Difference between revisions of "Main Page"

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<div id="MainCompBox" class="componentBox">
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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!]]
  
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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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[[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>
  
* GMOD Core (Chado database and tools)<br />
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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>
*; [[gmod-core]]
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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>-->
*: the schema and tools to install it. [[[/chado_from_cvs From cvs]]]<br />
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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>
*; [[XORT]]
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<news unique nominor nobot namespaces="main|talk">
*: a tool for loading and dumping chado-xml [[[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=148718 Download]]]<br />
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[[{{{pagename}}}]] &bull;
*; [[/gmodtools GMODTools]]
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</news> -->
*: a collection of tools for extracting data from a chado database and formatting it in common bulk download formats (GFF, Fasta, etc) [[[/chado_from_cvs Included in schema cvs]]]<br />
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</div>
* MOD website<br />
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*; [http://turnkey.sf.net gmod-web/Turnkey]
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<div class="intro">
*: a generic web front end for browsing database contents.<br />
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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]]. -->
* Genome Editing and Visualization<br />
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</div>
*; [[Apollo]]
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*: a Java application for viewing and editing genome annotations [[[http://www.fruitfly.org/annot/apollo/install.html Download]]]<br />
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=== Get Started ===
*; [[GBrowse]]
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*: a CGI application for displaying genome annotations [[[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513 Download]]]<br />
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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]].
* Comparative Genomics<br />
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*; [[Synbrowse]]
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=== Get Support ===
*: a GBrowse based synteny viewer [[[http://www.synbrowse.org/download.html Download]]]<br />
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*; [[CMap]]
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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.
*: a CGI application for displaying comparative maps [[[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129 Download]]]<br />
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* Literature curation<br />
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=== Get Involved ===
*; [[PubSearch]]
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*: a Java servlet web application for annotating genes from literature [[[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=100560 Download]]]<br />
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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]].
*; [[PubFetch]]
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*: a tool to facilitate literature collection for curators' use [[[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=126656 Download]]]<br />
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*; [[Textpresso]]
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*: a text mining system for scientific literature [[[http://textpresso.org/textpresso/downloads.html Download]]]<br />
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=== Popular GMOD Tools ===
* Database querying tools<br />
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*; [http://www.biomart.org/ BioMart]
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See the [[GMOD Components|full list of GMOD components]]
*: a query-oriented data management system [[[http://www.biomart.org/install.html Download]]]
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<div class="logos">
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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