GMOD Users

The following is a selection of the databases using GBrowse or Chado or some other popular component of GMOD. For a list of related publications see Publications. At the bottom of the page there is a list of GBrowse users.

Name	Description	URL	Chado	Year added/checked
http://agripestbase.org	Agripestbase	Agricultural pests		2013
http://agripestbase.org/hessianfly	Hessian fly	part of Agripestbase		2013
http://agripestbase.org/manduca	Manduca sexta	part of Agripestbase		2013
http://amoebadb.org	AmoebaDB	Amoeba (part of EupathDB)		2013
http://animalgenome.org	National Animal Genome Research Program	Animal genomes!	GBrowse	2013
http://www.aphidbase.com/	AphidBase	Pea aphid genome	Apollo, Chado, Galaxy, GBrowse, Cycs	2013
http://www.arabidopsis.org	TAIR			2013
http://arpcard.mcmaster.ca/	The Comprehensive Antibiotic Resistance Database	Bioinformatics database of resistance genes, their products and associated phenotypes.	Yes	2013
http://aspergillusgenome.org/	AspGD	Aspergillus	GBrowse, Sybil	2013
http://asrp.danforthcenter.org/	Arabidopsis Small RNA Project (ASRP)	Arabidopsis	JBrowse	2013
http://atidb.org	ATIDB	Arabidopsis		200x
http://banana-genome.cirad.fr/	Banana Genome Hub		Tripal	2013
http://beetlebase.org/	BeetleBase	Tribolium castaneum	Gbrowse, JBrowse, Chado	2013
http://bioinf.gen.tcd.ie/jbrowse/SL1344/	Salmonella	transcriptional map of S. Typhimurium	JBrowse	2013
http://bioinf.hutton.ac.uk/public/	SCRI Plant Bioinformatics Group		Yes	200x
http://bioinfo.cau.edu.cn/ProFITS/index.php	ProFITS	Protein Families Involved in the Transduction of Signalling (Maize)	JBrowse, GBrowse	2013
http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/	Rubber Genome Browser	(not accessible to public - Mar 2013)		2013
http://bioinformatics.ai.sri.com/ptools/	Pathway Tools		Home of Pathway Tools	2013
http://bovinegenome.org/	BGD	Bovine Genome Database		200x
http://www.brachybase.org/	Brachypodium		JBrowse	2013
http://butterflybase.ice.mpg.de/	ButterflyBase (part of InsectaCentral)	Butterflies and moths	GBrowse	2013
http://www.cacaogenomedb.org	Cacao Genome Database	Cacao	Tripal	2013
http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/	CGD	Candida Genome Database		200x
http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2/	Chromosome 7 Annotation Project			200x
http://www.chromdb.org/	ChromDB	Plant Chromatin Database		200x
http://www.ciliate.org/	TGD	Tetrahymena Genome Database		2013
http://www.citrusgenomedb.org	Citrus Genome Database	Citrus	Tripal	2013
http://citrusgreening.org/	Citrus Greening	pathogens causing citrus greening (Huanglongbing or HLB), esp. Liberibacter		2013
http://www.coccidia.icb.usp.br/eimeriatdb/	Eimeria transcript database	Annotated transcripts of protozoan parasites of the genus Eimeria		2013
http://compbio.dfci.harvard.edu/tgi/	TGI	The Gene Index Project: uses ESTs and gene sequences to predict genes and variants	GBrowse	2013
http://www.comparative-legumes.org/	LIS	Legume Information System	CMap	2013
http://www.cosmoss.org	cosmoss.org	The Bryophyte Genomics Resource - Physcomitrella patens Annotation		200x
http://www.cottongen.org/	Cottongen		Tripal	2013
http://aniseed-ibdm.univ-mrs.fr/	ANISEED	Ascidian Network for In Situ Expression and Embryological Data	GBrowse	2013
http://cryptodb.org	CryptoDB	Cryptosporidium (part of EupathDB)	GBrowse, Cyc	2013
http://db-mml.sjtu.edu.cn/ThioFinder/search.html	ThioBase	A database of thiopeptides featured in genetics and chemistry	GBrowse_syn	2013
http://diagcomputing.org/resources/software.php	Data-Intensive Academic Grid	Provides a VM/cloud image of bioinf. software	JBrowse, BioMart, Ergatis, etc.	2013
http://www.dictybase.org	DictyBase		Yes	2013
http://ecobrowser.biosino.org	EcoBrowser	E. coli transcriptome	JBrowse	2013
http://ecocyc.org/	EcoCyc			2013
http://ecoliwiki.net	EcoliWiki	E. coli		2013
http://www.endophyte.uky.edu/	UKY Genome Projects	University of Kentucky; numerous spp	GBrowse	2013
http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/	eQTL browser	eQTLs identified in recent studies in multiple tissues @ Pritchard lab, UChicago		2013
http://www.equinegenome.org/	Equine Genome	Equus caballus		200x
http://eupathdb.org	EupathDB	Eukaryotic pathogens, including Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma, and Vivraia		2013
http://fagaceae.org	Fagaceae Genomics Web	Fagaceae spp, including oak, beech, chestnut, etc.	Tripal	2013
http://www.flybase.org	FlyBase	A Database of Drosophila Genes & Genomes	Yes	2013
http://fungalgenomes.org/	Fungal Genomes	Fungal Genomics Resources		2013
http://fungidb.org/	FungiDB	Fungal Genomics Resources		2013
http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k	A. fumigatus TIGR/Sanger Assembly			2013
http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/S_nodorum_broad_tel_100k	S. nodorum Fungal Telomere Browser			2013
http://gabcsfl.org	Cool Season Food Legume Database	Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc.	Tripal	2013
http://gbrowse.jcvi.org/gbrowse/	JCVI	J. Craig Venter Institute; offers numerous species		2013
https://gdoc.georgetown.edu/gdoc/	G-DOC	Systems medicine platform for personalized oncology	JBrowse	2013
http://www.genedb.org	GeneDB	Pathogen Sequencing Unit	Chado, JBrowse	2013
http://www.generationcp.org/	Generation Challenge Programme
http://genomes.sapac.edu.au/bovineqtl/	Bovine QTL Viewer			2013
http://www.genomesunzipped.org/jbrowse/	Genomes Unzipped	Human -- personal genomic data made public	JBrowse	2013
http://www.genoscope.cns.fr/spip/Ressources-bioinformatiques-du.html	Genoscope	Multiple organisms	GBrowse	2013
http://genexpdb.ou.edu/main/	E. coli GenExpDB	E. coli Gene Expression Database	JBrowse	2013
http://giardiadb.org	GiardiaDB	Giardia (part of EupathDB)		2013
http://github.com/capsid	CaPSID	Computational Pathogen Sequence IDentification - open source platform for pathogen sequence identification	JBrowse	2013
http://gmod.mbl.edu/	JBPC Generic Model Organism Database servers	Huge set of GMOD/GBrowse resources covering many different species		2013
http://www.gramene.org	Gramene			2013
http://green.dna.affrc.go.jp/Og/	AfRicA DB	African Rice Annotation DataBase	GBrowse	2013
http://hapmap.ncbi.nlm.nih.gov/index.html.en	HapMap			2013
http://www.hardwoodgenomics.org	Hardwood Genomics Project	Hardwood tree spp	Tripal	2013
http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/	Human Genome Diversity Project	HGDP @ Pritchard lab, UChicago		2013
http://hymenopteragenome.org/beebase/	BeeBase	The secret life of bees	JBrowse	2013
http://hymenopteragenome.org/ant_genomes/	Ant Genomes Portal	Ants	GBrowse	2013
http://hymenopteragenome.org/nasonia/	NasoniaBase	Nasonia wasp	GBrowse	2013
http://icemangenome.net/	Ice Man Genome	The genome of Ötzi the Iceman	JBrowse	2013
http://ich.ciliate.org/	IchDB	Ichthyophthirius multifiliis genome		2013
http://informatics.jax.org/	MGI			2013
http://inra.fr/lepidodb	Lepido dB	Lepidoptera database; covers Helicoverpa armigera and Spodoptera frugiperda	GBrowse, CMap, Apollo, Chado	2012
http://www.inra.fr/meloidogyne_incognita	Meloidogyne incognita	Covers phytoparasitic root-knot nematode Meloidogyne incognita.	Chado, GBrowse, Apollo	2013
http://insectacentral.org	InsectaCentral	Repository of insect transcriptomes	Chado	2013
http://insects.eugenes.org/DroSpeGe/	DroSpeGe			200x
http://irfgc.irri.org/cgi-bin/gbrowse	OryzaSNP			200x
http://iubio.bio.indiana.edu/	IUBio Archive	Software and data from Indiana University; includes numerous resources, such as euGenes, DroSpeGe, wFleaBase, etc.	Argos	2013
http://www.jcvi.org	TIGR	The Institute for Genomic Research	Yes	200x
http://knowpulse2.usask.ca/portal/	KnowPulse: Pulse Crop Genomics & Breeding	Chickpea, lentil, common bean, pea	Tripal	2013
http://krithgenomics.drupalgardens.com/	K-RITH-Hopkins Genomics Web Portal		JBrowse	2013
http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/	GARFIELD	Genome Annotation Resource Field Felis catus	GBrowse	2013
http://www.livestockgenomics.csiro.au/	Livestock Genomics	CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines		2013
http://magi.plantgenomics.iastate.edu/	MAGI	Maize Assembled Genomic Island		200x
http://maizegdb.org	MaizeGDB	Maize Genetics and Genomics DB		2013
http://www.marinegenomics.org	Marine Genomics	Multispecies marine organism database	Tripal	2013
http://me.lzu.edu.cn/yak/	Yak Genome Database	Yak genome		2013
http://www.medicinalgenomics.com/the-jane-ome/	The Jane-Ome	Cannabis Genome Project, Medicinal Marijuana	JBrowse	2013
http://mg.dna.affrc.go.jp/	MgEST DB	Magnaporthe grisea ESTs	GBrowse	2013
http://microb215.med.upenn.edu/gb2/gbrowse/phage_metagenomics/	Phage metagenomics		GBrowse	2013
http://microsporidiadb.org	MicrosporidiaDB	Microsporidia (part of EupathDB)		2013
http://mips.helmholtz-muenchen.de/plant/triticeae/index.jsp	MIPS Triticeae genomes database	Barley, wheat, rye		2013
http://nabic.rda.go.kr/	NABIC RDA	Various plant and animal genomes	GBrowse_syn, GBrowse	2013
http://nypg.bio.nyu.edu/vicogenta/	Vicogenta	Viewer for Comparing Genomes to Arabidopsis		200x
http://oikoarrays.biology.uiowa.edu/Oiko/	OikoBase	genome expression database of Oikopleura dioica	GBrowse	2013
http://www.omap.org/	OMAP	Oryza Map Alignment Project		200x
http://www.opossumbase.org/	OpossumBase	Monodelphis domestica Genomic Resources Database	GBrowse, JBrowse	2013
http://orygenesdb.cirad.fr/	OryGenesDB			200x
http://paramecium.cgm.cnrs-gif.fr/	ParameciumDB		Yes	200x
http://patricbrc.org	PATRIC	Pathosystems Resource Integration Center	JBrowse	2013
http://phytozome.net/	Phytozome	Numerous green plants	GBrowse, BioMart	2013
http://piroplasmadb.org	PiroplasmaDB	Piroplasma (part of EupathDB)		2013
http://plasmodb.org	PlasmoDB	Plasmodium (part of EupathDB)		2013
http://popgenie.org/	PopGenIE	The Populus Genome Integrative Explorer		200x
http://www.possumbase.org.nz/	PossumBase	EST DB for the brushtail possum, Trichosurus vulpecula	GBrowse	2013
http://pseudomonas.com/	PseudoCAP	Pseudomonas Genome Database		200x
http://puma.princeton.edu/	PUMAdb	Princeton Microarray Database, Chado		200x
http://qtaro.abr.affrc.go.jp/	QTARO	QTL Annotation Rice Online	GBrowse	2013
http://rapdb.dna.affrc.go.jp/	Rice Annotation Project DB		GBrowse	2013
http://research.nhgri.nih.gov/mnemiopsis/	Mnemiopsis Genome Project	The ctenophore Mnemiopsis leidyi	JBrowse	2013
http://rgd.mcw.edu	RGD	Rat Genome Database		200x
http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice	MSU Rice Genome Browser			2013
http://rnaspace.org/	RNAspace	an integrated environment for non-coding RNA annotation	JBrowse	2013
http://www.rosaceae.org	Genome Database for Rosaceae	Rosaceae species	Tripal	2013
http://rulai.cshl.edu/cshlmpd/credit.html	CSHLmpd	Mammalian Promoter Database		2013
http://sgdlite.princeton.edu/	SGD Lite			200x
http://www.shigen.nig.ac.jp/barley/	BarleyDB	Barley!	GBrowse, CMap	2013
http://smedgd.neuro.utah.edu/	SmedGD	Planaria ESTs	Yes	2013
http://solgenomics.net/	Sol Genomics Network		Yes	2013
http://soybase.org/	SoyBase	USDA Soybean Genetics and Genomics Database	No	200x
http://soybeangenome.siu.edu/	Soybean Gbrowse Database		GBrowse	2013
http://spbase.org	SpBase	Genome sequence and annotations produced by the Baylor College of Medicine Human Genome Sequencing Center and the sea urchin research community.	GBrowse, BioMart, Textpresso	2013
http://www.spirodelagenome.org/	Spirodela Genome		GBrowse	2013
http://t1dbase.org/	T1DBase	DB focussed on type 1 diabetes		2013
http://www.tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl	TIGR Medicago BACs			200x
http://toxodb.org	ToxoDB	Toxoplasma (part of EupathDB)		2013
http://treetfdb.bmep.riken.jp/index.pl	TreeTFDB	transcription factors (TF) of papaya (Carica papaya), jatoropha (Jatropha curcas), cassava (Manihot esculenta), poplar (Populus trichocarpa), castor bean (Ricinus communis) and grape vine (Vitis vinifera)		2013
http://trichdb.org	TrichDB	Trichomonas (part of EupathDB)		2013
http://tritrypdb.org	TriTrypDB	Kinetoplastids (part of EupathDB)		2013
http://tropgenedb.cirad.fr/	TropGENE DB	genetic and genomic information about tropical crops studied by Cirad.		200x
http://www.vaccinium.org/	Genomic DB for Vaccinium	Blueberry, cranberry, lingonberry, other Vaccinium spp.	Tripal	2013
http://vectorbase.org	VectorBase	Chado, DAS, Apollo	Yes	2013
http://wfleabase.org/	wFleaBase	Daphnia	Yes	200x
http://wheat-urgi.versailles.inra.fr/Tools/Triannot-Pipeline/	TriAnnot Pipeline	TriAnnot pipeline for automated plant genome annotation	GBrowse	2013
http://wheat.pw.usda.gov/	GrainGenes		GBrowse, CMap	2013
http://www.wheatgenome.info/	Wheat Genome	Wheat		2013
http://www.wormbase.org	WormBase			2013
http://www.xenbase.org/	Xenbase	Xenopus		2013
http://xmap.ftdna.com/	Xmap	Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology	No	2013
http://yandell-lab.org/software/cgl/	CGL	Comparative Genomics Library		2013
http://yeastgenome.org/	SGD	S. cerevisiae resources		2013
http://ymap.ftdna.com/	Ymap	Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology	No	2013
http://zfin.org/	ZFIN	Zebrafish, Danio rerio	GBrowse	2013

GBrowse Users

This is a list of confirmed GBrowse users as of April 2004.

• Agricultural Biotechnology Center, Hungary
• AphidBase
• BAWI, S. Korea
• Baylor College of Medicine
• Biocrates GmbH, Innsbruck
• Brandeis University
• Bristol-Meyers Squibb
• British Columbia Centre for Diseaes Control
• CIRAD, France
• CSIRO, Australia
• Cambridge University (multiple labs)
• Center for Genomics & Bioinformatics, Stockholm
• Center for Genomics and Bioinformatics, Stockholm
• Centre de Genetique Moleculaire, CNRS
• Cold Spring Harbor Laboratory (multiple labs)
• Compugen
• Concordia University, Canada
• Cornell Medical School
• Cornell University
• DNA Landmarks, Inc.
• Donald Danforth Plant Sciences Center
• Duke University (multiple labs)
• EMBL, Heidelberg
• EuGenes (hacked copy)
• Faculdade de Medicina de Ribeiro Preto, So Paulo
• Family Tree DNA, Genealogy by Genetics Ltd.
• FlyBase
• Foundation for Research and Technology, Crete
• Fundao 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
• Medical University of South Carolina
• Michigan State University
• NHGRI, NIH
• National Cancer Institute, Frederick Cancer Center
• New York University (multiple labs)
• North Carolina State University
• Northern Illinois University
• Northwestern University
• Oklahoma State University
• Open 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
• SoyBase
• St. Jude Children's Research Hospital, Memphis
• Stowers Institute for Medical Research
• Texas A&M (multiple labs)
• Texas Biomedical Research Institute
• 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
• Universitt Giessen
• Universit de Lige, Belgium
• Wageningen Universiteit & Researchcentrum, Netherlands
• Washington University at St. Louis (multiple labs)
• WormBase
• Xenbase
• deVGen, Belgium