Difference between revisions of "GBrowse"

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{{ImageCenter|GBrowseLogo.png|GBrowse Logo|400|http://gmod.org/wiki/GBrowse#Logo}}
 
 
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[[File:GBrowseLogo.png|center|400px|alt=GBrowse logo]]
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The Generic Genome Browser (GBrowse) is a genome [[Visualization|viewer]] and is [[GMOD]]'s most popular [[GMOD Components|component]]. For a demo of its features, see [http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase], [http://flybase.org/cgi-bin/gbrowse/dmel FlyBase], and  [[GMOD_Users|others]].
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<div class="componentBox">
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<div class="compBoxHdr">Status</div>
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*Mature release
 +
*maintenance
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*active support
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<div class="compBoxHdr">Resources</div>
 +
*[http://gbrowse.org Home page]
 +
*[http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ Download]
 +
*[http://gmod.org/extras/2008GMODCommunitySurvey.html#GBrowse 2008 Survey]
 +
</div>
  
==Description==
+
==About Generic Genome Browser (GBrowse)==
[[image:GBrowse_screenshot1.png|right|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]]]]
+
  
GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Some of its features include:
+
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.
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* 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)
 
* 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)
  
==GBrowse Versions ==
+
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].
  
{{NeedsEditing}}
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===Screenshots===
  
'''GBrowse 1.X''' (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.
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[[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]]]]
  
'''GBrowse 2.0''' is a rewrite of the original GBrowse to add dynamic updating via AJAX and a smoother user experience. In addition, it provides administrators with the ability to attach a different genome database to each GBrowse track, making it much easier to manage and update tracks. It also provides a distributed backend system of "slave" renderers, allowing each track to be rendered in parallel on a different machine and significantly increasing performance. GBrowse 2.0 is considered stable, but does not have full internationalization support. In addition, there may be issues with older browsers that do not support newer JavaScript features.
+
==Downloads==
  
==Installation==
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Download GBrowse: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/]
  
{{NeedsEditing}}
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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.
  
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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==Using GBrowse==
  
 +
===System Requirements===
  
[[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
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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.
  
 +
===Installation===
  
[[GBrowse_Install_HOWTO|GBrowse 1.x installation guide]]
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* [[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
 +
* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]
 +
* [[GBrowse 2.0 Install Paths|Install Paths]]
  
* [[GBrowse_MacOSX_HOWTO|Install on MacOSX]]
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===Configuration===
* [[GBrowse_Windows_HOWTO|Install on Windows]]
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* [[GBrowse_Ubuntu_HOWTO|Install on Ubuntu and other Debian-based systems]]
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* [[GBrowse_RPM_HOWTO|Install on Fedora Core and other RPM-based systems]]
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* [[GBrowse_Gentoo_HOWTO|Install on Gentoo Linux system]]
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* [[GBrowse_Install_HOWTO|Source Code Install (for other Linux systems)]]
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==Documentation==
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* [[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
 +
** [[GBrowse Configuration/Authentication|Authentication]]
 +
** [[GBrowse Configuration/Balloons|Balloons]]
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** [[GBrowse Configuration/DAS|DAS]]
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** [[GBrowse Configuration/Feature frequency histograms|Feature Frequency Histograms]]
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** [[GBrowse Configuration/Glyphs|Glyphs]]
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** [[GBrowse Configuration/I18n|I18n]]
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** [[GBrowse Configuration/Images|Images]]
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** [[GBrowse Configuration/URL schema|URL schema]]
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* [[Creating and Managing Subtracks with GBrowse2|Subtracks]]
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* [[GBrowse Adaptors]]
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* [[GBrowse Backends]]
  
===On-line documentation===
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===Documentation===
  
 +
* [[GBrowse FAQ]]
 
* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
 
* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
* [[GBrowse Popup Balloons]]
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* Balloons:
* [[GBrowse FAQ]]
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** [[GBrowse Popup Balloons]]
 
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** [[GBrowse Balloon Tips|Balloon Tips]]
====GBrowse 2.x====
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* [[GBrowse Persistent Variables]]
 
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* [[GBrowse img]]
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
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* [[Glyphs and Glyph Options]]
*[[GBrowse 2.0 Install HOWTO|Installation guide]]
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* [[RubberBandSelection|Rubber Band Selection]]
*[[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
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* [[Gbrowse Benchmarking]]
*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
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* [[GBrowse User Uploads]]
 
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====GBrowse 1.x====
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*[http://www.openhelix.com/gbrowse Usage tutorial @ openhelix.com]
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*[[GBrowse Install HOWTO|Installation guide]]
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*[[GBrowse Configuration HOWTO|Configuration guide]]
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*{{SF_SVN|Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html Administration tutorial}}
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+
  
 
===POD documentation===
 
===POD documentation===
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GBrowse 2.x pod documents can also be viewed online at CPAN:
 
GBrowse 2.x pod documents can also be viewed online at CPAN:
  
* {{GBrowse_pod|FAQ}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/FAQ.pod FAQ]
* {{GBrowse_pod|INSTALL}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.pod INSTALL]
* {{GBrowse_pod|INSTALL.MacOSX}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.MacOSX.pod INSTALL.MacOSX]
* {{GBrowse_pod|README-chado}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/README-chado.pod README-chado]
* {{GBrowse_pod|README-gff-files}} (see also [[GFF]])
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* [http://search.cpan.org/dist/GBrowse/docs/pod/README-gff-files.pod README-gff-files] (see also [[GFF]])
* {{GBrowse_pod|README-lucegene}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/README-lucegene.pod README-lucegene]
* {{GBrowse_pod|BIOSQL_ADAPTER_HOWTO}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/BIOSQL_ADAPTER_HOWTO.pod BIOSQL_ADAPTER_HOWTO]
* {{GBrowse_pod|GENBANK_HOWTO}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/GENBANK_HOWTO.pod GENBANK_HOWTO]
* {{GBrowse_pod|PLUGINS_HOWTO}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/PLUGINS_HOWTO.pod PLUGINS_HOWTO]
* {{GBrowse_pod|DAS_HOWTO}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod DAS_HOWTO]
* {{GBrowse_pod|MAKE_IMAGES_HOWTO}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/MAKE_IMAGES_HOWTO.pod MAKE_IMAGES_HOWTO]
* {{GBrowse_pod|GBROWSE_IMG}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/GBROWSE_IMG.pod GBROWSE_IMG]
* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}
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* [http://search.cpan.org/dist/GBrowse/docs/pod/ORACLE_AND_POSTGRESQL.pod ORACLE_AND_POSTGRESQL]
  
==Downloads==
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==Publications, Tutorials, and Presentations==
  
=== Source Code Download (tar.gz file) ===
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===Publications on or mentioning GBrowse===
  
Download the source from the [https://sourceforge.net/projects/gmod/files/ SourceForge download page].
+
* 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]]
  
=== Net-based Installer Script ===
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===Tutorials===
  
The net installer script, called {{GitHub|GBrowse|master/bin/gbrowse_netinstall.pl|gbrowse_netinstall.pl at the GBrowse GitHub repository}} will automatically download and install GBrowse 1.70 ('''NOT GBrowse2''' and its Perl libraries for you. See [[#Installation|Installation]] for details on using this script.
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*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
 +
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
 +
*[[GBrowse_Tutorial|Links to numerous GBrowse tutorials]]
 +
* [http://www.openhelix.com/gbrowse Usage tutorial @ openhelix.com] - n.b. [[GBrowse 1.x]] tutorial
  
=== GitHub ===
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==Contacts and Mailing Lists==
  
{{NeedsEditing}}
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{| class="wikitable"
 +
|
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! Mailing List Link
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! Description
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! 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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|}
  
There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use the [https://github.com/GMOD/GBrowse GBrowse GitHub repository]. The recommended branch to use is ''master'', which is usually stable:
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Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291SourceForge Bug Tracker] (select 'Category: Gbrowse').
  
  git clone https://github.com/GMOD/GBrowse.git
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==GBrowse in the wild==
  
or, if you have commit privileges on the GBrowse repository, you can use:
+
Public installations of GBrowse:
 +
*[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]
  
  git clone git@github.com:GMOD/GBrowse.git
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==GBrowse Development==
  
which downloads significantly faster.
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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.
  
Once you have successfully cloned the GBrowse repository, fetch recent changes by executing <code>git pull</code> inside the <code>GBrowse</code> directory.
 
  
You can also browse the [https://github.com/GMOD/GBrowse GBrowse GitHub repository].
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==See also==
  
==== 1.x Development Version ====
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[[WebGBrowse]]
  
The link above will get you to the GBrowse2 development version.  To get to the GBrowse 1.x development branch, use the stable branch:
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==More on GBrowse==
  
  git clone https://github.com/GMOD/GBrowse.git
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See [[:Category:GBrowse]]
  cd GBrowse
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  git checkout -t -b stable origin/stable
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+
==== Further reading ====
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* [https://github.com/parrot/parrot/blob/master/docs/project/git_terminology.pod Git Terminology guide] (80% generic, 20% parrot specific).
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* [https://github.com/parrot/parrot/blob/master/docs/project/git_workflow.pod Git Workflow guide] (80% generic, 20% parrot specific).
+
 
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== About Databases ==
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{{:GBrowse Adaptors}}
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==Contacts==
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Please report bugs to the SourceForge [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291 Bug Tracker] (select 'Category: Gbrowse').
+
 
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{{MailingListsFor|GBrowse}}
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== Logo ==
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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].
 
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==
 
 
==See Also==
 
 
{{GBrowse}}
 
  
<references/>
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<references />
  
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]

Revision as of 15:53, 24 August 2012

__NOTITLE__

GBrowse logo
Status
  • Mature release
  • maintenance
  • active support
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

Download GBrowse: http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/

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.

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:

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

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:

GBrowse Development

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.


See also

WebGBrowse

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