Difference between revisions of "User:Girlwithglasses/Template:ToolData/gbrowse"

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<noinclude>
 
*[[User:Girlwithglasses/Template:ToolData/gbrowse|GBrowse tool data]]
 
*[[User:Girlwithglasses/Template:ToolData/gbrowse|GBrowse tool data]]
 
*[[User:Girlwithglasses/Template:StandardToolDisplay|tool template]]
 
*[[User:Girlwithglasses/Template:StandardToolDisplay|tool template]]
 
*[[User:Girlwithglasses/GBrowse|GBrowse page]]
 
*[[User:Girlwithglasses/GBrowse|GBrowse page]]
−
 
+
</noinclude>
  
 
{{ {{{template}}}
 
{{ {{{template}}}
−
| name     = GBrowse
+
| name = GBrowse
−
| status   = mature
+
| status = mature
−
| dev     = active
+
| dev = maintenance
 
| support  = active
 
| support  = active
−
| logo    = GBrowseLogo.png
+
| os_web = yes
−
| home    = http://gbrowse.org/
+
| os_mac = yes
−
| dl      = http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO
+
| os_linux = yes
−
| tutorial = http://www.openhelix.com/gbrowse
+
| os_win = yes
−
| mail    = Please report bugs to the SourceForge [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291 Bug Tracker] (select 'Category: Gbrowse').
+
| os_unix = yes
−
 
+
| logo = GBrowseLogo.png
−
{{MailingListsFor|GBrowse}}
+
| home = http://gbrowse.org
−
 
+
| note = The information on this page refers to GBrowse 2; [[GBrowse_1_x|GBrowse 1.x]] is recommended only for applications where legacy browser support is required and a single database is used.
−
| src      = http://sourceforge.net/project/showfiles.php?group_id=27707
+
| about = GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
−
| install  = 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.
+
−
 
+
−
[[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
+
−
 
+
−
[[GBrowse_Install_HOWTO|GBrowse 1.x installation guide]]
+
−
 
+
−
* [[GBrowse_MacOSX_HOWTO|Install on MacOSX]]
+
−
* [[GBrowse_Windows_HOWTO|Install on Windows]]
+
−
* [[GBrowse_Ubuntu_HOWTO|Install on Ubuntu and other Debian-based systems]]
+
−
* [[GBrowse_RPM_HOWTO|Install on Fedora Core and other RPM-based systems]]
+
−
* [[GBrowse_Gentoo_HOWTO|Install on Gentoo Linux system]]
+
−
* [[GBrowse_Install_HOWTO|Source Code Install (for other Linux systems)]]
+
−
| docs    = ===Online documentation===
+
  
 +
* 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)
 +
| scrnsht = [[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]]]]
 +
| dl = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
 +
| dl_src = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
 +
| dl_dev = [https://github.com/GMOD/GBrowse GBrowse repository on GitHub]
 +
| 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]]
 +
| config = [[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
 +
| doc =
 +
*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
 +
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
 
* [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]]
 
* [[GBrowse Popup Balloons]]
 
* [[GBrowse FAQ]]
 
* [[GBrowse FAQ]]
−
 
−
====GBrowse 2.x====
 
−
 
−
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
 
−
*[[GBrowse 2.0 Install HOWTO|Installation guide]]
 
−
*[[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
 
−
*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
 
−
 
−
 
−
====GBrowse 1.x====
 
−
 
−
*[http://www.openhelix.com/gbrowse Usage tutorial @ openhelix.com]
 
−
*[[GBrowse Install HOWTO|Installation guide]]
 
−
*[[GBrowse Configuration HOWTO|Configuration guide]]
 
−
*{{SF_SVN|Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html Administration tutorial}}
 
−
 
  
 
===POD documentation===
 
===POD documentation===
Line 71: Line 67:
 
* {{GBrowse_pod|GBROWSE_IMG}}
 
* {{GBrowse_pod|GBROWSE_IMG}}
 
* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}
 
* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}
−
 
+
| papers = publications
−
 
+
* 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 = interactive tutorials or workshops
 +
| presentations = non-interactive tutorials or workshops
 +
| mail = {{MailingListsFor|GBrowse}}
 +
| logo_info = 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].
 +
| wild_urls =
 +
*[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]
 +
| dev_ppl = who is developing the tool?
 +
| dev_status = what's going on at the moment
 +
| tool_type = tool type / features
 +
*Community Annotation
 +
*Comparative Genome Visualization
 +
*Database schema
 +
*Database (Chado) web front ends
 +
*Database tools
 +
*Gene Expression Visualization
 +
*Genome Annotation
 +
*Genome Visualization & Editing
 +
*Literature Tools
 +
*Middleware
 +
*Molecular Pathway Visualization
 +
*Ontology Visualization
 +
*Sequence Alignment
 +
*Tool Integration
 +
*Workflow Management
 +
| formats =
 
}}
 
}}

Latest revision as of 23:43, 10 August 2012


{{ {{{template}}} | name = GBrowse | status = mature | dev = maintenance | support = active | os_web = yes | os_mac = yes | os_linux = yes | os_win = yes | os_unix = yes | logo = GBrowseLogo.png | home = http://gbrowse.org | note = 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. | 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 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)
| scrnsht =
GBrowse running on HapMap.org Click to view at full resolution

| dl = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ | dl_src = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ | dl_dev = GBrowse repository on GitHub | getting_started_preamble = | req = 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. | install = GBrowse 2.x installation guide | config = Configuration guide | doc =

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:

| papers = publications

  • 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 = interactive tutorials or workshops | presentations = non-interactive tutorials or workshops | mail =

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

| logo_info = 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. | wild_urls =

| dev_ppl = who is developing the tool? | dev_status = what's going on at the moment | tool_type = tool type / features

  • Community Annotation
  • Comparative Genome Visualization
  • Database schema
  • Database (Chado) web front ends
  • Database tools
  • Gene Expression Visualization
  • Genome Annotation
  • Genome Visualization & Editing
  • Literature Tools
  • Middleware
  • Molecular Pathway Visualization
  • Ontology Visualization
  • Sequence Alignment
  • Tool Integration
  • Workflow Management

| formats = }}
Cite error: <ref> tags exist, but no <references/> tag was found

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