Difference between revisions of "GBrowse"

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__NOTITLE__
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{{Tool data
 
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|use template=yes
[[File:GBrowseLogo.png|center|400px|alt=GBrowse logo]]
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|name=GBrowse
 
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|full name=Generic Genome Browser
<div class="componentBox">
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|status=mature
<div class="compBoxHdr">Status</div>
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|dev=active
*Mature release
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|support=active
*maintenance
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|type=Genome Visualization & Editing
*active support
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|platform=web
<div class="compBoxHdr">Resources</div>
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|about=GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
*[http://gbrowse.org Home page]
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*[http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ Download]
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*[http://gmod.org/extras/2008GMODCommunitySurvey.html#GBrowse 2008 Survey]
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*[[GBrowse Tutorial]]
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</div>
+
 
+
==About Generic Genome Browser (GBrowse)==
+
 
+
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.
 
* Simultaneous bird's eye and detailed views of the genome.
Line 34: Line 25:
  
 
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.
 
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.
Visit the [http://gbrowse.org GBrowse website].
+
|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]]
  
===Screenshots===
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|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]]
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** [[GBrowse Configuration/Feature frequency histograms|Feature Frequency Histograms]]
 +
** [[GBrowse Configuration/Glyphs|Glyphs]]
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** [[GBrowse Configuration/I18n|I18n]]
 +
** [[GBrowse Configuration/Images|Images]]
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** [[GBrowse Configuration/URL schema|URL schema]]
 +
* [[Creating and Managing Subtracks with GBrowse2|Subtracks]]
 +
* [[GBrowse Adaptors]]
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* [[GBrowse Backends]]
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|doc=* [[GBrowse FAQ]]
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* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
 +
* Balloons:
 +
** [[GBrowse Popup Balloons]]
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** [[GBrowse Balloon Tips|Balloon Tips]]
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* [[GBrowse Persistent Variables]]
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* [[GBrowse img]]
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* [[Glyphs and Glyph Options]]
 +
* [[RubberBandSelection|Rubber Band Selection]]
 +
* [[Gbrowse Benchmarking]]
 +
* [[GBrowse User Uploads]]
  
[[image:GBrowse_screenshot1.png|none|thumb|350px|GBrowse running on [http://hapmap.ncbi.nlm.nih.gov/downloads/index.html HapMap.org] [[Media:GBrowse_screenshot1.png|Click to view at full resolution]]]]
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===POD documentation===
  
==Downloads==
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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.
  
Download GBrowse: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/]
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GBrowse 2.x pod documents can also be viewed online at CPAN:
  
The development version of GBrowse is found at https://github.com/GMOD/GBrowse. Please be aware that development versions may have new features that are not fully tested.
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* {{GBrowse_pod|FAQ}}
 
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* {{GBrowse_pod|INSTALL}}
Note that GBrowse can also be found on [http://search.cpan.org CPAN] and in the Debian sid ("unstable") apt package repository (so it is available to install via apt-get in Ubuntu since release 12.04).
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* {{GBrowse_pod|INSTALL.MacOSX}}
 
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* {{GBrowse_pod|README-chado}}
==Using GBrowse==
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* {{GBrowse_pod|README-gff-files}} (see also [[GFF]])
 
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* {{GBrowse_pod|README-lucegene}}
===System Requirements===
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* {{GBrowse_pod|BIOSQL_ADAPTER_HOWTO}}
 
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* {{GBrowse_pod|GENBANK_HOWTO}}
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.
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* {{GBrowse_pod|PLUGINS_HOWTO}}
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* {{GBrowse_pod|DAS_HOWTO}}
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* {{GBrowse_pod|MAKE_IMAGES_HOWTO}}
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* {{GBrowse_pod|GBROWSE_IMG}}
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* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}
  
 
===Installation===
 
===Installation===
Line 108: Line 159:
 
* [http://search.cpan.org/dist/GBrowse/docs/pod/GBROWSE_IMG.pod GBROWSE_IMG]
 
* [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]
 
* [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=
 +
}}
  
==Publications, Tutorials, and Presentations==
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{{SemanticLink
 
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|linkurl=http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
===Publications on or mentioning GBrowse===
+
|linktype=download
 
+
}}
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:19957275/>
+
{{SemanticLink
* SNP@Evolution: a hierarchical database of positive selection on the human genome. <ref name=PMID:19732458/> ([[GBrowse]]-related)
+
|linkurl=https://github.com/GMOD/GBrowse
* TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <ref name=PMID:19683474/> ([[GBrowse]]-related)
+
|linktype=source code
* FishMap: a community resource for zebrafish genomics. <ref name=PMID:18554176/> ([[GBrowse]]-related)
+
}}
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:18428797/>
+
{{SemanticLink
* 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].)
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|linkurl=http://gbrowse.org
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/>
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|linktype=website
* The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]
+
}}
 
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{{SemanticLink
===Tutorials===
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|linkurl=http://www.wormbase.org/tools/genome/gbrowse/c_elegans/
 
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|linktitle=WormBase
*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
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|linktype=wild URL
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
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}}
*[[GBrowse_Tutorial|Links to numerous GBrowse tutorials]]
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{{SemanticLink
* [http://www.openhelix.com/gbrowse Usage tutorial @ openhelix.com] - n.b. [[GBrowse 1.x]] tutorial
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|linkurl=http://flybase.org/cgi-bin/gbrowse/dmel
 
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|linktitle=FlyBase
==Contacts and Mailing Lists==
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|linktype=wild URL
 
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}}
{| class="wikitable"
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{{SemanticLink
|
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|linkurl=http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse
! Mailing List Link
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|linktitle=HapMap
! Description
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|linktype=wild URL
! Archive(s)
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}}
|-
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! rowspan="2" | [[GBrowse]] & [[GBrowse_syn]]
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| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse gmod-gbrowse]
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| [[GBrowse]] and [[GBrowse_syn]] users and developers.
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| [http://dir.gmane.org/gmane.science.biology.gmod.gbrowse Gmane], [http://gmod.827538.n3.nabble.com/GBrowse-f815907.html Nabble (2010/05+)], [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse Sourceforge]
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|-
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| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-cmts gmod-gbrowse-cmts]
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| Code updates.
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| [http://sourceforge.net/mailarchive/forum.php?forum_name=gmod-gbrowse-cmts Sourceforge]
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|}
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Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291 SourceForge Bug Tracker] (select 'Category: Gbrowse').
+
 
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==GBrowse in the wild==
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Public installations of GBrowse:
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*[http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase]
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*[http://flybase.org/cgi-bin/gbrowse/dmel FlyBase]
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*[http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse HapMap]
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+
==GBrowse Development==
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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.
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+
 
+
==See also==
+
 
+
[[WebGBrowse]]
+
 
+
==More on GBrowse==
+
 
+
See [[:Category:GBrowse]]
+
 
+
The [[:Image: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].
+
 
+
 
+
<references />
+
  
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]

Latest revision as of 17:18, 2 December 2013

GBrowse logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence
{{{PAGENAME}}} is open source

GPL 2.0, Artistic License 2.0

Resources


About Generic Genome Browser (GBrowse)

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.


Visit the GBrowse website.

Screenshots

Downloads

GBrowse can also be found on CPAN and in the Debian sid ("unstable") apt package repository and can be installed via apt-get in Ubuntu 12.04 and later.

Using GBrowse

System Requirements

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.

Installation

Configuration

Documentation

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:

Installation

Configuration

Documentation

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:

Publications, Tutorials, and Presentations

Publications on or mentioning GBrowse

  • Using the Generic Genome Browser (GBrowse). [1]
  • SNP@Evolution: a hierarchical database of positive selection on the human genome. [2] (GBrowse-related)
  • TBrowse: an integrative genomics map of Mycobacterium tuberculosis. [3] (GBrowse-related)
  • FishMap: a community resource for zebrafish genomics. [4] (GBrowse-related)
  • Using the Generic Genome Browser (GBrowse). [5]
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [6] (See YSB.)
  • Gbrowse Moby: a Web-based browser for BioMoby Services. [7]
  • The generic genome browser (GBrowse): a building block for a model organism system database. [8] PDF

Tutorials

GBrowse tutorial from 2012 GMOD Summer School. This relies heavily on the GBrowse2 Admin Tutorial.
Demonstrates setting up, configuring and using GBrowse with some sample data. GBrowse is provided on an Amazon Machine Image; see GMOD in the Cloud for more information on getting a GMOD AMI.
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 GBrowse2 Admin Tutorial.
GBrowse2 Admin Tutorial
Step by step guide on how to configure and load data into GBrowse. Administration tutorials are available for both the GBrowse2 Admin Tutorial, and the earlier 1.x versions.
Usage tutorial
GBrowse usage tutorial
GBrowse NGS Tutorial
Instructions on how to visualize next generation sequencing data in GBrowse using SAMtools. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
GBrowse video tutorial
Produced by EuPathDB; please direct praise and thanks to them!
GBrowse User Tutorial at OpenHelix
A Flash based tutorial on using GBrowse. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. NB: this tutorial is for GBrowse 1.x


Contacts and Mailing Lists

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').

GBrowse in the wild

Public installations of GBrowse:



See also

JBrowse, the successor to GBrowse, built with JavaScript for a faster, more interactive user experience; and WebGBrowse, a tool for configuring GBrowse.

More on GBrowse

See Category:GBrowse

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.

  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19957275
  2. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19732458
  3. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19683474
  4. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18554176
  5. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18428797
  6. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17389913
  7. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17147784
  8. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12368253
Facts about "GBrowse"RDF feed
Available on platformweb +
Has URLhttp://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 descriptionGBrowse is a combination of database and iGBrowse 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 statusactive +
Has full nameGeneric Genome Browser +
Has input formatGFF3 + and GFF2 +
Has licenceGPL2 + and Artistic License +
Has logoGBrowseLogo.png +
Has software maturity statusmature +
Has support statusactive +
Has titleWormBase +, FlyBase + and HapMap +
Has topicGBrowse +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Release date1 January 2001 +
Tool functionality or classificationGenome Visualization & Editing +
Written in languagePerl +
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 +