Difference between revisions of "Main Page"

From GMOD
Jump to: navigation, search
(<font color="navy blue">How do I Get Involved?</font>)
(<font color="navy blue">Welcome to GMOD</font>)
Line 7: Line 7:
 
|
 
|
 
;Genome Browsing and Editing
 
;Genome Browsing and Editing
:[[Apollo | The Apollo Genome Annotation Editor]] [http://www.fruitfly.org/annot/apollo/images/mainwindow.jpg [screenshot]]
+
:[[Apollo | Apollo: Genome annotation editor]] [http://www.fruitfly.org/annot/apollo/images/mainwindow.jpg [screenshot]]
:[[GBrowse | The GBrowse Genome Annotation Viewer]] [http://www.gmod.org/wiki/images/b/b6/Gbrowse_screenshot1.gif [screenshot]] [http://www.wormbase.org/db/seq/gbrowse/wormbase/?start=10671750;stop=10675964;ref=V;width=800;version=100;label=LOCI%3Aoverview-CG-MOTIFS-WABA-ESTB-RNAi_BEST-SAGE  [demo]]
+
:[[GBrowse | GBrowse: Genome annotation viewer]] [http://www.wormbase.org/db/seq/gbrowse/wormbase/?start=10671750;stop=10675964;ref=V;width=800;version=100;label=LOCI%3Aoverview-CG-MOTIFS-WABA-ESTB-RNAi_BEST-SAGE  [demo]]
 
;Comparative Genetic and Sequence Maps
 
;Comparative Genetic and Sequence Maps
:[[CMap | The CMap comparative genetic map viewer]] [http://www.gmod.org/wiki/index.php/Image:Cmap_sample1.jpg [screenshot]]
+
:[[CMap | CMap: Comparative genetic map viewer]] [http://www.gmod.org/wiki/index.php/Image:Cmap_sample1.jpg [screenshot]]
:[[Sybil | The Sybil comparative genome viewer]] [http://sybil.sourceforge.net/index.html#screenshots [screenshots]]
+
:[[Sybil | Sybil: Comparative genome viewer]] [http://sybil.sourceforge.net/index.html#screenshots [screenshots]]
:[[SynBrowse | The SynBrowse genome synteny viewer]] [http://www.synbrowse.org/cgi-perl/synbrowse?config=plant&relink=1&tname=5:22042000..22063000&name=Mt2:6658500..6709000&qry_species=Medicago&ref_species=Arabidopsis&key_align=Protein_Align&Mode=Coding_Exon [demo]]
+
:[[SynBrowse | SynBrowse: Genome synteny viewer]] [http://www.synbrowse.org/cgi-perl/synbrowse?config=plant&relink=1&tname=5:22042000..22063000&name=Mt2:6658500..6709000&qry_species=Medicago&ref_species=Arabidopsis&key_align=Protein_Align&Mode=Coding_Exon [demo]]
 
;Database Tools
 
;Database Tools
:[[BioMart | The BioMart genome data mining system ]] [http://www.biomart.org/ [overview]]
+
:[[Chado | Chado: Modular biological database schema]]
 +
:[[BioMart | BioMart: Genome data mining system ]] [http://www.biomart.org/ [overview]]
 
;Biological Pathways
 
;Biological Pathways
:[[Pathway Tools | The Pathway Tools biochemical pathways suite]] [http://biocyc.org/samples.shtml [demo]]
+
:[[Pathway Tools | Pathway Tools: Biochemical pathways suite]] [http://biocyc.org/samples.shtml [demo]]
 
;Infrastructure
 
;Infrastructure
:[[Chado | The Chado modular biological database schema]]
+
:[[GMODWeb | GMODWeb: Biological database website]]  
:[[GMODWeb | The GMODWeb biological database website]]  
+
 
:[http://gmod-ware.sourceforge.net Modware: Middleware for Chado]
 
:[http://gmod-ware.sourceforge.net Modware: Middleware for Chado]
 
|}
 
|}

Revision as of 09:43, 3 October 2007

Welcome to GMOD

Popular GMOD Tools
Genome Browsing and Editing
Apollo: Genome annotation editor [screenshot]
GBrowse: Genome annotation viewer [demo]
Comparative Genetic and Sequence Maps
CMap: Comparative genetic map viewer [screenshot]
Sybil: Comparative genome viewer [screenshots]
SynBrowse: Genome synteny viewer [demo]
Database Tools
Chado: Modular biological database schema
BioMart: Genome data mining system [overview]
Biological Pathways
Pathway Tools: Biochemical pathways suite [demo]
Infrastructure
GMODWeb: Biological database website
Modware: Middleware for Chado

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.

How do I Get Started?

Visit the projects described in the box to the right, or visit GMOD Components for a comprehensive list of all GMOD tools.

How do I Get Support?

We provide support via mailing lists, a set of FAQs, and a Help Desk.

How do I Get Involved?

See the GMOD Project Page for new projects in need of ideas and developers. Or join one of the GMOD Mailing Lists to get a feel for how the project is organized.

For information about the GMOD hackathon, see the Hackathon 2007 info page.

About the Project

The Generic Model Organism Database project is an open source project to develop a complete set of software for creating and administering an organism database, or MOD. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is funded by the NIH and the USDA Agricultural Research Service and National Science Foundation. Participation draws from members of several database projects including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, DictyBase, wFleaBase, NESCent, Saccharomyces Genome Database and BeeBase (See also MOD list).

Contributing Organizations

Fly_logo.png Wdb_small.gif Daphnia-wfleabase2.png Gramene_logo180.jpg TAIR_logo.gif Nescent_logo.gif SGD-t.gif Mgi_logo.jpg DictyLogo.png Rgd-logo.gif BioCycDC.gif Ecoliwiki.png