GBrowse/tool data

This page stores the data that populates the GBrowse wiki page.

{{ {{{template}}} | name = GBrowse | full_name = Generic Genome Browser | status = mature | dev = maintenance | support = active | type = | os_linux = y | os_mac = y | os_unix = y | os_win = y | os_web = y | logo = GBrowseLogo.png | home = http://gbrowse.org | about = GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:

• Simultaneous bird's eye and detailed views of the genome.
• Scroll, zoom, center.
• Use a variety of premade glyphs or create your own.
• Attach arbitrary URLs to any annotation.
• Order and appearance of tracks are customizable by administrator and end-user.
• Search by annotation ID, name, or comment.
• Supports third party annotation using GFF formats.
• Settings persist across sessions.
• DNA and GFF dumps.
• Connectivity to different databases, including BioSQL and Chado.
• Multi-language support.
• Third-party feature loading.
• Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)

Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.

| screenshot =

GBrowse running on HapMap.org Click to view at full resolution

| public_server = http://webgbrowse.cgb.indiana.edu/ | dl = | dl_url = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ | dl_src = | dl_src_url = | dl_dev = | dl_dev_url = https://github.com/GMOD/GBrowse | getting_started_preamble = | req = GBrowse is Perl-based and the GBrowse 2.x modules are hosted on CPAN. GBrowse can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. | install =

• GBrowse 2.x installation guide
• Advanced
• Install Paths

| config =

• Configuration guide
  • Authentication
  • Balloons
  • DAS
  • Feature Frequency Histograms
  • Glyphs
  • I18n
  • Images
  • URL schema
• Subtracks
• GBrowse Adaptors
• GBrowse Backends

| doc =

• GBrowse FAQ
• Annotation Help
• Balloons:
  • GBrowse Popup Balloons
  • Balloon Tips
• GBrowse Persistent Variables
• GBrowse img
• Glyphs and Glyph Options
• Rubber Band Selection
• Gbrowse Benchmarking
• GBrowse User Uploads

POD documentation

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod.

GBrowse 2.x pod documents can also be viewed online at CPAN:

• FAQ
• INSTALL
• INSTALL.MacOSX
• README-chado
• README-gff-files (see also GFF)
• README-lucegene
• BIOSQL_ADAPTER_HOWTO
• GENBANK_HOWTO
• PLUGINS_HOWTO
• DAS_HOWTO
• MAKE_IMAGES_HOWTO
• GBROWSE_IMG
• ORACLE_AND_POSTGRESQL

| papers = * Using the Generic Genome Browser (GBrowse).

• SNP@Evolution: a hierarchical database of positive selection on the human genome. (GBrowse-related)
• TBrowse: an integrative genomics map of Mycobacterium tuberculosis. (GBrowse-related)
• FishMap: a community resource for zebrafish genomics. (GBrowse-related)
• Using the Generic Genome Browser (GBrowse).
• Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. (See YSB.)
• Gbrowse Moby: a Web-based browser for BioMoby Services.
• The generic genome browser (GBrowse): a building block for a model organism system database. PDF

| presentations = | tutorials =

• Administration tutorial
• Usage tutorial
• Links to numerous GBrowse tutorials
• Usage tutorial @ openhelix.com - n.b. GBrowse 1.x tutorial

| wild_urls =

• WormBase
• FlyBase
• HapMap

| mail =

	Mailing List Link	Description	Archive(s)
GBrowse & GBrowse_syn	gmod-gbrowse	GBrowse and GBrowse_syn users and developers.	Gmane, Nabble (2010/05+), Sourceforge
	gmod-gbrowse-cmts	Code updates.	Sourceforge

Please report bugs to the Bug Tracker (select 'Category: Gbrowse').

| logo_info = The GBrowse logo was created by Alex Read, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College. | dev_ppl = | dev_status = GBrowse development is on hold, with the focus now being on developing JBrowse, which aims to perform the same tasks as GBrowse using a faster JavaScript-based implementation. | contact_email = | input = | output = | see_also = JBrowse, the successor to GBrowse, built with JavaScript for a faster, more interactive user experience; and WebGBrowse, a tool for configuring GBrowse. | demo_server = | survey_link = GBrowse }}