2007genomeinformaticsgmodposter.ppt - Main Page - GMOD by gjjur4356


									                                               Digesting the Genome Glut
                                      Promoting the Use and Extension of GMOD
                                           To Emerging Model Organisms
                 GMOD.org                    David Clements1 Brian Osborne2 Hilmar Lapp1 Xianhua Liu1
                                                  W. Owen McMillan3 Nassib Nassar4 Todd J. Vision1                                               NESCent.org
                     1National   Evolutionary Synthesis Center 2ZBio LLC 3North Carolina State University 4Renaissance Computing Institute

                                   Abstract                                                                 Getting Started with GMOD
An ever-increasing volume of genomic data is being generated from                                                                                      Contribute doc!
                                                                                       Start at GMOD.org
organisms well suited to comparative genomic, evolutionary and                                                                                        GMOD.org is a wiki.
ecological studies. More data offers more potential for discovery,                     Download software                                               The most popular
but it also makes it is harder to organize, visualize and annotate.                                                                                   GMOD components.
                                                                                       FAQs and HOWTOs
The Generic Model Organism Database                                                                                                                    GMOD Support
(GMOD, http://gmod.org) is a toolkit of                                               GMOD for the Biologist                                      Helpdesk: help@gmod.org
interconnected components that meet                                                                                                               and mailing lists for each
                                                                                       GMOD Mailing Lists                                             GMOD Component
many of the data management, analysis,
and visualization needs of these studies,                                              Feature requests &                                              Contribute code!
                                                                                          Bug Reports                                                GMOD is open source.
and on a small informatics budget.
GMOD has recently added a helpdesk to promote use of GMOD more
broadly in emerging model organism research communities. GMOD                                 In the past year, the GMOD web site has been revamped
has also been extended to better support evolutionary research.                               and a GMOD Helpdesk (help@gmod.org) has been created.

                       What Can GMOD Do?                                                               GMOD for Natural Diversity Data
GMOD is a collection of software tools for creating and managing                      Heliconius butterflies are a favored model for studying mimicry,
genome-scale biological databases. You can use it to create a small                   because geographically overlapping populations of different species
laboratory database of genome annotations, or a large web-                            frequently converge on similar wing color patterns. Complementing
accessible community database. GMOD includes a modular                                the long history of evolutionary genetic studies in the genus, an
database schema called Chado that supports many common needs.                         increasing amount of molecular marker and sequence data are being
    If you have         & you need to           then GMOD can help with
                        View               GBrowse                                    To capture the diversity data in a GMOD-compatible way, Chado
Genomic Sequence        Annotate           Apollo                                     (GMOD’s relational data model) has been extended with the
                        Organize           Chado Sequence Module                      ‘diversity’ module (see http://sf.net/projects/heliconiusdb). The
                        View               CMap,SynView,SynBrowse,Sybil               module supports stocks, individuals, pedigrees, cross experiments,
Physical, Genetic &                                                                   geolocations, and phenotype and genotype experiments. In
                        Annotate           Sybil
Comparative Maps
                        Organize           Chado Map Module                           addition, some of Chado’s core modules have been revised to
                        Organize           Chado Organism & Phylogeny modules         consolidate how organism relationships and phylogenetic trees are
Phylogenetic Trees
                        View               GMODWeb                                    represented.
Phenotype,              Organize           Chado Genetics Module
Genotype                View               GMODWeb
Microarray and          View               Java TreeView, Caryoscope, GeneXplorer
Expression              Organize           Chado Mage and Expression Modules
                        Curate             Chado CV module
                        View               GO Term Viewer, GMODWeb
                        Organize           Chado Organism & Phylogeny modules
Phylogenetic Trees
                        View               GMODWeb                                    Entity graph of the ‘diversity’ extension to Chado,
                        Curate, search     TextPresso, PubSearch                      and architecture and Web GUI for HeliconiusDB, an
Publications                                                                          evolutionary model database.
                        Organize           Chado Publication Module

    The National Evolutionary Synthesis Center (NESCent)
   Sponsors Synthetic, Interdisciplinary and Transformative
              Research in Evolutionary Biology.
The center hosts working groups,              NESCent is located in Durham
catalysis meetings, sabbaticals, post-        NC and is a collaborative
doctoral fellowships, and a short-            effort of Duke University,
term visitor program. NESCent’s               North Carolina State
informatics branch undertakes                 University, and the University
initiatives in support of software            of North Carolina at Chapel
interoperability, data sharing, and           Hill.
informatics training. The center also
solicits whitepapers for projects that
fall outside the scope of existing                                                                       The GMOD Helpdesk is hosted by NESCent and is
programs. More information on how                                                                       funded by a National Institutes of Health grant to
to apply or become involved at:                                                                           Ian Holmes and a USDA Agricultural Research
      http://www.nescent.org                  NESCent is supported by the National                               Service grant to Doreen Ware.
                                            Science Foundation (Grant # EF-0423641)

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