View source for GBrowse

{{Tool data
|use template=yes
|name=GBrowse
|full name=Generic Genome Browser
|status=mature
|dev=active
|support=active
|type=Genome Visualization & Editing
|platform=web
|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 [[GBrowse Configuration HOWTO#Glyphs and Glyph Options|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 [[GBrowse Plugins|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|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.
|open source=Yes
|licence=GPL2, Artistic License
|input=GFF3, GFF2
|language=Perl
|release date=2001/01/01
|logo=GBrowseLogo.png
|screenshot=[[image:GBrowse_screenshot1.png|none|thumb|500px|GBrowse running on [http://hapmap.ncbi.nlm.nih.gov/downloads/index.html HapMap.org] [[Media:GBrowse_screenshot1.png|Click to view at full resolution]]]]
|mail={{MailingListsFor|GBrowse}}Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291SourceForge Bug Tracker] (select 'Category: Gbrowse').
|dl src=GBrowse can also be found on [http://search.cpan.org CPAN] and in the Debian sid ("unstable") apt package repository and can be installed via apt-get in Ubuntu 12.04 and later.
|papers=* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:19957275/>
* SNP@Evolution: a hierarchical database of positive selection on the human genome. <ref name=PMID:19732458/> ([[GBrowse]]-related)
* TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <ref name=PMID:19683474/> ([[GBrowse]]-related)
* FishMap: a community resource for zebrafish genomics. <ref name=PMID:18554176/> ([[GBrowse]]-related)
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:18428797/>
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/>  (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].)
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/>
* The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]

|tutorials=; [[GBrowse Tutorial|GBrowse tutorial from 2012 GMOD Summer School]]. This relies heavily on the {{GBrowseAdminTutorialLink| GBrowse Administration Tutorial}}.
: Demonstrates setting up, configuring and using [[GBrowse]] with some sample data. GBrowse is provided on an Amazon Machine Image; see [[Cloud|GMOD in the Cloud]] for more information on getting a GMOD AMI.
; [[GBrowse Tutorial 2010|GBrowse tutorial from 2010 GMOD Summer School]]
: Set up and run [[GBrowse]] with sample data. It provides a VMware image to work on, and relies heavily on the {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}.
; {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}
: Step by step guide on how to configure and load data into [[GBrowse]].  Administration tutorials are available for both the {{GBrowseAdminTutorialLink|current version}}, and the earlier {{GBrowse1AdminTutorialLink|1.x versions}}.
;[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
:GBrowse usage tutorial
; [[GBrowse NGS Tutorial]]
: Instructions on how to visualize [[next generation sequencing]] data in GBrowse using [http://samtools.sourceforge.net SAMtools].  The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
; [http://youtu.be/jxA6VMN97Y8 GBrowse video tutorial]
: Produced by [http://eupathdb.org EuPathDB]; please direct praise and thanks to them!
; [http://www.openhelix.com/gbrowse GBrowse User Tutorial] at [http://www.openhelix.com OpenHelix]
: A Flash based tutorial on using GBrowse.  Provided by [http://www.openhelix.com OpenHelix].  Tutorial includes slides, handouts and exercises. NB: this tutorial is for [[GBrowse 1.x]]
|req=GBrowse is [[Glossary#Perl|Perl]]-based and the GBrowse 2.x modules are [http://search.cpan.org/dist/GBrowse/ 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_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]
* [[GBrowse 2.0 Install Paths|Install Paths]]
|config=* [[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
** [[GBrowse Configuration/Authentication|Authentication]]
** [[GBrowse Configuration/Balloons|Balloons]]
** [[GBrowse Configuration/DAS|DAS]]
** [[GBrowse Configuration/Feature frequency histograms|Feature Frequency Histograms]]
** [[GBrowse Configuration/Glyphs|Glyphs]]
** [[GBrowse Configuration/I18n|I18n]]
** [[GBrowse Configuration/Images|Images]]
** [[GBrowse Configuration/URL schema|URL schema]]
* [[Creating and Managing Subtracks with GBrowse2|Subtracks]]
* [[GBrowse Adaptors]]
* [[GBrowse Backends]]
|doc=* [[GBrowse FAQ]]
* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
* Balloons:
** [[GBrowse Popup Balloons]]
** [[GBrowse Balloon Tips|Balloon Tips]]
* [[GBrowse Persistent Variables]]
* [[GBrowse img]]
* [[Glyphs and Glyph Options]]
* [[RubberBandSelection|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:

* {{GBrowse_pod|FAQ}}
* {{GBrowse_pod|INSTALL}}
* {{GBrowse_pod|INSTALL.MacOSX}}
* {{GBrowse_pod|README-chado}}
* {{GBrowse_pod|README-gff-files}} (see also [[GFF]])
* {{GBrowse_pod|README-lucegene}}
* {{GBrowse_pod|BIOSQL_ADAPTER_HOWTO}}
* {{GBrowse_pod|GENBANK_HOWTO}}
* {{GBrowse_pod|PLUGINS_HOWTO}}
* {{GBrowse_pod|DAS_HOWTO}}
* {{GBrowse_pod|MAKE_IMAGES_HOWTO}}
* {{GBrowse_pod|GBROWSE_IMG}}
* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}

===Installation===

* [[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]
* [[GBrowse 2.0 Install Paths|Install Paths]]

===Configuration===

* [[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
** [[GBrowse Configuration/Authentication|Authentication]]
** [[GBrowse Configuration/Balloons|Balloons]]
** [[GBrowse Configuration/DAS|DAS]]
** [[GBrowse Configuration/Feature frequency histograms|Feature Frequency Histograms]]
** [[GBrowse Configuration/Glyphs|Glyphs]]
** [[GBrowse Configuration/I18n|I18n]]
** [[GBrowse Configuration/Images|Images]]
** [[GBrowse Configuration/URL schema|URL schema]]
* [[Creating and Managing Subtracks with GBrowse2|Subtracks]]
* [[GBrowse Adaptors]]
* [[GBrowse Backends]]

===Documentation===

* [[GBrowse FAQ]]
* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
* Balloons:
** [[GBrowse Popup Balloons]]
** [[GBrowse Balloon Tips|Balloon Tips]]
* [[GBrowse Persistent Variables]]
* [[GBrowse img]]
* [[Glyphs and Glyph Options]]
* [[RubberBandSelection|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:

* [http://search.cpan.org/dist/GBrowse/docs/pod/FAQ.pod FAQ]
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.pod INSTALL]
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.MacOSX.pod INSTALL.MacOSX]
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-chado.pod README-chado]
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-gff-files.pod README-gff-files] (see also [[GFF]])
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-lucegene.pod README-lucegene]
* [http://search.cpan.org/dist/GBrowse/docs/pod/BIOSQL_ADAPTER_HOWTO.pod BIOSQL_ADAPTER_HOWTO]
* [http://search.cpan.org/dist/GBrowse/docs/pod/GENBANK_HOWTO.pod GENBANK_HOWTO]
* [http://search.cpan.org/dist/GBrowse/docs/pod/PLUGINS_HOWTO.pod PLUGINS_HOWTO]
* [http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod DAS_HOWTO]
* [http://search.cpan.org/dist/GBrowse/docs/pod/MAKE_IMAGES_HOWTO.pod MAKE_IMAGES_HOWTO]
* [http://search.cpan.org/dist/GBrowse/docs/pod/GBROWSE_IMG.pod GBROWSE_IMG]
* [http://search.cpan.org/dist/GBrowse/docs/pod/ORACLE_AND_POSTGRESQL.pod ORACLE_AND_POSTGRESQL]
|logo info=The [[:File:GBrowseLogo.png|GBrowse logo]] was created by [mailto:alexisnb1@yahoo.com Alex Read], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].
|see also=[[JBrowse]], the successor to GBrowse, built with JavaScript for a faster, more interactive user experience; and [[WebGBrowse]], a tool for configuring GBrowse.
|extra={{GitcComponent}}
|survey link=GBrowse
|contact email=lincoln.stein@gmail.com; scott@scottcain.net
|integration=
|dev status=
}}

{{SemanticLink
|linkurl=http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
|linktype=download
}}
{{SemanticLink
|linkurl=https://github.com/GMOD/GBrowse
|linktype=source code
}}
{{SemanticLink
|linkurl=http://gbrowse.org
|linktype=website
}}
{{SemanticLink
|linkurl=http://www.wormbase.org/tools/genome/gbrowse/c_elegans/
|linktitle=WormBase
|linktype=wild URL
}}
{{SemanticLink
|linkurl=http://flybase.org/cgi-bin/gbrowse/dmel
|linktitle=FlyBase
|linktype=wild URL
}}
{{SemanticLink
|linkurl=http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse
|linktitle=HapMap
|linktype=wild URL
}}

[[Category:GBrowse]]
[[Category:GMOD Components]]
Available on platform	web +
Date published	2009 +, 2008 +, 2007 +, 2006 + and 2002 +
Has DOI	10.1002/0471250953.bi0909s28 +, 10.1186/1471-2148-9-221 +, 10.1016/j.tube.2009.07.005 +, 10.1089/zeb.2008.0531 +, 10.1002/0471250953.bi0909s17 +, 10.1371/journal.pone.0000322 +, 10.1186/1751-0473-1-4 + and 10.1101/gr.403602 +
Has PMCID	PMC2755008 +, PMC1829191 +, PMC1636335 + and PMC187535 +
Has PMID	19957275 +, 19732458 +, 19683474 +, 18554176 +, 18428797 +, 17389913 +, 17147784 + and 12368253 +
Has URL	http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, https://github.com/GMOD/GBrowse +, http://gbrowse.org +, http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, http://flybase.org/cgi-bin/gbrowse/dmel + and http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +
Has author	Donlin MJ +, Cheng F +, Chen W +, Richards E +, Deng L +, Zeng C +, Bhardwaj A +, Bhartiya D +, Kumar N +, Open Source Drug Discovery Consortium +, Scaria V +, Meli R +, Prasad A +, Patowary A +, Lalwani MK +, Maini J +, Sharma M +, Singh AR +, Kumar G +, Jadhav V +, Sivasubbu S +, Schacherer J +, Ruderfer DM +, Gresham D +, Dolinski K +, Botstein D +, Kruglyak L +, Wilkinson M +, Stein LD +, Mungall C +, Shu S +, Caudy M +, Mangone M +, Day A +, Nickerson E +, Stajich JE +, Harris TW +, Arva A + and Lewis S +
Has description	GBrowse is a combination of database and i … 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.is required and a single database is used. +
Has development status	active +
Has full name	Generic Genome Browser +
Has input format	GFF3 + and GFF2 +
Has licence	GPL2 + and Artistic License +
Has logo	GBrowseLogo.png +
Has publication details	Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 9: Unit 9.9 +, BMC evolutionary biology 9: 221 +, Tuberculosis (Edinburgh, Scotland) 89: 386-7 +, Zebrafish 5: 125-30 +, PloS one 2: e322 +, Source code for biology and medicine 1: 4 + and Genome research 12: 1599-610 +
Has software maturity status	mature +
Has support status	active +
Has title	WormBase +, FlyBase +, HapMap +, Using the Generic Genome Browser (GBrowse). +, SNP@Evolution: a hierarchical database of positive selection on the human genome. +, TBrowse: an integrative genomics map of Mycobacterium tuberculosis. +, FishMap: a community resource for zebrafish genomics. +, Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. +, Gbrowse Moby: a Web-based browser for BioMoby Services. + and The generic genome browser: a building block for a model organism system database. +
Has topic	GBrowse +
Is open source	Yes +
Link type	download +, source code +, website + and wild URL +
Published in	Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] +, BMC evolutionary biology +, Tuberculosis (Edinburgh, Scotland) +, Zebrafish +, PloS one +, Source code for biology and medicine + and Genome research +
Release date	1 January 2001 +
Tool functionality or classification	Genome Visualization & Editing +
Written in language	Perl +
Has subobjectThis property is a special property in this wiki.	GBrowse#http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, GBrowse#https://github.com/GMOD/GBrowse +, GBrowse#http://gbrowse.org +, GBrowse#http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, GBrowse#http://flybase.org/cgi-bin/gbrowse/dmel + and GBrowse#http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +