Below is a list of WheatIS nodes and related information
Core node of the wheat information system with Links to various servers and nodes
Leader(s): Hadi Quesneville, Mario Caccamo, David Edwards, Gerard Lazo
WheatIS EWG firstname.lastname@example.org
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
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
Data Infrastructure group http://www.earlham.ac.uk/davey-group
Grassroots Infrastructure https://wheatis.tgac.ac.uk
Open data http://opendata.earlham.ac.uk
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
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/)
Service focused on the wheat breeder community (genetic diversity)
Leader(s): Robert Davey
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
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)
Monogram parallel Search http://www.monogram.ac.uk/ressrch.php
KnetMiner 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. Knetminer 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
Integrated resource of sequence, transcriptome, QTL, pathway, ontologies, interaction, literature, annotation, variation http://knetminer.rothamsted.ac.uk
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
Ensembl Plants http://plants.ensembl.org
Wheat genome browsers (Aegilops tauschii, Triticum aestivum, Triticum urartu)
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
CIMMYT-Wheat Germplasm Bank 1.9.1 http://wgb.cimmyt.org/gringlobal/search.aspx
GrainGenes USDA-ARS USA http://wheat.pw.usda.gov
T3 wheat USDA-ARS USA 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
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