Difference between revisions of "GBrowse"

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(Add our new database to the GBrowse.conf)
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{{SessionHead}}
+
{{Tool data
{| class="tutorialheader"
+
|use template=yes
| {{TutorialTitleLine|GBrowse}}<br />
+
|name=GBrowse
[[2011 GMOD Spring Training]]<br />
+
|full name=Generic Genome Browser
8-12 March 2011<br />
+
|status=mature
[[User:Scott|Scott Cain]]
+
|dev=active
| align="right" | {{#icon: GBrowseLogo.png|GBrowse|200|gmod:GBrowse}}
+
|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)
  
{{TocRight}}
+
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.
=Prerequisites=
+
|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]]
  
Installed before using apt or cpan.
+
|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]]
  
=Install GBrowse=
+
===POD documentation===
  
Easily installed via the cpan shell:
+
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.
  <span class="enter">sudo cpan</span>
+
  cpan> <span class="enter">install Bio::Graphics::Browser2</span>
+
  
Which gets all of the prereqs that aren't installed on the machine.
+
GBrowse 2.x pod documents can also be viewed online at CPAN:
  
=Tutorial=
+
* {{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}}
  
Go to http://localhost/gbrowse2
+
===Installation===
  
=Basic [[Chado]] Configuration (if we have time)=
+
* [[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
 +
* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]
 +
* [[GBrowse 2.0 Install Paths|Install Paths]]
  
{{CPAN|Bio::DB::Das::Chado}} was installed when we created the image.  Sample configuration files are available with GBrowse, and we'll get the sample Chado file:
+
===Configuration===
  
  <span class="enter">wget http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/contrib/conf_files/07.chado.conf -O pythium.conf</span>
+
* [[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]]
  
Some simple tweaks and additions:
+
===POD documentation===
  
*Change description
+
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.
*Get rid of <tt>database = main</tt>
+
*Remove or change examples (yeast examples don't help anybody)
+
*Add initial landmark (<tt>initial landmark = scf1117875582023</tt>)
+
  
==DB connection info==
+
GBrowse 2.x pod documents can also be viewed online at CPAN:
  
[annotation:database]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/FAQ.pod FAQ]
db_adaptor    = Bio::DB::Das::Chado
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.pod INSTALL]
db_args      = -dsn dbi:Pg:dbname=chado
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.MacOSX.pod INSTALL.MacOSX]
                -user gmod
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-chado.pod README-chado]
                -inferCDS 1
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-gff-files.pod README-gff-files] (see also [[GFF]])
                -srcfeatureslice 1
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-lucegene.pod README-lucegene]
search options = default
+
* [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=
 +
}}
  
==Add a BAM data source==
+
{{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
 +
}}
  
[bam_sample:database]
+
[[Category:GBrowse]]
db_adaptor    = Bio::DB::Sam
+
[[Category:GMOD Components]]
db_args        = -fasta /var/www/gbrowse2/databases/pythium/scf1117875582023.fasta
+
                  -bam  /var/www/gbrowse2/databases/pythium/simulated-sorted.bam
+
search options = default
+
 
+
==Add track defaults==
+
 
+
[TRACK DEFAULTS]
+
glyph      = generic
+
database    = annotation
+
height      = 8
+
bgcolor    = cyan
+
fgcolor    = black
+
label density = 25
+
bump density  = 100
+
 
+
Note particularly the "database" entry--for most tracks we'll be using the annotation database, but the bam_sample data source will be available when we want it.
+
 
+
==Add some tracks==
+
 
+
[Genes]
+
feature      = gene
+
glyph        = gene
+
ignore_sub_part = polypeptide
+
#bgcolor      = yellow
+
forwardcolor = yellow
+
reversecolor = turquoise
+
label        = sub { my $f = shift;
+
                    my $name = $f->display_name;
+
                    my @aliases = sort $f->attributes('Alias');
+
                    $name .= " (@aliases)" if @aliases;
+
                    $name;
+
  }
+
height      = 6
+
description  = 0
+
key          = Named gene
+
+
[CDS]
+
feature      = mRNA
+
glyph        = cds
+
description  = 0
+
ignore_sub_part = polypeptide exon
+
height      = 26
+
sixframe    = 1
+
label        = sub {shift->name . " reading frame"}
+
key          = CDS
+
citation    = This track shows CDS reading frames.
+
+
[repeats]
+
feature      = match:repeatmasker
+
glyph        = generic
+
bgcolor      = black
+
key          = Repeats
+
+
[ests]
+
feature      = expressed_sequence_match
+
glyph        = segments
+
stranded    = 1
+
bgcolor      = green
+
key          = EST matches
+
+
[proteins]
+
feature      = protein_match
+
glyph        = segments
+
stranded    = 1
+
bgcolor      = pink
+
fgcolor      = red
+
key          = protein matches
+
+
[CoverageXyplot]
+
feature        = coverage
+
glyph          = wiggle_xyplot
+
database      = bam_sample
+
height        = 50
+
fgcolor        = black
+
bicolor_pivot  = 20
+
pos_color      = blue
+
neg_color      = red
+
key            = Coverage (xyplot)
+
+
[Reads]
+
feature        = match
+
glyph          = segments
+
draw_target    = 1
+
show_mismatch  = 1
+
mismatch_color = red
+
database      = bam_sample
+
bgcolor        = blue
+
fgcolor        = white
+
height        = 5
+
label density  = 50
+
bump          = fast
+
key            = Reads
+
+
[Pair]
+
feature      = read_pair
+
glyph        = segments
+
database      = bam_sample
+
draw_target  = 1
+
show_mismatch = 1
+
bgcolor      = sub {
+
                my $f = shift;
+
                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
+
                }
+
fgcolor      = green
+
height        = 3
+
label        = sub {shift->display_name}
+
label density = 50
+
bump          = fast
+
connector    = dashed
+
balloon hover = sub {
+
                my $f    = shift;
+
                return '' unless $f->type eq 'match';
+
                return 'Read: '.$f->display_name.' : '.$f->flag_str;
+
                }
+
key          = Read Pairs
+
 
+
==Add our new database to the GBrowse.conf==
+
 
+
To let GBrowse know that there is a new database available, we have to add a few lines to GBrowse.conf.  Add this to the bottom:
+
 
+
[pythium]
+
description  = Pythium ultimum
+
path          = pythium.conf
+
 
+
===Updating SAMtools===
+
 
+
The version of SAMtools may need to be updated.  Get the samtools release:
+
 
+
  cd ~/Documents/Software
+
  wget -O samtools-0.1.13.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.13/samtools-0.1.13.tar.bz2/download
+
  tar jxvf samtools-0.1.13.tar.bz2
+
  cd samtools-0.1.13
+
  make
+
 
+
Install Bio::DB::Sam:
+
 
+
  sudo cpan
+
  cpan> install Bio::DB::Sam
+
 
+
when asked "Please enter the location of the bam.h and compiled libbam.a files:", answer:
+
 
+
  /home/gmod/Documents/Software/samtools-0.1.13
+
 
+
==Add semantic zooming for the BAM tracks==
+
 
+
Not doing this for very dense data (like BAM) is probably the number one performance killers for GBrowse; asking GBrowse to draw a track that has thousands of glyphs is time consuming (and ultimately, probably not very informative).
+
 
+
[Reads:5001]
+
feature        = coverage
+
glyph          = wiggle_density
+
height        = 15
+
+
[Pair:5001]
+
feature        = coverage
+
glyph          = wiggle_density
+
height        = 15
+
bgcolor        = purple
+
 
+
==Add "show summary" functionality==
+
 
+
For other tracks, when zoomed way out (100kb or 1MB), performance can similarly suffer, with a decreasing "information" content.  Newer versions of GBrowse provide the ability to automatically generate density plots when zoomed out.  This functionality is available from Chado and {{CPAN|Bio::DB::SeqFeature::Store}} data adaptors.  To prepare our Chado database to do this semantic zooming, we need to run a script that comes with Bio::DB::Das::Chado:
+
 
+
  cd ~/Documents/Software/gbrowse-adaptors/Chado
+
  svn update
+
  perl bin/gmod_create_summary_statistics.pl
+
 
+
and then add to the pythium.conf file, somewhere near the top (ie, not in the track definitions):
+
 
+
  show summary = 99999
+
 
+
==Enabling full text searching==
+
 
+
If we try searching for "<tt>gene 7.92</tt>", we'll get "Not Found" as a result, even though genemark-scf1117875582023-abinit-gene-7.92 does exist.  To look for partial strings, we need to enable full text searching.  To do so, we need to run another script that comes with Bio::DB::Das::Chado:
+
 
+
  perl /home/gmod/Documents/Software/gbrowse-adaptors/Chado/bin/gmod_chado_fts_prep.pl
+
 
+
This does several things (including poorly estimating how long it will take to finish), including creating materialized views, using a tool provided by [[gmod:Category:SGN|SOL Genomics Network (SGN)]].  In practice, it would be a good idea to read the documentation of <tt>gmod_materialized_view_tool.pl</tt> for information on keeping the view up to date.
+
 
+
We also have to tell GBrowse that this Chado database can now do full text searching, by adding this to the Chado database stanza:
+
 
+
  -fulltext 1
+
 
+
Now we can search for "<tt>gene 7.92</tt>" and we'll find our gene (plus it's mRNA and exons) and we can click on the gene to see it in GBrowse.
+
 
+
= Evaluation =
+
 
+
{{Feedback}}
+
 
+
{{NextSession|Apollo|Apollo}}
+

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.

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Facts about "GBrowse"RDF feed
Available on platformweb +
Date published2009 +, 2008 +, 2007 +, 2006 + and 2002 +
Has DOI10.1002/0471250953.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 PMCIDPMC2755008 +, PMC1829191 +, PMC1636335 + and PMC187535 +
Has PMID19957275 +, 19732458 +, 19683474 +, 18554176 +, 18428797 +, 17389913 +, 17147784 + and 12368253 +
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 authorDonlin 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 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 publication detailsCurrent 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 statusmature +
Has support statusactive +
Has titleWormBase +, 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 topicGBrowse +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Published inCurrent 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 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 +