User:Girlwithglasses/Template:ToolData/gbrowse
- 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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