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__NOTOC__
 
__NOTOC__
<!-- Define the right hand sidebar.
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<div id="MainCompBox" class="componentBox">
  - News: List from GMOD News RSS feed, defined on GMOD News page.
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<div class="compBoxHdr clear">GMOD is Social</div>
  -    Lists first 9 news items
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<div class="zero">
  - New & Revised pages: Automatically populated from Special:Recentchanges.
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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!]]
  -    Lists last 10 changes/additions and EXCLUDES minor edits.
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  - Popular GMOD Tools: This list changes slowly and is manually maintained
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  -    by the GMOD help desk.
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  -->
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{| align="right" class="toc plainlinks" style="margin-left: 0.5em; width: 20em"
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|- align="center"
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| {{#icon: April2012MeetingLogo.png|April 2012 GMOD Meeting|170|April 2012 GMOD Meeting}}<br />Following [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012]<br />[[April 2012 GMOD Meeting|Registration is open]]
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|- align="center" bgcolor="lightblue"
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| <div style="float: left; padding-left: 6em">'''[[GMOD News]]''' {{#icon: RSSIcon16x16.gif|RSS feed||{{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed}}</div> <div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div><br />
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|- align="center"
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| <rss time="1800" number="10" desc="off" title="off">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>
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|- align="center" bgcolor="lightblue"
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| '''[[Special:Recentchanges|New &amp; Revised Pages]]'''  {{#icon: RSSIcon16x16.gif|All recent changes feed||http://gmod.org/mediawiki/index.php?title=Special:Recentchanges&feed=rss}}
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|- align="center"
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|
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<news unique nominor nobot namespaces="main|talk">
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&bull; [[{{{pagename}}}]]
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</news>
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|- align="center" bgcolor="lightblue"
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| '''Popular [[GMOD Components|GMOD Tools]]'''
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|-
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|
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'''Genome Browsing and Editing'''
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<br />&nbsp;&nbsp;[[GBrowse|GBrowse: Genome annotation viewer]]
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<br />&nbsp;&nbsp;[[Apollo|Apollo: Genome annotation editor]]
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<br />'''Comparative Genomics'''
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<br />&nbsp;&nbsp;[[CMap|CMap: Comparative map viewer]]
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<br />&nbsp;&nbsp;[[GBrowse_syn|GBrowse_syn: Synteny viewer]]
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<br />'''Database Tools'''
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<br />&nbsp;&nbsp;[[Chado|Chado: Biological database schema]]
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<br />&nbsp;&nbsp;[[BioMart|BioMart: Data mining system]]
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<br />&nbsp;&nbsp;[[GMODTools|GMODTools: Chado to Fasta, GFF, ...]]
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<br />&nbsp;&nbsp;[[InterMine|InterMine: Data warehousing]]
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<br />&nbsp;&nbsp;[[Tripal|Tripal: Chado web interface]]
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<br />'''Analysis and Annotation'''
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<br />&nbsp;&nbsp;[[Galaxy|Galaxy: Data analysis & integration]]
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<br />&nbsp;&nbsp;[[MAKER|MAKER: Genome annotation pipeline]]
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<br />'''Biological Pathways'''
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<br />&nbsp;&nbsp;[[Pathway Tools|Pathway Tools: Metabolic, regulatory]]
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<br />'''Publication Curation'''
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<br />&nbsp;&nbsp;[[Textpresso|Textpresso: text mining]]
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|}
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=Welcome to GMOD=
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[http://twitter.com/gmodproject Follow '''The Tweet of GMOD''']<br>
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[http://twitter.com/gmodproject @gmodproject]
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</div>
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<div class="zero clear">
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[[File:LinkedInLogo-60px.png|left|link=http://www.linkedin.com/groups?gid=131368&trk=group-name|GMOD group on LinkedIn]]
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[http://www.linkedin.com/groups?gid=131368&trk=group-name Join other '''GMOD users''' on LinkedIn]
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</div>
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<div class="zero clear">
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[[File:MendeleyLogo-horiz.jpg|50px|right|link=http://mnd.ly/WwRe8F|GMOD group on Mendeley]]
  
'''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. GMOD tools are in use at [[MOD|many large and small community databases]].
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Keep up with GMOD papers and contribute your own in the '''[http://mnd.ly/WwRe8F GMOD group on Mendeley]'''
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</div>
 +
<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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<!-- <rss max="10">http://gmod.org/mediawiki/index.php?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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<news unique nominor nobot namespaces="main|talk">
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[[{{{pagename}}}]] &bull;
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</news> -->
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</div>
  
=== How do I Get Started? ===
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<div class="intro">
 +
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]]. -->
 +
</div>
  
See [[Overview]] for the big picture.  For an introduction to specific GMOD components see the list of the most popular tools at the right, 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]].
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=== Get Started ===
  
=== How do I Get Support? ===
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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]].
 +
 
 +
=== 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.
 
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.
  
=== How do I Get Involved? ===
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=== Get Involved ===
<!-- {{ImageRight|GMODAmericas2011Logo.jpg|GMOD Americas 2011|90|GMOD Americas 2011}} -->
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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 next project meeting will be held in [[April 2012 GMOD Meeting|April 2012]] in Washington, DC.
+
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]].
 +
 
 +
 
 +
 
 +
=== Popular GMOD Tools ===
 +
 
 +
See the [[GMOD Components|full list of GMOD components]]
 +
 
 +
<div class="logos">
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[[File:GitcLogo.png|250px|thumb|none|link=Cloud|GMOD in the Cloud toolset]]
 +
[[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]]
 +
[[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]]
 +
[[File:ChadoLogo.png|250px|thumb|none|link=Chado|Chado: Biological database schema]]
 +
[[File:JBrowseLogo.png|250px|thumb|none|link=JBrowse|JBrowse: Super-fast genome annotation viewer]]
 +
[[File:Biomart250.png|250px|thumb|none|link=BioMart|BioMart: Data mining system]]
 +
[[File:WebApolloLogo.png|250px|thumb|none|link=WebApollo|WebApollo: browser-based annotation editor]]
 +
[[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]]
 +
</div>
 +
 
  
==== Contributing Organizations ====
 
  
<!-- Please scale any icons to be the same size as the
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<!-- {{Template:Organisations}} -->
  - existing icons when adding it to this list.
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  -->
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<div class="imagecloud"><center>
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{{#icon: FlyBaseMainPageIcon.png|FlyBase||http://www.flybase.org/}}
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{{#icon: Wdb_small.gif|WormBase||http://www.wormbase.org/}}
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{{#icon: WFleaBaseMainPageIcon.png|wFleaBase||http://wfleabase.org/}}
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{{#icon: CSHL_Logo75x75.gif|CSHL||http://www.cshl.edu/}}
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{{#icon: GrameneMainPageIcon.jpg|Gramene||http://www.gramene.org/}}
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{{#icon: NESCentMainPageIcon.png|NESCent||http://www.nescent.org/}}
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{{#icon: SGD-t.gif|SGD||http://www.yeastgenome.org/}}
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{{#icon: MgiMainPageLogo.jpg|MGI||http://www.informatics.jax.org/}}
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{{#icon: DictyMainPageLogo.png|DictyBase||http://dictybase.org/}}
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{{#icon: RgdRatLogo.png|RGD||http://rgd.mcw.edu/}}&nbsp;&nbsp;
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{{#icon: BioCycMainPageLogo.gif|BioCyc||http://www.biocyc.org/}}
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{{#icon: UtahLogoU75.png|University of Utah|60|http://www.genetics.utah.edu/}}
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{{#icon: Ecoliwiki.png|EcoliWiki||http://ecoliwiki.net/}}
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{{#icon: Lbl_logo.png|Berkeley Lab|95|http://berkeleybop.org/}}
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{{#icon: ParameciumDBIcon133x42.png|ParameciumDB||http://paramecium.cgm.cnrs-gif.fr/}}
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{{#icon: Sgn small tag.png|SGN||http://www.sgn.cornell.edu/}}
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{{#icon: FlyMineLogo.png|FlyMine|65|http://flymine.org/}}
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{{#icon: OICRlogo.png|OICR||http://www.oicr.on.ca/}}
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{{#icon: CUGILogoHomePage.png|CUGI||http://www.genome.clemson.edu/}}
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{{#icon: PennState.gif|Penn State University||http://usegalaxy.org/}}
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{{#icon: IPlant Logo Trans Small.png|iPlant||http://iplantcollaborative.org/}}
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{{#icon: Cgb-logo-transparent.png|Center for Genomics and Bioinformatics|55|http://cgb.indiana.edu/}}
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{{#icon: EmoryLogoSmall.gif|Emory University||http://usegalaxy.org}}
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{{#icon: Berkeley-text.png|University of California Berkeley|120|http://biowiki.org/}}
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{{#icon: TAIR_logo.gif|TAIR||http://www.arabidopsis.org/}}
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{{#icon: 150px-WSULogo.png|Washington State University||http://www.bioinfo.wsu.edu/}}
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{{#icon: 150px-USLogo.png|University of Saskatchewan||http://www.usask.ca/}}
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</center></div>
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Latest revision as of 14:41, 3 November 2016

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

GMOD in the Cloud toolset
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