Difference between revisions of "GBrowse"

From GMOD
Jump to: navigation, search
m (converting to tool_data-generated page)
m
Line 2: Line 2:
  
 
{{ :GBrowse/tool_data | template = Template:ToolDisplay }}
 
{{ :GBrowse/tool_data | template = Template:ToolDisplay }}
 +
 +
{{Tool data
 +
|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.
 +
|gmod date=2002?
 +
|release date=2001
 +
|open source=yes
 +
|licence=
 +
|language=Perl
 +
|input=[[GFF3]], [[GFF2]]
 +
|output=
 +
|audience=
 +
|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]]]]
 +
|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.
 +
|survey link=GBrowse
 +
|mail={{MailingListsFor|GBrowse}}
 +
 +
Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291SourceForge Bug Tracker] (select 'Category: Gbrowse').
 +
|contact email=lincoln.stein@gmail.com; scott@scottcain.net
 +
|integration=
 +
|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===
 +
 +
*[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
 +
|presentations=
 +
|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]]
 +
|getting started preamble=
 +
|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]
 +
|dev ppl=
 +
|dev status=
 +
|dl tracking=
 +
|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}}
 +
}}
 +
{{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:GBrowse]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]

Revision as of 23:04, 4 October 2013



GBrowse logo
Status
  • Mature release
  • Development: active
  • Support: active
Resources

Included in

Cloud component

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


  • 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 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:

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

Raw tool data at GBrowse/tool data





"yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property., "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property.

"yes" is not in the list of possible values (Yes, No, Caveats apply) for this property.

"yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property. "yes" is not in the list of possible values (Yes, No, Caveats apply) for this property.

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 download URLhttp://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +
Has full nameGeneric Genome Browser +
Has input formatGFF3 + and GFF2 +
Has logoGBrowseLogo.png +
Has software maturity statusmature +
Has support statusactive +
Has titleWormBase +, FlyBase + and HapMap +
Has topicGBrowse +
Has websitehttp://gbrowse.org +
Link typedownload +, source code +, website + and wild URL +
Release date2001 +
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 +