gmod: genomics resources for emerging model...
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GMOD: Genomics Resources forEmerging Model Organisms
AbstractAs genomics technologies have become widely available, manyemerging model organism communities have accumulated anunprecedented volume of data on sequences, genotypes, expressionpatterns, etc. Much of this data is from organisms well suited tocomparative genomic, evolutionary and ecological studies. Moredata offers more potential for discovery, but it also makes it isharder to organize, visualize and annotate. GMOD is a collection ofinteroperable open source software, including tools for managing,annotating and visualizing genomic data. GMOD tools are used indiverse contexts, from genome annotation projects withinindividual labs to major model organism databases.
Comparative GenomicsGMOD supports visualizing compara-tive genomics data. Sybil displayssyntenic regions and whole genomecomparisons. CMap shows compara-tive maps of any type (genetic,physical, sequence, …). SynView,GBrowse_syn and SynBrowse areGBrowse-based synteny browsers.
Dave Clements, Hilmar Lapp, Todd J. VisionNational Evolutionary Synthesis Center (NESCent), Durham, NC, USA
http://nescent.org [email protected]
The GMOD Help Desk is hosted by NESCent and is funded byNational Institutes of Health grants to Ian Holmes at UC Berkeley
and James Hu at Texas A&M.
Getting Started with GMOD
Start at GMOD.org
Download Software
FAQs and HOWTOs
Project Events
Project News
Contribute Doc!GMOD.org is a Wiki
Support: Help Desk& mailing lists
Contribute Code!We’re open source
Popular GMOD Components
http://gmod.org
GMOD for Biologists
GBrowse Genome Browser
GBrowse is a web-based viewer fordisplaying genomes and their
annotation. It is highly configurable byend-users and site administrators. Ifyou have sequence and/or genomic
annotation, GBrowse can show it.
Apollo Genome EditorThe Apollo genome editor is used toannotate genomic sequences. Apollosupports adding new annotations andrefining computational annotations.It is used in several communityannotation efforts.
Chado Database SchemaChado is the unifying data model for GMOD. It is a modular andextensible database design for biological data. Chado supportssequence, genetic, phenotypic, ontology, gene expression, andmany other datatypes.
GMOD records behaviors asphenotypes by combiningontologies such as GO andPATO (the Gene and Phenotypeontologies) in Chado, GMOD'sdatabase schema. These canthen be displayed or queried.You can also use (or create)more specific ontologies suchas the Social Insect BehaviorOntology (SIBO) or anatomyontologies for specificorganisms.
TextPresso, PubSearchChado Publication Module
Curate/searchOrganize
Publications
Java TreeView, Caryoscope,GeneXplorerChado Mage, Expression Modules
View
Organize
Microarray andExpression
Chado Genetics ModuleGMODWeb
OrganizeView
Phenotype,Genotype
Chado Organism, Phylogeny modulesGMODWeb
OrganizeView
PhylogeneticTrees
Pathway ToolsView, predict,organizePathways
Chado CV moduleGO Term Viewer
CurateView
Ontologies
CMap, SynView, SynBrowse, SybilSybilChado Map Module
ViewAnnotateOrganize
Comparative,Synteny
GBrowseApolloChado Sequence Module
ViewAnnotateOrganize
GenomicSequence
then GMOD can help with& you need toIf you have
What Can GMOD Do?
Chado has recently been extendedwith the Natural Diversity module,which supports stocks, individuals,pedigrees, crosses, geolocations,and phenotype and genotypeexperiments. Taxonomy andphylogenetic trees in Chado’s coremodules have also beenrationalized.
Behavior and Phenotype in GMOD
An allele page at ParameciumDB showingphenotype information integrated withsequence, genetic, and stock data.
Natural Diversity in GMOD