the gmod project lincoln stein cold spring harbor laboratory
TRANSCRIPT
The GMOD Project
Lincoln SteinCold Spring Harbor Laboratory
FRANCIS HARRY COMPTON CRICK1916-2004
The GMOD Project
Lincoln SteinCold Spring Harbor Laboratory
What’s a MOD?o Model Organism Databaseo Repository for reagents
o Stocks, vectors, cloneso Genetic & physical maps
o Large-scale data setso Genomeo EST sets, microarray results, 2-cell hybrid
interactionso Literatureo Ontologies & Nomenclatureo Meetings, announcements
Example MOD: WormBase
Gene
Genome
Comparative Genomics
Citation
Demand for CuratedDatabases is High
o Actinomyceteso Barleyo Chlamydiao Cowo HIVo Honeybeeo Parameciumo Planaria
o Plasmodiao Pseudomonaso Staphylococcio Schistosomao Soybeano Tetrahymenao Volvox
The GMOD Project
o Portable, open source software to support model organism databases
o Multiple MODs involvedo Worm, fly, yeast, mouse, arabidopsis,
rat, monocot, fugu, E. coli
o Funded by NIH as of June 2002o Programmers, coordinator, quarterly
meetings
http://www.gmod.org
The GMOD Pyramid
Open Source DBMS& Middleware
Modular Schema
ModularApplications
A MOD Construction Set
genome geneticmaps
liter-ature
genomesMiddlewareLayer
DatabaseLayer
AppplicationLayer
maps citations
genomebrowser
genomeeditor
mapbrowser
mapeditor
citationbrowser
citationeditor
BioperlBioJavaBioPython
annotationpipeline
Chado – Modular Schema
o Common schema for use by MODso Ontology Driven
o Small number of generic tables driven by a controlled vocabulary
o Evidence-Savvyo Extensible
o A collection of application-driven modules
www.gmod.org
Genome Management
Genbank
Chado
Apollo (desktop) Gbrowse (web site)
BioPipe
OtherFormats
OtherFormats
OtherFormats
loaders
Genome Annotation
and Visualization
Apollo – BDGP/Sanger
Adding a Transcript
Apollo Exon Editor
Apollo Macrosynteny Viewer
Apollo Microsynteny Viewer
Genome Management
Genbank
Chadobioperl
Apollo (desktop) Gbrowse (web site)
BioPipe
GBrowse – Low Magnification
Zoom – Medium Magnification
Zoom – High Magnification
Zoom – Highest Magnification
Sequence dumps & other reports
Extensively Customizable
DAS: Gbrowse on UCSC
DAS: Gbrowse on EnsEMBL
DAS: Gbrowse on both
Distributed GBrowse
Gbrowse 1Gbrowse 3
Gbrowse 2
MyGbrowse
EmbeddableEmbedding Capable
Internationalizable
Genetic, Sequenceand Physical Map
Management
CMap: Map Comparisons
Metabolic PathwayVisualization &Management
Pathway Tools - SRI
Citation Managementand Searching
PubSearch/PubFetch
TextPresso - WormBase
PDFs
Pattern recognition &Markup engine
TextPresso Db
Search Interface
Future Attractions
Interaction Browser
Turnkey Website
Known GMOD UsersAgricultural Biotechnology Center, HungaryBAWI, S. KoreaBaylor College of MedicineBiocrates GmbH, InnsbruckBrandeis UniversityBristol-Meyers SquibbBritish Columbia Centre for Diseaes Control CIRAD, FranceCSIRO, AustraliaCambridge University (multiple labs)Center for Genomics & Bioinformatics, StockholmCentre de Genetique Moleculaire, CNRSCold Spring Harbor Laboratory (multiple labs)CompugenConcordia University, CanadaCornell Medical SchoolCornell UniversityDNA Landmarks, Inc.Donald Danforth Plant Sciences CenterDuke University (multiple labs)EMBL, HeidelbergFaculdade de Medicina de Ribeirão PretoFlyBase Foundation for Research and Technology, Crete
Fundação Hemocentro, Sao Paolo Genoscope, France GrainGenes Harvard University Hospital for Sick Kids, Toronto Illinois Institute of Technology Incyte Corporation Inpharmatica, Ltd. Institute for Systems Biology, Seattle Institute of Molecular and Cell Biology, Singapore International Rice Research Institute, Phillipines John Innes Centre KEGG Kansas State University Karolinska Institute Kennedy Krieger Institute Lawrence Berkeley Laboratories Marine Biological Laboratories, Woods Hole Massachusetts Institute of Technology (multiple labs)Mayo Institute McGill University Meat Animal Research Center, University of Nebraska
Known GMOD UsersOpen Informatics Consulting Corp. Oxagen Corp. Pasteur Institute, Paris Pioneer Corporation QIAGEN Operon Corp. RIKEN (multiple labs) RatDB Regulome, Inc. Rhobio (Bayer CropScience SA & Biogemma joint venture) Rigshospitalet, Copenhagen Rockefeller University Roslin Institute, Edinburgh Russian Academy Medical Sciences Serono International Corp, Geneva Simon Frasier University South Africa National Bioinformatics Institute Southern Illinois University St. Jude Children's Research Hospital, Memphis Stowers Institute for Medical Research Texas A&M (multiple labs) The Institute for Genome Research Tulane University
University California Davis University of Arizona (multiple labs) University of British Columbia University of California Santa Barbara University of Georgia (multiple labs) University of Minnesota University of Muenster University of New South Wales, Australia University of Oklahoma (multiple labs) University of Pennsylvania (multiple labs) University of Southern California University of Texas University of Toronto University of Virginia University of Washington Universität Giessen Université de Liège, Belgium Wageningen Universiteit & Researchcentrum, Netherlands Washington University at St. Louis (multiple labs) WormBase deVGen, Belgium
Find out more about GMOD
o Go to www.gmod.orgo Examine software matrixo Find a project you’re interested ino Contact project leader
o Or contact Scott Cain: [email protected] Or mail gmod-
CreditsCSHLAdrian ArvaShuly AvrahamScott CainKen ClarkAllen DayXiaokang Pan
BDGPNomi Harris Suzanna LewisChris MungallJohn RichterShengQiang ShuColin Weil
http://www.gmod.org
Broad InstituteMichele ClampCarnegie InstituteSue RheeDanny Yoo
HarvardDavid EmmertStan Letovsky
CaltechEimear KennyHans-Michael Muller
UCLAAllen DayBrian O’Connor
MCWSimon Twigger
SRI InternationalPeter Karp