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:StandardToolDisplay|tool template]] | ||
+ | *[[User:Girlwithglasses/GBrowse|GBrowse page]] | ||
+ | </noinclude> | ||
+ | |||
{{ {{{template}}} | {{ {{{template}}} | ||
− | | name | + | | name = GBrowse |
− | | status | + | | status = mature |
− | | dev | + | | dev = maintenance |
| support = active | | support = active | ||
− | | logo | + | | os_web = yes |
− | | | + | | os_mac = yes |
− | | | + | | os_linux = yes |
− | | tutorial = http:// | + | | 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|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 [[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] | ||
+ | * [[GBrowse Popup Balloons]] | ||
+ | * [[GBrowse FAQ]] | ||
+ | |||
+ | ===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}} | ||
+ | | 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
- GBrowse tool data
- tool template
- GBrowse page
{{ {{{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)
| 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:
- 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
| 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 =
}}
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