GMOD Users
From GMOD
Revision as of 01:03, 8 March 2013 by Girlwithglasses (Talk | contribs)
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://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