GMOD: Difference between revisions
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[http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source 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. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases. | [http://gmod.org/ '''GMOD'''] is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase project, a collection of open source 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. [http://gmod.org/wiki/GMOD_Components GMOD tools] are in use at many large and small community databases. | ||
== GMOD Tools == | |||
GMOD has a wide variety of tools for many different purposes: | |||
{| | |||
| valign="top" | | |||
'''Community Annotation''' | |||
* [http://gmod.org/wiki/Apollo Apollo] | |||
* Wiki [http://gmod.org/wiki/Table Editor Table Editor] | |||
'''Comparative Genome Visualization''' | |||
*[http://gmod.org/wiki/CMap CMap] | |||
*[http://gmod.org/wiki/GBrowse_syn GBrowse_syn] | |||
*[http://gmod.org/wiki/SynView SynView] | |||
*[http://gmod.org/wiki/SynBrowse SynBrowse] | |||
*[http://gmod.org/wiki/Sybil Sybil] | |||
'''Database schema''' | |||
*[http://gmod.org/wiki/Chado Chado] | |||
Chado web front ends: | |||
* [http://gmod.org/wiki/GMODWeb GMODWeb] | |||
* [http://gmod.org/wiki/Tripal Tripal] | |||
'''Database tools''' | |||
*[http://gmod.org/wiki/Argos Argos] | |||
*[http://gmod.org/wiki/BioMart BioMart] | |||
*[http://gmod.org/wiki/Genome_grid Genome grid] | |||
*[http://gmod.org/wiki/GMODTools GMODTools] | |||
*[http://gmod.org/wiki/InterMine InterMine] | |||
*[http://gmod.org/wiki/LuceGene LuceGene] | |||
*[http://gmod.org/wiki/XORT XORT] | |||
| valign="top" | | |||
'''Gene Expression Visualization''' | |||
*[http://gmod.org/wiki/Caryoscope Caryoscope] | |||
*[http://gmod.org/wiki/GeneXplorer GeneXplorer] | |||
*[http://gmod.org/wiki/Java_TreeView Java TreeView] | |||
'''Genome Annotation''' | |||
*[http://gmod.org/wiki/Apollo Apollo] | |||
*[http://gmod.org/wiki/MAKER MAKER] | |||
'''Genome Visualization & Editing''' | |||
*[http://gmod.org/wiki/Apollo Apollo] | |||
*[http://gmod.org/wiki/Flash_GViewer Flash GViewer] | |||
*[http://gmod.org/wiki/GBrowse GBrowse] | |||
*[http://gmod.org/wiki/GMODWeb GMODWeb] | |||
*[http://gmod.org/wiki/JBrowse JBrowse] | |||
*[http://gmod.org/wiki/Restriction Graphic Viewer Restriction Graphic Viewer] | |||
'''Literature Tools''' | |||
* [http://gmod.org/wiki/PubSearch PubSearch] | |||
* [http://gmod.org/wiki/Textpresso Textpresso] | |||
| valign="top" | | |||
'''Molecular Pathway Visualization''' | |||
* [http://gmod.org/wiki/Pathway_Tools Pathway Tools] | |||
'''Ontology Visualization''' | |||
* [http://gmod.org/wiki/GO_Graphic_Viewer|Go Graphic Viewer GO_Graphic_Viewer|Go Graphic Viewer] | |||
'''Workflow Management''' | |||
*[http://gmod.org/wiki/TIGR-Workflow_/_Ergatis Ergatis] | |||
'''Middleware''' | |||
*[http://gmod.org/wiki/Modware Modware] | |||
*[http://gmod.org/wiki/Chado::AutoDBI Chado::AutoDBI] | |||
'''Tool Integration''' | |||
*[http://gmod.org/wiki/Galaxy Galaxy] | |||
'''Sequence Alignment''' | |||
*[http://gmod.org/wiki/BLAST_Graphic_Viewer|Blast Graphic BLAST_Graphic_Viewer|Blast Graphic] | |||
'''Utilities''' | |||
*[http://gmod.org/wiki/org.bdgp org.bdgp] | |||
|} | |||
Revision as of 17:41, 24 June 2009
| Link/URL: | |
|---|---|
| What: |
An open source project for creating and managing genome-scale biological databases. See the project overview for more. |
| Who: |
Community Based |
| Updates: |
Daily |
| Upcoming events: | |
| Web Services: |
None |
| edit table |
GMOD is the Generic Model Organism Database project, a collection of open source 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 many large and small community databases.
GMOD Tools
GMOD has a wide variety of tools for many different purposes:
|
Community Annotation Comparative Genome Visualization Database schema Chado web front ends: Database tools |
Gene Expression Visualization Genome Annotation Genome Visualization & Editing Literature Tools |
Molecular Pathway Visualization Ontology Visualization Workflow Management Middleware Tool Integration Sequence Alignment Utilities |