Difference between revisions of "GBrowse"
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− | + | [[File:GBrowseLogo.png|center|400px|alt=GBrowse logo]] | |
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− | + | <div class="componentBox"> | |
+ | <div class="compBoxHdr">Status</div> | ||
+ | *Mature release | ||
+ | *maintenance | ||
+ | *active support | ||
+ | <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> | ||
− | == | + | ==About Generic Genome Browser (GBrowse)== |
− | + | ||
− | GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. | + | 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) | ||
− | + | 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]. | ||
− | + | ===Screenshots=== | |
− | + | [[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]]]] | |
− | + | ==Downloads== | |
− | + | Download GBrowse: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ 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. | |
− | GBrowse | + | ==Using GBrowse== |
+ | ===System Requirements=== | ||
− | [[ | + | 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_2.0_Install_HOWTO|GBrowse 2.x installation guide]] |
+ | * [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]] | ||
+ | * [[GBrowse 2.0 Install Paths|Install Paths]] | ||
− | + | ===Configuration=== | |
− | + | ||
− | + | ||
− | + | ||
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− | + | ||
− | + | * [[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] | * [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help] | ||
− | * [[GBrowse Popup Balloons]] | + | * Balloons: |
− | * [[GBrowse | + | ** [[GBrowse Popup Balloons]] |
− | + | ** [[GBrowse Balloon Tips|Balloon Tips]] | |
− | + | * [[GBrowse Persistent Variables]] | |
− | + | * [[GBrowse img]] | |
− | *[ | + | * [[Glyphs and Glyph Options]] |
− | *[[GBrowse | + | * [[RubberBandSelection|Rubber Band Selection]] |
− | *[[ | + | * [[Gbrowse Benchmarking]] |
− | *[ | + | * [[GBrowse User Uploads]] |
− | + | ||
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− | *[[ | + | |
− | *[[GBrowse | + | |
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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: | ||
− | * | + | * [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] |
− | == | + | ==Publications, Tutorials, and Presentations== |
− | === | + | ===Publications on or mentioning GBrowse=== |
− | + | * 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 | ||
− | == | + | ==Contacts and Mailing Lists== |
− | { | + | {| class="wikitable" |
+ | | | ||
+ | ! Mailing List Link | ||
+ | ! Description | ||
+ | ! Archive(s) | ||
+ | |- | ||
+ | ! rowspan="2" | [[GBrowse]] & [[GBrowse_syn]] | ||
+ | | [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse gmod-gbrowse] | ||
+ | | [[GBrowse]] and [[GBrowse_syn]] users and developers. | ||
+ | | [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] | ||
+ | |- | ||
+ | | [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-cmts gmod-gbrowse-cmts] | ||
+ | | Code updates. | ||
+ | | [http://sourceforge.net/mailarchive/forum.php?forum_name=gmod-gbrowse-cmts Sourceforge] | ||
+ | |} | ||
− | + | Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291SourceForge Bug Tracker] (select 'Category: Gbrowse'). | |
− | + | ==GBrowse in the wild== | |
− | + | Public installations of GBrowse: | |
+ | *[http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase] | ||
+ | *[http://flybase.org/cgi-bin/gbrowse/dmel FlyBase] | ||
+ | *[http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse HapMap] | ||
− | + | ==GBrowse Development== | |
− | which | + | 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]] | |
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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]. | ||
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− | <references/> | + | <references /> |
[[Category:GBrowse]] | [[Category:GBrowse]] | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] |
Revision as of 15:53, 24 August 2012
__NOTITLE__
Contents
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
- GBrowse FAQ
- Annotation Help
- Balloons:
- 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
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
- Administration tutorial
- Usage tutorial
- Links to numerous GBrowse tutorials
- Usage tutorial @ openhelix.com - n.b. GBrowse 1.x tutorial
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
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.
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