Difference between revisions of "Main Page"

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The Generic Model Organism Database (GMOD) Project is a largely open source project to develop a complete set of software for creating and administering a model organism database. 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 NIH and the USDA Agricultural Research Service, with participation from members of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. For more information, please see http://www.gmod.org/ or contact [[mailto:cain@cshl.edu Scott Cain <cain@cshl.edu>]].
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* GMOD Core (Chado database and tools)<br />
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*; [[gmod-core]]
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*: the schema and tools to install it. [[[/chado_from_cvs From cvs]]]<br />
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*; [[XORT]]
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*: 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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*; [[/gmodtools GMODTools]]
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*: 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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* MOD website<br />
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*; [http://turnkey.sf.net gmod-web/Turnkey]
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*: a generic web front end for browsing database contents.<br />
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* Genome Editing and Visualization<br />
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*; [[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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*; [[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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* Comparative Genomics<br />
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*; [[Synbrowse]]
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*: a GBrowse based synteny viewer [[[http://www.synbrowse.org/download.html Download]]]<br />
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*; [[CMap]]
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*: 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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*; [[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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*; [[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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* Database querying tools<br />
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*; [http://www.biomart.org/ BioMart]
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*: a query-oriented data management system [[[http://www.biomart.org/install.html Download]]]

Revision as of 18:13, 25 January 2007


  • GMOD Core (Chado database and tools)
    gmod-core
    the schema and tools to install it. [[[/chado_from_cvs From cvs]]]
    XORT
    a tool for loading and dumping chado-xml [[Download]]
    /gmodtools GMODTools
    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]]]
  • MOD website
    gmod-web/Turnkey
    a generic web front end for browsing database contents.
  • Genome Editing and Visualization
    Apollo
    a Java application for viewing and editing genome annotations [[Download]]
    GBrowse
    a CGI application for displaying genome annotations [[Download]]
  • Comparative Genomics
    Synbrowse
    a GBrowse based synteny viewer [[Download]]
    CMap
    a CGI application for displaying comparative maps [[Download]]
  • Literature curation
    PubSearch
    a Java servlet web application for annotating genes from literature [[Download]]
    PubFetch
    a tool to facilitate literature collection for curators' use [[Download]]
    Textpresso
    a text mining system for scientific literature [[Download]]
  • Database querying tools
    BioMart
    a query-oriented data management system [[Download]]