitHub. Please feel very free to fork the source code on GitHub and make modifications and improvements, submitting GitHub [pull requests
The lead developer of JBrowse is Robert Buels. Much of the code was originally written by Mitch Skinner.
Developer Communication
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 Ian Holmes if you want to participate in the call.
Presentations
- Talk at the April 21, 2010 UCSC genome browser group ("genecats") meeting.
- JBrowse: A next-generation genome browser - Presentation by Ian Holmes at the August 2009 GMOD Meeting. See the talk's summary for more.
- JBrowse - Presentation by Mitch Skinner at the January 2009 GMOD Meeting. See the talk's summary for more.
- Presentation by Ian Holmes at July 2008 GMOD Meeting. See the talk's summary for more.
See also
- JBrowse Home Page
- JBrowse Quick Tutorial - JBrowse administration.
- JBrowseDev/Upcoming Future JBrowse features
