WheatIS nodes :: WheatIS

URGI is a research unit in genomics and bioinformatics at Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), 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.inrae.fr
Wheat sequence repository: BLAST, browsers, download http://wheat-urgi.versailles.inrae.fr/Seq-Repository
Transposable elements analysis https://urgi.versailles.inrae.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.inrae.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

KnetMiner UK

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

Links:
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): Sarah Dyer, 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