Difference between revisions of "GMOD"
From Christoph's Personal Wiki
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
'''GMOD''' is the '''Generic Model Organism Database Toolkit''', a collection of software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at FlyBase, WormBase, SGD, BeeBase and many other large and small community databases (see: [[Genome projects]]). | '''GMOD''' is the '''Generic Model Organism Database Toolkit''', a collection of software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at FlyBase, WormBase, SGD, BeeBase and many other large and small community databases (see: [[Genome projects]]). | ||
| + | |||
| + | ==GBrowse== | ||
| + | The Generic Genome Browser written by Lincoln Stein with collaboration from many member of the community.<ref name="Stein2002">Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002). "The generic genome browser: a building block for a model organism system database". ''Genome Res, 12(10) 1599-1610''. {{doi|10.1101/gr.403602}} PMID:12368253.</ref> The project [http://www.gmod.org/gbrowse webpage] provides some example installations. It is deployed for many Model Organism Databases or MODs as well as disease and process specific databases. See the publication highlighting its design [1]. | ||
| + | |||
| + | Also see the [http://gmod.org/wiki/index.php/Gbrowse GBrowse page at www.gmod.org]. | ||
==See also== | ==See also== | ||
| + | *[http://www.sanger.ac.uk/Software/formats/GFF/ GFF] | ||
*[http://www.gmod.org/wiki/index.php/GBrowse GBrowse] — the most popular viewer in GMOD | *[http://www.gmod.org/wiki/index.php/GBrowse GBrowse] — the most popular viewer in GMOD | ||
| − | *[http://biowiki.org/view/GBrowse/PrototypeGBrowse Prototype Generic Genome Browser] — extending the GenericGenomeBrowser (GBrowse) with AJAX, community annotation and other "Web 2.0"-y ideas. | + | *[http://biowiki.org/view/GBrowse/PrototypeGBrowse Prototype Generic Genome Browser] — extending the GenericGenomeBrowser (GBrowse) with AJAX, community annotation and other "Web 2.0"-y ideas. |
| + | *[http://genome.biowiki.org/ AJAX GBrowse] | ||
| + | *[http://genome.ucla.edu/turnkey/ Turnkey] | ||
| + | *[http://www.gmod.org/Chado Chado] | ||
| + | *[http://www.gmod.org/Textpresso Textpresso] | ||
| + | *[http://www.gmod.org/wiki/index.php/Standard_URL GMOD: Standard URL] | ||
| + | *[[GenomeDiagram]] | ||
| + | *[http://www.genomic.unimelb.edu.au/varivis/index.html VariVis] — a visualisation tool for variation databases | ||
| + | ==References== | ||
| + | <references/> | ||
==External links== | ==External links== | ||
*[http://www.gmod.org/ GMOD.org] | *[http://www.gmod.org/ GMOD.org] | ||
Latest revision as of 08:41, 18 May 2008
GMOD is the Generic Model Organism Database Toolkit, a collection of software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at FlyBase, WormBase, SGD, BeeBase and many other large and small community databases (see: Genome projects).
Contents
GBrowse
The Generic Genome Browser written by Lincoln Stein with collaboration from many member of the community.[1] The project webpage provides some example installations. It is deployed for many Model Organism Databases or MODs as well as disease and process specific databases. See the publication highlighting its design [1].
Also see the GBrowse page at www.gmod.org.
See also
- GFF
- GBrowse — the most popular viewer in GMOD
- Prototype Generic Genome Browser — extending the GenericGenomeBrowser (GBrowse) with AJAX, community annotation and other "Web 2.0"-y ideas.
- AJAX GBrowse
- Turnkey
- Chado
- Textpresso
- GMOD: Standard URL
- GenomeDiagram
- VariVis — a visualisation tool for variation databases
References
- ↑ Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002). "The generic genome browser: a building block for a model organism system database". Genome Res, 12(10) 1599-1610. DOI:10.1101/gr.403602 PMID:12368253.
External links
- GMOD.org
- About GFF files — shows how to convert different file formats.
