Difference between revisions of "Main Page"

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m (→‎<font color="navy blue">Welcome to GMOD</font>)
(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)
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=<font color="navy blue">Welcome to GMOD</font>=
 
=<font color="navy blue">Welcome to GMOD</font>=
 
__NOTOC__
 
__NOTOC__
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<big>Click for information about the [[November 2007 GMOD Meeting]].</big>
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<!-- Define the right hand sidebar.
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<hr/>
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  - All sections of the sidebarhis bar are MANUALLY maintained. 
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{| align="right" class="toc" style="margin-left: 0.5em"
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  - The GMOD Help Desk, a.k.a., Dave Clements, attempts to maintain News and
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  - New/Updated Pages twice a week.
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  - 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]]
 
|- align="center" bgcolor="lightblue"
 
|- align="center" bgcolor="lightblue"
 
| '''Popular GMOD Tools'''
 
| '''Popular GMOD Tools'''
 
|-  
 
|-  
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|
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|  
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;Genome Browsing and Editing
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'''Genome Browsing and Editing'''
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:[[Apollo | Apollo: Genome annotation editor]] [http://www.fruitfly.org/annot/apollo/images/mainwindow.jpg [screenshot]]
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<br />&nbsp;&nbsp;[[Apollo|Apollo: Genome annotation editor]]
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:[[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]]
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<br />&nbsp;&nbsp;[[GBrowse|GBrowse: Genome annotation viewer]]  
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:[[Pathway Tools | Pathway Tools microbial genome browser]] [http://biocyc.org/samples.shtml [demo]]
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<br />'''Comparative Maps'''
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;Comparative Genetic and Sequence Maps
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<br />&nbsp;&nbsp;[[CMap|CMap: Comparative map viewer]]  
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:[[CMap | CMap: Comparative genomic map viewer]] [http://www.gmod.org/wiki/index.php/Image:Cmap_sample1.jpg [screenshot]]
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<br />&nbsp;&nbsp;[[Sybil|Sybil: Comparative genome viewer]]  
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:[[Sybil | Sybil: Comparative genome viewer]] [http://sybil.sourceforge.net/index.html#screenshots [screenshots]]
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<br />'''Database Tools'''
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:[[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]]
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<br />&nbsp;&nbsp;[[Chado|Chado: Biological database schema]]
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;Database Tools
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<br />&nbsp;&nbsp;[[BioMart|BioMart: Data mining system]]  
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:[[Chado | Chado: Modular biological database schema]]
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<br />&nbsp;&nbsp;[[GMODTools|GMODTools: Chado to Fasta, GFF, ...]]  
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:[[BioMart | BioMart: Genome data mining system ]] [http://www.biomart.org/ [overview]]
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<br />'''Biological Pathways'''
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;Biological Pathways
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<br />&nbsp;&nbsp;[[Pathway Tools|Pathway Tools: Metabolic, regulatory]]
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:[[Pathway Tools | Pathway Tools: Metabolic and regulatory pathways]] [http://biocyc.org/samples.shtml [demo]]
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<br />'''Infrastructure'''
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;Infrastructure
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<br />&nbsp;&nbsp;[[GMODWeb|GMODWeb: Website for Chado DBs]]  
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:[[GMODWeb | GMODWeb: Biological database website]]  
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<br />&nbsp;&nbsp;[[Modware|Modware: Middleware for Chado]]
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:[[Modware | Modware: Middleware for Chado]]
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|}
 
|}
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'''GMOD''' is the '''G'''eneric '''M'''odel '''O'''rganism '''D'''atabase 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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'''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]].
  
 
===<font color="navy blue">How do I Get Started?</font>===
 
===<font color="navy blue">How do I Get Started?</font>===
  
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For a project overview see [[GMOD for the Biologist]].  For an introduction to specific GMOD components see the list at the right, or visit [[GMOD_Components|GMOD Components]] for a comprehensive list of GMOD tools.
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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.
  
 
===<font color="navy blue">How do I Get Support?</font>===
 
===<font color="navy blue">How do I Get Support?</font>===
  
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We provide support via [[GMOD_Mailing_Lists | mailing lists]], a set of [[: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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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.
  
 
===<font color="navy blue">How do I Get Involved?</font>===
 
===<font color="navy blue">How do I Get Involved?</font>===
  
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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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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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For information about the GMOD hackathon, see the [[Hackathon 2007 info]] page.
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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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===<font color="navy blue">About the Project</font>===
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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).
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====<font color="navy blue">Contributing Organizations</font>====
 
====<font color="navy blue">Contributing Organizations</font>====
  
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[http://www.flybase.org/ http://www.gmod.org/wiki/images/3/38/FlyBaseMainPageIcon.png]&nbsp;&nbsp;
 
[http://www.flybase.org/ http://www.gmod.org/wiki/images/3/38/FlyBaseMainPageIcon.png]&nbsp;&nbsp;
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[http://rgd.mcw.edu/ http://gmod.org/wiki/images/c/c7/RgdMainPageIcon.gif]&nbsp;&nbsp;
 
[http://rgd.mcw.edu/ http://gmod.org/wiki/images/c/c7/RgdMainPageIcon.gif]&nbsp;&nbsp;
 
[http://www.biocyc.org/ http://gmod.org/wiki/images/8/8f/BioCycMainPageLogo.gif]&nbsp;&nbsp;
 
[http://www.biocyc.org/ http://gmod.org/wiki/images/8/8f/BioCycMainPageLogo.gif]&nbsp;&nbsp;
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[http://smedgd.neuro.utah.edu/ http://gmod.org/wiki/images/1/12/InfinityPlanaria58x72.png]&nbsp;&nbsp;&nbsp;
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[http://ecoliwiki.net/ http://gmod.org/wiki/images/e/ed/Ecoliwiki.png]&nbsp;&nbsp;
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[http://parameciumdb.org/ http://gmod.org/wiki/images/2/24/ParameciumDBIcon133x42.png]
 
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Revision as of 18:50, 14 December 2007

Welcome to GMOD

GMOD News RSSIcon16x16.gif

Modware Feedback Wanted
November 2007 GMOD Meeting
GMODTools 1.1 Released
GMOD Help Desk is Back
FlyBase Converts to Chado
Pathway Tools 11.5 Released
ISMB/Bioinformatics Chado Paper
BioMart 0.6 Released
GBrowse 1.68 Released

New & Revised Pages

Glossary • PostgreSQL • Databases and GMOD • Computing Requirements • Materialized views • GMOD News • Finding Support • GMOD Mailing Lists • Installing Chado on Ubuntu HOWTO • GBrowse/AJAXhandlerScript

Popular GMOD Tools

Genome Browsing and Editing
  Apollo: Genome annotation editor
  GBrowse: Genome annotation viewer
Comparative Maps
  CMap: Comparative map viewer
  Sybil: Comparative genome viewer
Database Tools
  Chado: Biological database schema
  BioMart: Data mining system
  GMODTools: Chado to Fasta, GFF, ...
Biological Pathways
  Pathway Tools: Metabolic, regulatory
Infrastructure
  GMODWeb: Website for Chado DBs
  Modware: Middleware for Chado

GMOD is the Generic Model Organism Database 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 many large and small community databases.

How do I Get Started?

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 for a comprehensive list of GMOD tools.

How do I Get Support?

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.

How do I 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. The GMOD Project Page lists projects in need of ideas and developers.

You can also attend project meetings. See November 2007 GMOD Meeting and Hackathon 2007 info for summaries of the two most recent meetings.

Contributing Organizations

FlyBaseMainPageIcon.png   Wdb_small.gif WFleaBaseMainPageIcon.png   GrameneMainPageIcon.jpg     TAIR_logo.gif NESCentMainPageIcon.png SGD-t.gif MgiMainPageLogo.jpg DictyMainPageLogo.png   RgdMainPageIcon.gif   BioCycMainPageLogo.gif   InfinityPlanaria58x72.png    Ecoliwiki.png   ParameciumDBIcon133x42.png

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