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<div class="compBoxHdr clear">GMOD is Social</div>
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[[File:Gmod-bird.jpg|50px|right|link=http://twitter.com/gmodproject|It's a bird! It's a plane! It's the GMOD project on Twitter!]]
  
{| align="right" class="toc"
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[http://twitter.com/gmodproject Follow '''The Tweet of GMOD''']<br>
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[http://twitter.com/gmodproject @gmodproject]
| '''Popular GMOD Tools'''
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</div>
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[[File:LinkedInLogo-60px.png|left|link=http://www.linkedin.com/groups?gid=131368&trk=group-name|GMOD group on LinkedIn]]
;Genome Browsing and Editing
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[http://www.linkedin.com/groups?gid=131368&trk=group-name Join other '''GMOD users''' on LinkedIn]
:[[Apollo | The Apollo Genome Annotation Editor]] [http://www.fruitfly.org/annot/apollo/images/mainwindow.jpg [screenshot]]
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</div>
:[[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]]
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;Comparative Genetic and Sequence Maps
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:[[CMap | The CMap comparative genetic map viewer]] [http://www.gmod.org/wiki/index.php/Image:Cmap_sample1.jpg [screenshot]]
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:[[Sybil | The Sybil comparative genome viewer]] [http://sybil.sourceforge.net/index.html#screenshots [screenshots]]
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:[[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]]
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;Database Tools
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:[[BioMart | The BioMart genome data mining system ]] [http://www.biomart.org/ [overview]]
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;Biological Pathways
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:[[Pathway Tools | The Pathway Tools biochemical pathways suite]] [http://biocyc.org/samples.shtml [demo]]
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;Infrastructure
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:[[Chado | The Chado modular biological database schema]]
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:[[GMODWeb | The GMODWeb biological database website]]
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|}
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==<font color="navy blue">What is GMOD?</font>==
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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.
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<div class="compBoxHdr">[[GMOD News]][[File:RSSIcon16x16.gif|right|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]]<div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div></div><rss time="1800" number="10" desc="off" title="off">http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>
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<!-- <div class="compBoxHdr">[[Special:Recentchanges|New &amp; Revised Pages]][[File:RSSIcon16x16.gif|right|link=http://gmod.org/mediawiki/index.php?title=Special:Recentchanges&feed=rss|All recent changes feed]]</div>
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[[{{{pagename}}}]] &bull;
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</div>
  
==<font color="navy blue">How do I Get Started?</font>==
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<div class="intro">
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Welcome to the '''Generic Model Organism Database''' project, a collection of open source software tools for managing, visualising, storing, and disseminating genetic and genomic data.<!-- 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 [[MOD|many large and small community databases]]. -->
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</div>
  
Visit the projects described in the box to the right, or visit
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=== Get Started ===
[[GMOD_Components|GMOD Components]] for a comprehensive list of all GMOD tools.
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==<font color="navy blue">How do I Get Support?</font>==
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Read the [[Overview|GMOD overview]] for the big picture, or visit [[GMOD Components]] for a comprehensive list of GMOD tools.  If GMOD looks promising for your needs, consider attending the next [[Meetings|GMOD community meeting]].
  
We provide support via [[GMOD_Mailing_Lists | mailing lists]], a set of [http://gmod.org/wiki/index.php/Category:FAQ FAQs], and a [[GMOD Help Desk|Help Desk]]. <!--Please mail inquiries to [mailto:help@gmod.org help@gmod.org].-->
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=== Get Support ===
  
==<font color="navy blue">How do I Get Involved?</font>==
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GMOD support is available from several different sources. [[Support]] introduces each support option (this web site, [[GMOD Mailing Lists]], [[Training and Outreach]] activities (including [[GMOD Schools]]), and the [[GMOD Help Desk]]) and offers guidance on which one is the most appropriate for your question.
  
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.
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=== Get Involved ===
  
==<font color="navy blue">About the Project</font>==
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As an open source project GMOD relies on the [[GMOD Membership|donation of time and software]] by groups and individuals.  Contribution of new tools, adoption of existing ones, and [[Site Guidelines|improving the documentation]] are all welcome. [[MOD|Existing]] and potential users are encouraged to provide feedback via [[GMOD Mailing Lists|mailing lists]] or the [[GMOD Help Desk|help desk]]. <!-- The [[GMOD Project Page]] lists projects in need of ideas and developers.--> You can also attend project [[meetings]].
  
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 [http://www.nih.gov NIH] and the [http://www.ars.usda.gov/ USDA Agricultural Research Service] and [http://www.nsf.gov/ National Science Foundation].  Participation draws from members of several database projects including [http://wormbase.org WormBase], [http://flybase.org FlyBase], [http://www.informatics.jax.org/ Mouse Genome Informatics], [http://gramene.org Gramene], the [http://rgd.mcw.edu/ Rat Genome Database], [http://arabidopsis.org TAIR], [http://ecocyc.org EcoCyc], [http://dictybase.org DictyBase], [http://wfleabase.org wFleaBase], [http://www.nescent.org NESCent], [http://yeastgenome.org Saccharomyces Genome Database] and [http://racerx00.tamu.edu/bee_resources.html BeeBase] (See also [[MOD]] list).
 
  
===<font color="navy blue">Contributing Organizations</font>===
 
  
<span class="plainlinks">
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=== Popular GMOD Tools ===
[http://www.flybase.org/ http://www.gmod.org/wiki/images/e/e0/Fly_logo.png]
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[http://www.wormbase.org/ http://www.gmod.org/wiki/images/9/9d/Wdb_small.gif]
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[http://wfleabase.org/ http://www.gmod.org/wiki/images/4/4d/Daphnia-wfleabase2.png]
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[http://www.gramene.org/ http://www.gmod.org/wiki/images/5/59/Gramene_logo180.jpg]
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[http://www.arabidopsis.org/ http://www.gmod.org/wiki/images/7/7c/TAIR_logo.gif]
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[http://www.nescent.org/ http://www.gmod.org/wiki/images/d/dc/Nescent_logo.gif]
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[http://www.yeastgenome.org/ http://www.gmod.org/wiki/images/8/8f/SGD-t.gif]
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[http://www.informatics.jax.org/ http://www.gmod.org/wiki/images/0/07/Mgi_logo.jpg]
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[http://dictybase.org/ http://www.gmod.org/wiki/images/6/69/DictyLogo.png]
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[http://rgd.mcw.edu/ http://www.gmod.org/wiki/images/e/ed/Rgd-logo.gif]
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[http://www.biocyc.org/ http://www.gmod.org/wiki/images/6/65/BioCycDC.gif]
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[http://ecoliwiki.net/ http://gmod.org/wiki/images/e/ed/Ecoliwiki.png]
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</span>
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<!--
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See the [[GMOD Components|full list of GMOD components]]
<blockquote style="background: white; border: 1px solid aquamarine; padding: 1em;">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[Image:All-Mods.png]]
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<div class="logos">
</blockquote>
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[[File:Jbrowse2_logo.png|250px|thumb|none|link=JBrowse|JBrowse 2: New super-fast genome annotation viewer]]
-->
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[[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]]
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[[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]]
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[[File:ChadoLogo.png|250px|thumb|none|link=Chado|Chado: Biological database schema]]
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[[File:JBrowseLogo.png|250px|thumb|none|link=JBrowse|JBrowse: Super-fast genome annotation viewer]]
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[[File:Biomart250.png|250px|thumb|none|link=BioMart|BioMart: Data mining system]]
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[[File:WebApolloLogo.png|250px|thumb|none|link=WebApollo|WebApollo: browser-based annotation editor]]
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[[File:MAKERLogo.png|250px|thumb|none|link=MAKER|MAKER: Genome annotation pipeline]]
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[[File:GBrowse_syn_logo.png|250px|thumb|none|link=GBrowse_syn|GBrowse_syn: Synteny viewer]]
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[[File:TripalLogo.png|250px|thumb|none|link=Tripal|Tripal: Chado web interface]]
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[[File:InterMineLogo.png|250px|thumb|none|link=InterMine|InterMine: Data warehousing]]
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[[File:CMapLogo-horiz.png|250px|thumb|none|link=CMap|CMap: Comparative map viewer]]
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[[File:PathwayTools.png|250px|thumb|none|link=Pathway_Tools|Pathway Tools: Metabolic, regulatory pathways]]
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[[File:CantoTextLogo.png|250px|thumb|none|link=Canto|Canto: literature annotation tool]]
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</div>
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<!-- {{Template:Organisations}} -->

Latest revision as of 18:22, 30 March 2021

Welcome to the Generic Model Organism Database project, a collection of open source software tools for managing, visualising, storing, and disseminating genetic and genomic data.

Get Started

Read the GMOD overview for the big picture, or visit GMOD Components for a comprehensive list of GMOD tools. If GMOD looks promising for your needs, consider attending the next GMOD community meeting.

Get Support

GMOD support is available from several different sources. Support introduces each support option (this web site, GMOD Mailing Lists, Training and Outreach activities (including GMOD Schools), and the GMOD Help Desk) and offers guidance on which one is the most appropriate for your question.

Get Involved

As an open source project GMOD relies on the donation of time and software by groups and individuals. Contribution of new tools, adoption of existing ones, and improving the documentation are all welcome. Existing and potential users are encouraged to provide feedback via mailing lists or the help desk. You can also attend project meetings.


Popular GMOD Tools

See the full list of GMOD components

JBrowse 2: New super-fast genome annotation viewer
GBrowse: Genome annotation viewer
Galaxy: Data analysis & integration
Chado: Biological database schema
JBrowse: Super-fast genome annotation viewer
BioMart: Data mining system
WebApollo: browser-based annotation editor
MAKER: Genome annotation pipeline
GBrowse_syn: Synteny viewer
Tripal: Chado web interface
InterMine: Data warehousing
CMap: Comparative map viewer
Pathway Tools: Metabolic, regulatory pathways
Canto: literature annotation tool