tri-fold brochure - Main Page - GMOD by gjjur4356


									GMODWeb : Pathway Tools : Flash GViewer : Tripal : TableEdit : GBrowse_syn : Apollo : InterMine : GBrowse : MAKER

           Databases                          Community Meetings   

GMOD has several choices for creating         The GMOD community meets semi-
web-accessible biological databases.          annually to discuss GMOD components,
Chado is a modular and extensible             best practices, and project direction.
relational database schema that               These meetings often occur immediately
supports many common biological               before or after a major conference of
data types. Chado integrates sequence         interest to community members. Meetings
data and annotation, ontologies and           are open to everyone: developers, users,
controlled vocabularies, publication,         and potential users. Registration is often                  
strains, microarray data, libraries, and      free. GMOD also sponsors a few other
several other data types into an integrated   types of meetings such as hackathons.
whole. Websites
large (FlyBase)
and small
use Chado to                                                                                                genom
                                                                                             If you need to visualize, annotate,
                                                                                             integrate or share your data, then GMOD
                                                                                             can help you. GMOD is a collection of
manage and
integrate their data.
Tripal and GMODWeb are customizable
web front ends for Chado. Many
                                                                                             interoperable, open source software
                                                                                             tools for common data-related tasks in
                                                                                             biological research.
organizations also create their own web
interfaces using Chado APIs.
                                                           Training                          GMOD is used in hundreds of organiza-
                                         tions from major model organism
                                                                                             databases to smaller communities and
                   GMOD includes              GMOD offers training through multi-day         individual labs. Many GMOD components
                   BioMart and InterMine      hands-on courses, workshops at                 can be installed and maintained with only
                   for data mining and        conferences, and online tutorials and          minimal informatics support.
                   warehousing tasks.         documentation. Training sessions and
InterMine and BioMart are end-to-end          workshops are also offered on individual       In addition to software, GMOD is also an
packages that include relational database     GMOD components such as Galaxy,                active community of developers and
back ends, web front ends, and                Pathway Tools, MAKER and InterMine.            users that are addressing common
middleware to connect them. These                                                            challenges with their biological data.
packages give end users the ability to        GMOD offers summer courses at                  GMOD has mailing lists, regular meetings,
build custom and arbitrarily complex          NESCent in North Carolina, and at one          project staff, a wiki-based web site, and
queries using web interfaces.                 non-US location per year, when possible.       training workshops for new users.

modENCODE : SmedGD : TAIR : AphidBase : Gramene : SGN : GNPAnnot : wFleaBase : SoyBase : MGI : dictyBase
Ergatis : Galaxy : DIYA : Textpresso : LuceGene : GMODTools : Sybil :Genome Grid : Chado : CMap : JBrowse : BioMart

         Visualization                                                                      Annotation                                 GMOD Support                                              

GMOD can visualize                                                              Supporting annotation                             GMOD has an active community of users,
genomic data with                                                               of biological data is a                           developers and staff. GMOD support is
the GBrowse and                                                                 central goal of GMOD                              available from several different sources.
JBrowse genome                                                                  and many tools sup-
browsers. GBrowse is                                                            port it. Apollo is a                                             We       b Site
widely used, and is                                                             popular genome                                          
highly configurable. It                                                         annotation editor that allows users to  
allows users to                                                                 manually add and update genomic                   includes FAQs
integrate data from                                                             annotations. Many organism communities            & HOWTOs,
many sources,                                                                   use Apollo in community annotation efforts        component
                                                    QuickTime™ and a

including their own
                                             are neede d to see this picture.
                                                                                to maintain and update genomic annotation.        documentation,
uploaded files.                                                                 Efforts are underway to build a wiki based        community
JBrowse is a fast                                                               front end to the Chado database using             calendar &
AJAX-based browser.                                                             TableEdit, a MediaWiki extension for              news and
Any type of data                                                                updating tabular and database data.               information about the GMOD project.
associated with a
genomic region can                                                                                  GMOD has tools                              Mailing Lists
be integrated and                                                                                   for generating          
visualized in either                                                            annotation computationally. MAKER and                  The GMOD project has active mailing
browser.                                                                        DIYA are pipeline tools for automatically              lists for user questions, troubleshooting,
                                                                                annotating genomes. Ergatis, Galaxy and           best practices, and announcements. These
                                                                                Genome Grid are all tools for building,           20+ lists (some for the project as a whole
genomics data is
                                                                                running and reusing custom pipelines on           and some for specific components) have
visualized with CMap,
                                                                                one or a cluster of computers.                    almost 1000 threads per year. Questions are
GBrowse_syn, Sybil,
                                                                                                                                  answered by GMOD users, developers, and
and SynView.                                                                    The Textpresso package does automatic             staff.
Pathway information,                                                            annotation of publications by searching
                                                                                abstracts and the full text of publications for                   Help Desk
both metabolic and                                                                                                                      
regulatory, can be                                                              relevant terms and concepts.
                                                                                                                                  The GMOD Help Desk answers support
visualized using Pathway Tools.                                                 GBrowse and JBrowse are being extended
                                                                                                                                  questions, maintains and develops
Several database components (see                                                to include user authentication and
                                                                                                                                  documentation and the web site, and
"Databases") also provide web front ends.                                       annotation uploading and sharing.
                                                                                                                                  offers training.

GeneDB : FlyBase : ParameciumDB : BioCyc : SGD : BeetleBase : SpBase : VectorBase : LepidoDB : WormBase : RGD

To top