WheatIS

WheatIS nodes

WheatIS Nodes:
  • WheatIS
  • URGI
  • Earlham Institute (EI)
  • Edwards group @ UWA
  • CerealsDB
  • UCW
  • MonoGram
  • QTLNetMiner
  • EBI
  • CIMMYT
  • GrainGenes
  • T3 wheat
  • PGSB
  • CSHL
  • Below is a list of WheatIS nodes and related information


    WheatIS           http://www.wheatis.org/

    Core node of the wheat information system with Links to various servers and nodes

    Leader(s): Hadi Quesneville, Mario Caccamo, David Edwards, Gerard Lazo

    Links:
    WheatIS http://www.wheatis.org/
    WheatIS EWG    wheatis-ewg@listes.inra.fr

     


    URGI     France    http://wheat-urgi.versailles.inra.fr/

    URGI is a research unit in genomics and bioinformatics at Institut National de la Recherche Agronomique (INRA), dedicated to plants and crop parasites. The URGI research activity covers genome structure and dynamics. URGI hosts a bioinformatics platform , which belongs to the French national network of bioinformatics platforms ( ReNaBi ).

    Leader(s): Michael Alaux, Hadi Quesneville

    Links:
    GnpIS Information System http://wheat-urgi.versailles.inra.fr
    Wheat sequence repository: BLAST, browsers, download http://wheat-urgi.versailles.inra.fr/Seq-Repository
    Transposable elements analysis https://urgi.versailles.inra.fr/Tools/REPET
    Genomics, genetics and phenomics data integration sequences, physical maps, genetic maps, markers, QTL, SNP, germplasm, phenotypes, genes and repeats annotations http://wheat-urgi.versailles.inra.fr/

     


    Earlham Institute (EI)     UK    http://www.earlham.ac.uk

    The Earlham Institute (formerly The Genome Analysis Centre, TGAC) is a research institute focused on the application of state of the art genomics and bioinformatics to advance plant, animal and microbial research to promote a sustainable bioeconomy. We explore living systems by applying computational science and biotechnology to answer ambitious biological questions and generate enabling resources.EI is a hub for innovative bioinformatics founded on research, analysis and interpretation of multiple, complex data sets. We host one of the largest computing hardware facilities dedicated to life science research in Europe.

    Leader(s): Robert Davey

    Links:
    Data Infrastructure group http://www.earlham.ac.uk/davey-group
    Grassroots Infrastructure https://wheatis.tgac.ac.uk
    Open data http://opendata.earlham.ac.uk
    HPC http://www.earlham.ac.uk/high-performance-computing
    Sequencing http://www.earlham.ac.uk/genomic-services
    Training http://www.earlham.ac.uk/scientific-training

     


    Edwards group @ UWA     Australia   http://www.appliedbioinformatics.com.au/

    David Edwards is Winthrop Professor of cereal genomics at the University of Western Australia where he leads an applied bioinformatics group with a focus on crop genomics and bioinformatics

    Leader(s): David Edwards

    Links:
    Edwards group portal http://www.appliedbioinformatics.com.au/
    TAGdb: access to wheat NGS raw data http://sequencetagdb.info/
    Edwards wheat portal: Links to GBrowse and SNP data genome, annotation and SNPs http://www.wheatgenome.info/
    CMAP3D genetic maps http://www.appliedbioinformatics.com.au/cmap/
    T3 database. Host database for Australian wheat breeding data, linked to the US data with aims to integrate with IBP (temporary address: http://t3.wheatis.org/)

     


    CerealsDB     UK   

    Service focused on the wheat breeder community (genetic diversity)

    Leader(s): Robert Davey

    Links:
    CerealsDB http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php
    SNPs, genotyping, sequences http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php

     


    UCW     UC Davis    USA

    Wheat research and breeding laboratory

    Leader(s): Jorge Dubcovsky

    Links:
    Protocols for MAS http://maswheat.ucdavis.edu/Index.htm
    Access to transcriptome files: Diploid and Tetraploid wheat transcriptome files http://maswheat.ucdavis.edu/Transcriptome/index.htm
    Acces to Puccinia triiformis genome: Stripe rust genome http://maswheat.ucdavis.edu/plosonepst130/index.htm

     


    MonoGram     UK    http://www.monogram.ac.uk/

    Monogram aims to promote coordination and information flow amongst the community and ensure its visibility at the national and international level, thereby strengthening UK efforts in these species. Monogram is the focal point for integration of the UK grass and cereals community and represents it at the UK Plant Sciences Federation. We also hope to integrate more closely with the wider plant sciences community and provide a link to help lower the entry barriers for new researchers in the area.

    Leader(s): Cristobal Uauay (steering group), Nathalie Castells-Brooke (web site)

    Links:
    Monogram parallel Search http://www.monogram.ac.uk/ressrch.php
    Resources: http://www.monogram.ac.uk/all.php
    Publications: http://www.monogram.ac.uk/papers.php
    Databases: http://www.monogram.ac.uk/databases.php
    News: http://www.monogram.ac.uk/announce.php
    Vacancies: http://www.monogram.ac.uk/vacancies.php
    Events: http://www.monogram.ac.uk/events.php

     


    QTLNetMiner     UK

    QTLNetMiner was designed to help with the challenging task of prioritising candidate genes from genetics and transcriptomic studies which typically identify many (often hundreds) of potential genes. QTLNetminer provides users with a single point of entry to an integrated knowledge base created by the Ondex system using comparative analysis of wheat and other plant gene function data, gene-trait associations mined from the scientific literature, plant trait and gene ontologies and protein function resources such as Interpro, Uniprot and BioCyc.

    Leader(s): Keywan Hassani-Pak

    Links:
    Integrated resource of sequence, transcriptome, QTL, pathway, ontologies, interaction, literature, annotation, variation https://ondex.rothamsted.ac.uk/QTLNetMinerWheat

     


    EBI     EMBL UK    http://www.ebi.ac.uk

    The European Bioinformatics Institute (EBI) is Europe's premier centre for bioinformatics, a global leader in the storage, interrogation and dissemination of large biological datasets. The EBI maintains the world's most comprehensive range of biological databases, facilitating the provision of services to the scientific community.

    Leader(s): Paul Kersey, Dan Bolser

    Links:
    Ensembl Plants http://plants.ensembl.org
    Wheat genome browsers (Aegilops tauschii, Triticum aestivum, Triticum urartu)

     


    CIMMYT International Wheat Improvement Network     Mexico    http://orderseed.cimmyt.org/iwin-fb.php
    CIMMYT Wheat Germplasm Bank GRIN-Global     Mexico    http://wgb.cimmyt.org/gringlobal/search.aspx

    The International Wheat Information System (IWIS), curated by CIMMYT, contains data gathered from 1976 to the present, from multiple providers situated in countries throughout the world. International Wheat Improvement Network cooperators and partners have provided the genotypic and phenotypic data contained in IWIS.

    Leader(s): Tom Payne

    Links:
    IWIN http://orderseed.cimmyt.org/iwin-fb.php
    CIMMYT-Wheat Germplasm Bank 1.9.1 http://wgb.cimmyt.org/gringlobal/search.aspx

     


    GrainGenes     USDA-ARS  USA    http://wheat.pw.usda.gov

    GrainGenes is resource for Triticeae and Avena related information

    Leader(s): Gerard Lazo, Taner Sen

    Links:
    GrainGenes http://wheat.pw.usda.gov

     


    T3 wheat     USDA-ARS  USA    http://triticeaetoolbox.org/wheat

    T3 wheat houses germplasm, allele, and phenotype information

    Leader(s): Jean-Luc Jannink, David Matthews

    Links:
    T3-wheat http://triticeaetoolbox.org/wheat

     


    PGSB     Helmholtz Center Munich  Germany    http://mips.helmholtz-muenchen.de/plant/

    Plant genome and systems-oriented bioinformatics. Focus towards analyzing genomic encryption, expression patterns, functional and systems biology of plants. PGSB maintains a large data set of plant genomes structured in databases and makes them publically available along with comparative analyses.

    Leader(s): Manuel Spannagl, Klaus Mayer

    Links:
    PGSB PlantsDB http://mips.helmholtz-muenchen.de/plant/

     


    CSHL     CSHL, USDA-ARS  USA    www.gramene.org

    The Ware laboratory is part of the United State Department of Agriculture (USDA), Agriculture Research Service (ARS). The Ware labs focus is on collaborative research in the area of Plant Genomics and Bioinformatics. We are located on the Cold Spring Harbor Laboratory (CSHL) campus. CSHL is a preeminent international research institution in molecular biology and genetics.

    Leader(s): Marcela Monaco, Doreen Ware

    Links:
    Gramene http://www.gramene.org