Difference between revisions of "Main Page"

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(Revamped home page. Tweaked text, dropped about project section as redundant, added news and new/revised pages to right bar and narrowed right bar. Added parameciumDB icon)
(Popular GMOD Tools)
 
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=<font color="navy blue">Welcome to GMOD</font>=
 
 
__NOTOC__
 
__NOTOC__
<!-- Define the right hand sidebar.
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<div id="MainCompBox" class="componentBox">
  - All sections of the sidebarhis bar are MANUALLY maintained. 
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<div class="compBoxHdr clear">GMOD is Social</div>
  - The GMOD Help Desk, a.k.a., Dave Clements, attempts to maintain News and
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<div class="zero">
  - New/Updated Pages twice a week.
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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!]]
  - Why manually maintain these lists?
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  -  News: Some news ages more quickly than others.  These items
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  -        will be dropped from the sidebar sooner than others.
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  -  New & Revised pages: Not every new page is ready for announcement
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  -        when it is created, and not every new page is important
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  -        enough to go on the home page
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  -  Popular GMOD Tools: This list changes slowly.
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  -->
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{| align="right" class="toc" style="margin-left: 0.5em; width: 19em"
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|- align="center" bgcolor="lightblue"
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| <span class="plainlinks">'''[[GMOD News]]''' [http://gmod.org/wiki/index.php?title=GMOD_News&action=feed&feed=rss http://gmod.org/wiki/images/4/47/RSSIcon16x16.gif]</span>
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|- align="center"
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|
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[[GMOD News#Modware Feedback Wanted|Modware Feedback Wanted]]
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<br />[[GMOD News#November 2007 GMOD Meeting|November 2007 GMOD Meeting]]
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<br />[[GMOD News#GMODTools 1.1 Released|GMODTools 1.1 Released]]
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<br />[[GMOD News#GMOD Help Desk is Back|GMOD Help Desk is Back]]
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<br />[[GMOD News#FlyBase Converts to Chado|FlyBase Converts to Chado]]
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<br />[[GMOD News#Pathway Tools 11.5 Released|Pathway Tools 11.5 Released]]
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<br />[[GMOD News#ISMB/Bioinformatics Chado Paper|ISMB/Bioinformatics Chado Paper]]
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<br />[[GMOD News#BioMart 0.6 Released|BioMart 0.6 Released]]
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<br />[[GMOD News#GBrowse 1.68 Released|GBrowse 1.68 Released]]
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|- align="center" bgcolor="lightblue"
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| '''New &amp; Revised Pages'''
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|- align="center"
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|
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[[Glossary]]
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&bull; [[PostgreSQL]]
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&bull; [[Databases and GMOD]]
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&bull; [[Computing Requirements]]
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&bull; [[Materialized views]]
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&bull; [[GMOD News]]
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&bull; [[Finding Support]]
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&bull; [[GMOD Mailing Lists]]
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&bull; [[Installing Chado on Ubuntu HOWTO]]
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&bull; [[GBrowse/AJAXhandlerScript]]
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|- align="center" bgcolor="lightblue"
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| '''Popular 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;[[Apollo|Apollo: Genome annotation editor]]
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<br />&nbsp;&nbsp;[[GBrowse|GBrowse: Genome annotation viewer]]
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<br />'''Comparative Maps'''
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<br />&nbsp;&nbsp;[[CMap|CMap: Comparative map viewer]]
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<br />&nbsp;&nbsp;[[Sybil|Sybil: Comparative genome 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 />'''Biological Pathways'''
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<br />&nbsp;&nbsp;[[Pathway Tools|Pathway Tools: Metabolic, regulatory]]
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<br />'''Infrastructure'''
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<br />&nbsp;&nbsp;[[GMODWeb|GMODWeb: Website for Chado DBs]]  
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<br />&nbsp;&nbsp;[[Modware|Modware: Middleware for Chado]]
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|}
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'''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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[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>
  
===<font color="navy blue">How do I Get Started?</font>===
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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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<!-- <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>
  
For a project overview see [[GMOD for the Biologist]]. For an introduction to specific GMOD components see the list of the most popular tools at the right, or visit [[GMOD_Components|GMOD Components]] for a comprehensive list of GMOD tools.
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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>
  
===<font color="navy blue">How do I Get Support?</font>===
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=== Get Started ===
  
GMOD support is available from several different sources. [[Finding Support]] introduces each support option (this web site, [[GMOD Mailing Lists]], and the [[GMOD Help Desk]]) and offers guidance on which one is the most appropriate for your question.
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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]].
  
===<font color="navy blue">How do I Get Involved?</font>===
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=== Get Support ===
  
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.  [[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.
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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.
  
You can also attend project meetings.  See [[November 2007 GMOD Meeting]] and [[Hackathon 2007 info]] for summaries of the two most recent meetings.
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=== Get Involved ===
  
====<font color="navy blue">Contributing Organizations</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]].
  
<!-- Please scale any icons to be the same size as the
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  - existing icons before adding it to this list.
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  -->
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=== Popular GMOD Tools ===
<span class="plainlinks"><center>
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[http://www.flybase.org/ http://www.gmod.org/wiki/images/3/38/FlyBaseMainPageIcon.png]&nbsp;&nbsp;
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See the [[GMOD Components|full list of GMOD components]]
[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/1/15/WFleaBaseMainPageIcon.png]&nbsp;&nbsp;
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<div class="logos">
[http://www.gramene.org/ http://www.gmod.org/wiki/images/4/49/GrameneMainPageIcon.jpg]&nbsp;&nbsp;&nbsp;&nbsp;
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[[File:Jbrowse2_logo.png|250px|thumb|none|link=JBrowse|JBrowse 2: New super-fast genome annotation viewer]]
[http://www.arabidopsis.org/ http://www.gmod.org/wiki/images/7/7c/TAIR_logo.gif]
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[[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]]
[http://www.nescent.org/ http://www.gmod.org/wiki/images/c/c7/NESCentMainPageIcon.png]
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[[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]]
[http://www.yeastgenome.org/ http://www.gmod.org/wiki/images/8/8f/SGD-t.gif]
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[[File:ChadoLogo.png|250px|thumb|none|link=Chado|Chado: Biological database schema]]
[http://www.informatics.jax.org/ http://www.gmod.org/wiki/images/4/4f/MgiMainPageLogo.jpg]
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[[File:JBrowseLogo.png|250px|thumb|none|link=JBrowse|JBrowse: Super-fast genome annotation viewer]]
[http://dictybase.org/ http://www.gmod.org/wiki/images/a/a8/DictyMainPageLogo.png]&nbsp;&nbsp;
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[[File:Biomart250.png|250px|thumb|none|link=BioMart|BioMart: Data mining system]]
[http://rgd.mcw.edu/ http://gmod.org/wiki/images/c/c7/RgdMainPageIcon.gif]&nbsp;&nbsp;
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[[File:WebApolloLogo.png|250px|thumb|none|link=WebApollo|WebApollo: browser-based annotation editor]]
[http://www.biocyc.org/ http://gmod.org/wiki/images/8/8f/BioCycMainPageLogo.gif]&nbsp;&nbsp;
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[[File:MAKERLogo.png|250px|thumb|none|link=MAKER|MAKER: Genome annotation pipeline]]
[http://smedgd.neuro.utah.edu/ http://gmod.org/wiki/images/1/12/InfinityPlanaria58x72.png]&nbsp;&nbsp;&nbsp;
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[[File:GBrowse_syn_logo.png|250px|thumb|none|link=GBrowse_syn|GBrowse_syn: Synteny viewer]]
[http://ecoliwiki.net/ http://gmod.org/wiki/images/e/ed/Ecoliwiki.png]&nbsp;&nbsp;
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[[File:TripalLogo.png|250px|thumb|none|link=Tripal|Tripal: Chado web interface]]
[http://parameciumdb.org/ http://gmod.org/wiki/images/2/24/ParameciumDBIcon133x42.png]
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[[File:InterMineLogo.png|250px|thumb|none|link=InterMine|InterMine: Data warehousing]]
</center></span>
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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