Data access and analysis

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

The large-scale genomic, phenotypic and regulatory datasets emerging from the Designing Future Wheat BBSRC Strategic Programme (DFW), will be annotated, integrated and disseminated to generate critical reference resources supporting interpretation and driving new avenues of investigation. These activities will comprise the UK contribution to the international Wheat Information System (WheatIS), a unified global infrastructure for wheat biology being developed under the auspices of the G20 International Wheat Initiative. Wheat resources and information generated within the DFW programme will be presented in an easily accessible form, allowing ready access for UK and international plant researchers not directly working on wheat.

Publications

10 25 50
 
Title Slideshare Presentation of Knetminer 
Description This is online presentation introducing the knetminer software application. 
Type Of Art Film/Video/Animation 
Year Produced 2017 
Impact It helps with presentation to potential collaborators. 
URL https://www.slideshare.net/KeywanHassaniPak/knetminer-overview-oct-2017
 
Description During the year, we have provided BBSRC Swindon office with a Google Spreadsheet, which lists all our DFW outputs (including data access sites, germplasm generated, datasets generated, publications, and public engagement activities as they occur). This document is updated by us on a regular basis. All the objectives during the DFW reporting period have been met, and many exceeded. All the committees within DFW are running well including the key data coordination task force (DCTF) and Breeder's toolkit committees.

Rob Davey chairs the Data Coordination Task Force (DCTF), where researchers from all work packages, and external stakeholders, coordinate efforts to ensure that data flows from experiments into the DFW Data Portal, gets shared within the project, and to the community in a timely way. DCTF meetings have been held every month since project start.
We have investigated the recombination landscape of wheat, identifying more prevalent and longer gene conversion/double crossover events than in other plants, and a candidate REQ gene regulating either frequency or length of these events. This is likely to impact breeding (Gardiner, L.-J., et al. http://doi.org/10.1101/539684).

We designed, optimised, and used promoter exon capture to identify large amounts of variation in DNA methylation across wheat landraces and correlated some of this variation with changes in gene expression and phenotypic variation. We took advantage of the newly release IWGSC assembly to further improve our capture design. Both studies are available in Genome Research (http://doi.org/10.1101/gr.233551.117) and GigaScience (http://doi.org/10.1093/gigascience/giz018). All data sets are publicly available on the DFW Data Portal (https://opendata.earlham.ac.uk/wheat/under_license/toronto/).

We have developed CropSight to house and display integrated phenotyping data from small interconnected internet-enabled devices (Reynolds, D. et al. https://doi.org/10.1093/gigascience/giz009). CropSight collates data from CropQuant devices, providing automated indoor and in-field phenotyping and climate data collation, storage, and management through distributed IoT sensors. It has monitored in-field wheat experiments since 2016 and is publicly available (https://github.com/Crop-Phenomics-Group/CropSight/releases).

Continuing to develop the Grassroots platform at EI, we have built the first iteration of a DFW-wide Field Trial database and search service. EI DFW developers have also improved and extended the JIC Germplasm Resource Unit's (GRU) website, so that other services can use computer programs to query the extensive database of germplasm quickly and easily from their own tools. This has led to collaborative work across Bristol, EI, EBI and JIC to create a CerealsDB tool for exploring QTL data. As a prototype based on traits scored in Paragon x Watkins NAM lines, users can view QTL peak and flanking markers, Crop Ontology identifiers, and a genome browser view at Ensembl: http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/select_QTL.php. This has also allowed us to create links to GRU SeedStor for varieties genotyped on the Axiom 820 & 35K platforms: http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/select_varietal_info_SeedStor.php.
Exploitation Route The main outputs of this award are focused on providing software and data for the wheat community, comprising biologists, bioinformaticians, breeders, and external stakeholders. We have produced a project website, as well as an open data portal, for sharing DFW outputs with this community. We are actively interacting with the wheat community through the organisation of DFW stakeholder workshops to demonstrate and train users in our resources.

Clear and accessible representation of complex and extensive datasets from wheat can be used by wheat breeders and the research community. Examples include: Extracting gene content of key loci from the genome sequence of Chinese Spring in Ensembl Plants; downloading high density genotypic data on modern varieties compared to DFW germplasm in CerealsDB; Searching the genomes of modern UK varieties like Paragon, Robigus and Claire in the DFW Data Portal; studying the pedigree and graphical genotype of the Breeders Toolkit on the DFW website; quickly and efficiently requesting seed from the Germplasm Resource Unit using Seedstor.

We host visitors to our sites to demonstrate the latest technology and software for crop phenotyping and for analysis and sharing of data. We run training courses on the data resources and software that we are developing for wheat scientists.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)

 
Description The promoter exon capture platform is now being used by UK and international wheat researchers and breeders. We are also in discussions with AHDB about adding re-sequencing as a step for breeders for use on the UK recommended list of varieties. We are currently collaborating with the Wendy Harwood to generate transgenic plants, where we aim to write a Pathfinder and Follow-on Fund grant to develop REQ7 as tool for breeders to increase recombination frequency and break down linkage drag. We have been awarded a EAGER-Technology breakthrough award to take forward DNA methylation as a tool for breeders. These approaches potentially offer a new level of genetic variation for breeders to use. We are working with LGC to develop an assay and with IBM to apply ML and AI to develop algorithms to characterise, identify and associate methylation with changes in gene expression. We have continued to develop the Grassroots infrastructure system at EI, which underpins the DFW Data Portal. We are able to house all data types from small granular information to very large datasets and present them with rich metadata to the community. We currently house 21TB of wheat datasets that have been accessed by nearly 2000 researchers from 64 countries. We have built the first iteration of a DFW-wide Field Trial database and search service which will provide a simple mechanism for researchers and breeders to see what is being grown and where, and it what conditions and treatments, across the whole of DFW. This provides the basis for all downstream datasets, e.g., genotypes, sequence data, and recorded phenotypes, to be linked to a seed packet, accession, and growing conditions. We have continued to develop eirods-dav (https://github.com/billyfish/eirods-dav), a tool to interact with both iRODS data grids and Apache httpd web servers to allow for easy sharing of data and metadata from a standard web interface. We have added a number of features including the ability to greatly modify the page layout to make it more user-friendly, expose the metadata for viewing, searching and editing, and adding a REST API to allow for programmatic access to the underlying data and metadata. Our further developments of eirods-dav used by the DFW Data Portal has allowed access for any developers or users to write programs and scripts to query and interact with the datasets, along with their associated metadata. Similarly, the development of the GRU Application Programming Interface (API) for programmatic access to DFW germplasm metadata has unlocked the potential for this vital information resource to be integrated with other services. Users of CerealsDB and the DFW Data Portal, and indeed any other web-based service, can now query the GRU SeedStor database quickly and easily. We use this resource to power our DFW Field Trial search service, now in testing, and to allow QTL searches from within the CerealsDB infrastructure. All EI DFW infrastructure, including the DFW Data Portal, is housed on the CyVerse UK, our public research cloud that is funded by EI's National Capability in e-Infrastructure (NC3). We have deployed an upgraded OpenNebula virtualisation management platform, and created the required networking and operating system inventory so that we can now provide compute and storage resources within the CyVerse UK cloud to DFW researchers. We have made this available this year (http://cyverseuk.org/about/collaborations/designing-future-wheat/) and have since already completed one data analysis project for a UK wheat researcher, with more discussions currently underway.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)
Impact Types Cultural,Societal,Economic

 
Description A member of the Science Board of the G20 wheat initiative set up by the G20 agricultural ministers to coordinate wheat research across the G20 countries
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact By coordinating wheat research to address food security issues across the G20 countries, it makes more effect use of the funding by G20 government agencies
 
Description BEIS/UKRI/RCUK Cloud Workshop, London, 24-10-2017
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description Particapited in parliamentary debate on CRISPR CAS and post-BREXIT genetic engineering in crops -APPG Science & Technology in Agriculture
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description 16ALERT
Amount £283,383 (GBP)
Funding ID BB/R000662/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2017 
End 08/2018
 
Description 18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES
Amount £273,500 (GBP)
Funding ID B/S020942/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description Artificial intelligence and deep learning in image based crop phenomics for predicting seed quality
Amount £99,034 (GBP)
Funding ID BB/S507441/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
Description Bayer Grants4Traits
Amount £20,661 (GBP)
Organisation Bayer 
Department Bayer CropScience Ltd
Sector Private
Country United Kingdom
Start 01/2018 
End 12/2018
 
Description China Partnering Awards - Forge a long-term UK-China relationship in phenotyping, Agri-Tech innovation and crop research for Rice and Wheat
Amount £124,448 (GBP)
Funding ID BB/R021376/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description IPA Industrial Partnering Award - China Partnering Awards - Forge a long-term UK-China relationship in phenotyping, Agri-Tech innovation and crop research for Rice and Wheat
Amount £30,429 (GBP)
Funding ID BB/R021376/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description Integration of COPO and CGCore Schemas and Associated Repositories
Amount £62,968 (GBP)
Funding ID 2018X329.EI 
Organisation International Food Policy Research Institute (IFPRI) 
Sector Charity/Non Profit
Country United States
Start 09/2018 
End 01/2019
 
Description John Innes Centre Institute Strategy Funding - The elucidation of transcription factor networks underling internode extension in wheat
Amount £13,911 (GBP)
Organisation John Innes Centre 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2018
 
Description NRP Seed fund - A GPU-accelerated machine-learning based agricultural vehicle navigation system for crop monitoring and trait analysis
Amount £2,500 (GBP)
Funding ID SLSF 74 
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 03/2018 
End 08/2018
 
Description NRP Seed fund - A collaboration between the Earlham Institute (EI) and the University of East Anglia (UEA) to understand the role of small RNAs in complex gene regulatory networks in bread wheat
Amount £15,000 (GBP)
Funding ID SLSF 68 
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 01/2018 
End 01/2019
 
Description Open plant fund - Single cell pollen meiosis screening in wheat
Amount £4,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 08/2017 
End 07/2018
 
Description OpenPlant: Comparative analysis of cell free and in planta protein synthesis systems
Amount £4,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 02/2018 
End 12/2018
 
Description UK-China Newton Network+ Round 1 - AirSurf for automated image analysis and UAV-deployed remote sensors
Amount £30,000 (GBP)
Funding ID Newton Network+ SM003 
Organisation Newton Fund 
Sector Public
Country United Kingdom
Start 03/2018 
End 07/2018
 
Title CropSight - an automated data collation, storage, and phenotyping management system 
Description CropSight is a PHP and SQL based server platform, which provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralised data management. Data transfer and annotation are accomplished automatically though an HTTP accessible RESTful API installed on both device-side and server-side of the CropSight system, which synchronise daily representative crop growth images for visual-based crop assessment and hourly microclimate readings for GxE studies. CropSight also supports the comparison of historical and ongoing crop performance whilst different experiments 
Type Of Material Improvements to research infrastructure 
Year Produced 2019 
Provided To Others? Yes  
Impact CropSight is a scalable and open-source information management system that can be used to maintain and collate important crop performance and microclimate information. Big data captured by diverse technologies known collectively as the Internet of Things (IoT) is extremely difficult to calibrate, annotate and aggregate. This presents a major challenge for plant scientists trying to understand the dynamics between crop performance, genotypes and environmental factors and for agronomists and farmers monitoring crops in fluctuating agricultural conditions. The new system developed by researchers from the Earlham Institute, John Innes Centre, and University of East Anglia (UEA) provides near real time environmental and crop growth monitoring. 
URL https://github.com/Crop-Phenomics-Group/CropSight
 
Title Development of ChIP-Seq protocols in bread wheat 
Description The investigation of epigenetic marks enables deeper understanding of the gene expression regulation and the annotation of non coding functional sequences. Histone modifications (methylation, acetylation) are among the epigenetic marks most commonly assayed and specific modifications can be associated with biochemical activity (transcription, repression) and genomic elements (enhancers, promoters, coding regions). The protocols for chromatin immunoprecipation and sequencing have previously been developed for the model organism Arabidopsis thaliana, but never successfully applied to complex plant genomes such as the bread wheat. The protocols aimed to 1) improve the efficiency of chromatin extraction, 2) assay the antibodies, 3) evaluate yield and suitability of different tissues (leaves, root, spikelet, internode) fresh or frozen. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? No  
Impact The protocols will enable in depth understanding of gene expression regulation in bread wheat and relative crops. The protocols will directly be used to deliver objectives within the Designing Future Wheat (BBS/E/T/000PR9783), Signatures of Domestication and Adaptation (BBS/E/T/000PR9818), Regulatory interactions and Complex Phenotypes (BBS/E/T/000PR9819) awards. The protocols will be made available to the communities through the Supporting EI's ISPs and the UK Community with Genomics and Single Cell Analysis (BBS/E/T/000PR9816) award. 
 
Title Methyl-seq methods for wheat 
Description Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high- quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact As yet not known 
 
Title promoter exon capture platform 
Description Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Currently being used by DFW, CIMMYT and US CAPS projects 
 
Title AirSurf - a deep learning based aerial image analytic platform 
Description Derived from DFW's aerial image analysis work, AirSurf-Lettuce is an automated and open-source aerial image analysis platform that combines modern computer vision, up-to-date machine learning, and modular software engineering to measure yield-related phenotypes of millions of lettuces across the field. Utilising ultra-large normalized difference vegetation index (NDVI) images acquired by fixed-wing light aircrafts together with a deep-learning classifier trained with over 100,000 labelled lettuce signals, the platform is capable of scoring and categorising iceberg lettuces with high accuracy (>98%). Furthermore, novel analysis functions have been developed to map lettuce size distribution in the field, based on which global positioning system (GPS) tagged harvest regions can be derived to enable growers and farmers' precise harvest strategies and marketability estimates before the harvest. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact Aerial imagery is regularly used by farmers and growers to monitor crops during the growing season. To extract meaningful phenotypic information from large-scale aerial images collected regularly from the field, high-throughput analytic solutions are required, which not only produce high-quality measures of key crop traits, but also support agricultural practitioners to make reliable management decisions of their crops. We collaborate with the UK's second largest growers, G's Growers, and developed AirSurf-Lettuce that can measure millions of lettuces in the field, which has also helped the firm to improve the actual yield of iceberg lettuce in real-world agricultural practices. 
URL https://github.com/Crop-Phenomics-Group/AirSurf-Lettuce/releases
 
Title CropSight - a crop phenotyping management system 
Description As a scalable and open-source information management system, CropSight can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current experiment comparison through an integrated cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a personal computer, CropSight has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future. 
Type Of Material Data handling & control 
Year Produced 2018 
Provided To Others? Yes  
Impact CropSight can enable the accessibility of locally in the field through smart devices and remotely in an office using a personal computer. It has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future. We have used the CropSight system in our collaboration with BASF and Bayer Crop Science. 
URL https://github.com/Crop-Phenomics-Group/CropSight
 
Title Epigenomic variation across a polyploid wheat diversity collection 
Description We survey genotype and DNA methylation across the core Watkins bread wheat landrace collection. We observe high transposable element variability and expansion, most frequently in retrotransposons, alongside high epigenomic diversity; while there is an association between methylation and genotype, methylation is a standalone source of variation between closely related accessions. Both methylation and genotype are influenced by geographic origin. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Lead to an EAGER grant to translate the research 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB23320
 
Title Field trial database schema for DFW 
Description Database schema for recording field trial data for DFW, stored in the Grassroots Infrastructure. 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? Yes  
Impact Standardise the data structure and schema for recording field trial data. 
URL https://github.com/TGAC/grassroots-field-trial-database-schema
 
Title Genotyping of 150 CIMMYT wheat lines (paper DOI 
Description 35K affymetrix array data for the High Biomass Association Panel of 150 spring wheat lines from CIMMYT. A paper explaining the panel and the use we made of these snps is available here: http://dx.doi.org/10.1111/pbi.13052 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Facilitated the identification of multiple marker trait associations which have now been incorporated into CIMMYT spring wheat marker assisted selection program. 
 
Title Recombination landscape of hexaploid bread wheat 
Description Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of open access data from 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We find that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel candidate RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions conserved across recombination sparse centromeric regions. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Demonstrates high rates of recombination in wheat previously not seen 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB28231
 
Title Watkins core collection re-sequencing data 
Description Re-sequence data for the Watkins collection 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact International collabration 
URL https://grassroots.tools/data/under_license/toronto/
 
Title promoter exon capture data 
Description The data contain the design space for the promoter and exon used in our capture 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. 
URL https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c...
 
Description A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls
Collaborator Contribution See above
Impact This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls
Start Year 2018
 
Description China-UK Plant Phenomics Centre 
Organisation Aberystwyth University
Department Institute of Biological, Environmental and Rural Sciences (IBERS)
Country United Kingdom 
Sector Academic/University 
PI Contribution Coordinated the MoU for jointly establishing a China-UK Plant Phenomics Centre (CUPPC) between NANJING AGRICULTURAL UNIVERSITY (China), HUAZHONG AGRICULTURAL UNIVERSITY (China), Aberystwyth UNIVERSITY (IBERS, UK), Earlham institute (BBSRC UK), Rothamsted Research (Plant Sciences Dept., BBSRC UK), University of East Anglia (UK), and University of Nottingham (UK).
Collaborator Contribution Signed MoU as well as initiated research visits between the seven research organisations.
Impact The establishment of the China-UK Plant Phenomics Centre (CUPPC) in Nanjing and Wuhan. The MoU signed between seven leading research organisations in China and the UK. The detailed research agreement is being signed between NAU and UEA/EI. The first NAU-NRP research workshop at Norwich Research Park in Jan 2019.
Start Year 2018
 
Description China-UK Plant Phenomics Centre 
Organisation Huazhong Agricultural University
Country China 
Sector Academic/University 
PI Contribution Coordinated the MoU for jointly establishing a China-UK Plant Phenomics Centre (CUPPC) between NANJING AGRICULTURAL UNIVERSITY (China), HUAZHONG AGRICULTURAL UNIVERSITY (China), Aberystwyth UNIVERSITY (IBERS, UK), Earlham institute (BBSRC UK), Rothamsted Research (Plant Sciences Dept., BBSRC UK), University of East Anglia (UK), and University of Nottingham (UK).
Collaborator Contribution Signed MoU as well as initiated research visits between the seven research organisations.
Impact The establishment of the China-UK Plant Phenomics Centre (CUPPC) in Nanjing and Wuhan. The MoU signed between seven leading research organisations in China and the UK. The detailed research agreement is being signed between NAU and UEA/EI. The first NAU-NRP research workshop at Norwich Research Park in Jan 2019.
Start Year 2018
 
Description China-UK Plant Phenomics Centre 
Organisation Nanjing Agricultural University
Country China 
Sector Academic/University 
PI Contribution Coordinated the MoU for jointly establishing a China-UK Plant Phenomics Centre (CUPPC) between NANJING AGRICULTURAL UNIVERSITY (China), HUAZHONG AGRICULTURAL UNIVERSITY (China), Aberystwyth UNIVERSITY (IBERS, UK), Earlham institute (BBSRC UK), Rothamsted Research (Plant Sciences Dept., BBSRC UK), University of East Anglia (UK), and University of Nottingham (UK).
Collaborator Contribution Signed MoU as well as initiated research visits between the seven research organisations.
Impact The establishment of the China-UK Plant Phenomics Centre (CUPPC) in Nanjing and Wuhan. The MoU signed between seven leading research organisations in China and the UK. The detailed research agreement is being signed between NAU and UEA/EI. The first NAU-NRP research workshop at Norwich Research Park in Jan 2019.
Start Year 2018
 
Description China-UK Plant Phenomics Centre 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution Coordinated the MoU for jointly establishing a China-UK Plant Phenomics Centre (CUPPC) between NANJING AGRICULTURAL UNIVERSITY (China), HUAZHONG AGRICULTURAL UNIVERSITY (China), Aberystwyth UNIVERSITY (IBERS, UK), Earlham institute (BBSRC UK), Rothamsted Research (Plant Sciences Dept., BBSRC UK), University of East Anglia (UK), and University of Nottingham (UK).
Collaborator Contribution Signed MoU as well as initiated research visits between the seven research organisations.
Impact The establishment of the China-UK Plant Phenomics Centre (CUPPC) in Nanjing and Wuhan. The MoU signed between seven leading research organisations in China and the UK. The detailed research agreement is being signed between NAU and UEA/EI. The first NAU-NRP research workshop at Norwich Research Park in Jan 2019.
Start Year 2018
 
Description China-UK Plant Phenomics Centre 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution Coordinated the MoU for jointly establishing a China-UK Plant Phenomics Centre (CUPPC) between NANJING AGRICULTURAL UNIVERSITY (China), HUAZHONG AGRICULTURAL UNIVERSITY (China), Aberystwyth UNIVERSITY (IBERS, UK), Earlham institute (BBSRC UK), Rothamsted Research (Plant Sciences Dept., BBSRC UK), University of East Anglia (UK), and University of Nottingham (UK).
Collaborator Contribution Signed MoU as well as initiated research visits between the seven research organisations.
Impact The establishment of the China-UK Plant Phenomics Centre (CUPPC) in Nanjing and Wuhan. The MoU signed between seven leading research organisations in China and the UK. The detailed research agreement is being signed between NAU and UEA/EI. The first NAU-NRP research workshop at Norwich Research Park in Jan 2019.
Start Year 2018
 
Description Developing CropQuant Phenotyping Robot and Intel's AI Technologies to Gain Insights of Wheat GxE Interactions in Changeable Environmental Conditions 
Organisation Intel Corporation
Department Intel Corporation (UK) Ltd
Country United Kingdom 
Sector Private 
PI Contribution Led and was selected for CASE PhD studentship - Developing CropQuant Phenotyping Robot and AI Technologies to Gain Insights of Wheat GxE Interactions in Changeable Environmental Conditions (ZHOUE19DTP).
Collaborator Contribution Standard CASE industrial cash and in-kind contribution.
Impact No yet.
Start Year 2019
 
Description EAGER - Eduard Akhunov 
Organisation Kansas State University
Country United States 
Sector Academic/University 
PI Contribution Joint funding and publications, method development
Collaborator Contribution Access to material and bioinformatics methods
Impact EAGER -BBSRC grant A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES Gardiner, L.-J., Brabbs, T., Akhunov, A., Jordan, K., Budak, H., Richmond, T., et al. (2019). Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. GigaScience. http://doi.org/10.1093/gigascience/giz018 IWGS Consortium, Jordan, K. W., Wang, S., Lun, Y., Gardiner, L.-J., MacLachlan, R., et al. (2015). A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16(1), 680. http://doi.org/10.1186/s13059-015-0606-4
Start Year 2018
 
Description HPE AI workshop 2019 
Organisation Hewlett Packard Enterprise (HPE)
Country United Kingdom 
Sector Private 
PI Contribution We worked with HPE staff to organise and host an AI Workshop at EI. We opened the course up for national delegates to attend and discover more about how AI and Machine Learning techniques can be applied to biological research data.
Collaborator Contribution HPE provided the trainers and staff to teach the materials.
Impact We will continue to work with HPE to supply our institutlonal HPE equipment. We have also put forward HPE as a potential partner in the upcoming DTP3 bid.
Start Year 2019
 
Description IBM 
Organisation IBM
Department IBM UK Ltd
Country United Kingdom 
Sector Private 
PI Contribution This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars. The project aims to: 1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools. 2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars 3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture 4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars. This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project.
Collaborator Contribution IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks.
Impact No outputs to data
Start Year 2017
 
Description KWS 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work
Collaborator Contribution Know of the techniques and approaches we are using, early access to the data we generate
Impact Double haploid seed population
Start Year 2017
 
Description MIAPPE metadata for DFW Phenotypes 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Public 
PI Contribution This has been an interaction with the wider group of MIAPPE standards team, but largely with Cyril Pommier at INRA Versailles to improve the recording of field-based phenotyping metadata so that the MIAPPE standard evolves into something that DFW can adopt fully.
Collaborator Contribution They have visited Rothamsted several times and participated in a project workshop in February 2018
Impact DIscussions and contributions have led to changes to the MIAPPE standard which has now been updated ..
Start Year 2018
 
Description Moussa Benhamed 
Organisation University of Paris-Saclay
PI Contribution WE are collaborating with Moussa Benhamed to develop Next generation sequencing technology to explore the 3D structural organisation in the wheat nucleus and epigenetic regulation in wheat.
Collaborator Contribution The have built sequencing libraries for design future wheat and are providing staff training
Impact Production of sequencing libraries analysis of histone modification, 3D genome structural organisation and Chromatin accessibility.
Start Year 2018
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution Identify key material for our EAGER project and Design future wheat. Support for collaboration with IBM.
Collaborator Contribution Discussion of methods and analysis of material relevant to RAGT.
Impact none yet
Start Year 2018
 
Description Syngenta Seeds Case Collaboration 
Organisation Syngenta International AG
Department Syngenta Seeds
Country Switzerland 
Sector Private 
PI Contribution Led the application of artificial intelligence and deep learning in Image-based crop phenomics for predicting seed quality with EI and Syngenta. Was awarded the grant (BB/S507441/1) for a case PhD studentship between Oct/2018 and Sep/2022.
Collaborator Contribution Standard CASE PhD studentship cash and in-kind contribution.
Impact A manuscript is being prepared between EI, JIC and Syngenta for machine-learning based software solution, SeedGerm.
Start Year 2018
 
Description Wheat Information System (WheatIS) 
Organisation Cold Spring Harbor Laboratory (CSHL)
Country United States 
Sector Charity/Non Profit 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Zentrum Munchen
Country Germany 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of California, Davis
Department UC Davis College of Biological Sciences
Country United States 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of Western Australia
Country Australia 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Title CropQuant - data processing of crop images 
Description Field of the invention: the present invention relates to data processing of images of a crop, in particular a cereal crop such as wheat, maize or rice, for use in image-based field phenotyping. The method comprises retrieving a series of images of a crop captured over a period of time and identifying, in an image (or "initial image") selected from the series of images to be used as a reference image, a reference system against which other images can be compared, the reference system including an extent of a crop plot and/or one or more reference points. The method also comprises, for each of at least one other image in the series of images, calibrating or adjusting the image using the reference system, and determining a height of a canopy of the crop in the image, a main orientation of the crop and/or a value indicative of vegetative greenness (for example, a normalised green value in an RGB colour space and/or excessive greenness). This can afford greater flexibility when monitoring a crop, particularly large numbers of crops, over periods of months. For example, the method can be used to process images of a crop which have been captured in the field and, thus, subject to vagaries of weather. Moreover, the method can be used for each crop and, thus, allow large data to be processed for large numbers of crops. 
IP Reference UKIPO, GB1709756.9 (application ref: PJP/81353GB1) 
Protection Patent application published
Year Protection Granted 2018
Licensed Commercial In Confidence
Impact CropQuant technology has been reported by UK national and EU media over a dozen of times since 2016. It has been featured as a stand-out example of UK-based Agri-Tech innovations and was presented BBSRC's Harvest 2050 and other industry-related activities. Recently, our bespoke farming robot CropQuant Sheila was invited to exhibit at REAP 2017, an event organised by Agri-Tech East, KTN and Innovate UK.
 
Title API for SeedStor 
Description API for https://www.seedstor.ac.uk to improve the programmatic access. Used in the Grassroots Infrastructure and CerealsDB. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2018 
Impact Grassroots Infrastructure and CerealsDB can now query SeedStor programatically instead of browsing the web page. 
URL https://github.com/TGAC/grassroots-seedstor-api
 
Title AirSurf-Lettuce: an aerial image analysis platform for ultra-scale field phenotyping and precision agriculture using computer vision and deep learning 
Description Aerial imagery is regularly used by farmers and growers to monitor crops during the growing season. To extract meaningful phenotypic information from large-scale aerial images collected regularly from the field, high-throughput analytic solutions are required, which not only produce high-quality measures of key crop traits, but also support agricultural practitioners to make reliable management decisions of their crops. Here, we report AirSurf-Lettuce, an automated and open-source aerial image analysis platform that combines modern computer vision, up-to-date machine learning, and modular software engineering to measure yield-related phenotypes of millions of lettuces across the field. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact Utilising ultra-large normalised difference vegetation index (NDVI) images acquired by fixed-wing light aircrafts together with a deep-learning classifier trained with over 100,000 labelled lettuce signals, the platform is capable of scoring and categorising iceberg lettuces with high accuracy (>98%). Furthermore, novel analysis functions have been developed to map lettuce size distribution in the field, based on which global positioning system (GPS) tagged harvest regions can be derived to enable growers and farmers' precise harvest strategies and marketability estimates before the harvest. 
URL https://www.biorxiv.org/content/10.1101/527184v1
 
Title CerealsDB Webtool Update 
Description Providing access to the Axiom chip data 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact It is a system used by researchers and breeders 
URL http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/axiom_extractor.php
 
Title Collaborative Open Plant Omics (COPO) 
Description COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories. COPO facilitates the links to data analysis platforms such as CyVerse UK and Galaxy. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces. This improvement output represents the beta release of the COPO platform in 2017. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact COPO has been added to the ELIXIR-UK roadmap for ELIXIR core data services, and is currently being used by EI and JIC researchers to deposit real, large scale sequencing datasets into the European Nucleotide Archive. COPO is also being investigated as a potential data entry tool for the CGIAR Big Data project, and this will be explored in a joint EAGER submission with CIMMYT. COPO has also been selected to act as one of the data ingestion pipelines for data arising from the Designing Future Wheat programme, depositing open data into the Grassroots repository. COPO is also being included in grant submissions to assist vertebrate and wheat communities in effective metadata management. COPO runs within the CyVerse UK National Capability infrastructure. 
URL https://copo-project.org
 
Title CropQuant Software System 
Description The CropQuant in-field phenotyping platform provides a cost-effective Internet of Things (IoT) powered crop monitoring system for wheat and other cereal crops, designed to be easily used and widely deployed in any environment. To manage and process data generated by the platform, we developed an automatic control system, high-throughput trait analysis algorithms, and machine-learning based modelling to explore the dynamics between genotypes, phenotypes and environment. This technology can be applied to breeding, cultivation, crop research, and digital agriculture. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2017 
Impact Since September 2017, the preprint of the CropQuant manuscript has been tweeted for 35 times, downloaded for more than 1272 times. CropQuant was reported by BBSRC and other industry-related activities such as Syngenta and Bayer Internal Seminar Series. CropQuant has also been featured as a stand-out example of UK-based Agri-Tech innovations. Recently, our bespoke farming robot using the CropQuant software system, Project Sheila, was invited to exhibit at REAP 2017, an event organised by Agri-Tech East, KTN and Innovate UK. 
URL https://github.com/Crop-Phenomics-Group/CropQuant/releases
 
Title CropSight - a scalable and open-source information management system for distributed plant phenotyping and IoT-based crop management 
Description CropSight is a PHP and SQL based server platform, which provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralised data management. Data transfer and annotation are accomplished automatically though an HTTP accessible RESTful API installed on both device-side and server-side of the CropSight system, which synchronise daily representative crop growth images for visual-based crop assessment and hourly microclimate readings for GxE studies. CropSight also supports the comparison of historical and ongoing crop performance whilst different experiments are being conducted. 
Type Of Technology Webtool/Application 
Year Produced 2019 
Open Source License? Yes  
Impact As a scalable and open-source information management system, CropSight can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current experiment comparison through an integrated cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a personal computer, CropSight has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future. 
URL https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giz009/5304887
 
Title DFW cloud HPC resources 
Description Designing Future Wheat researchers are able to request virtual machines within CyVerse UK to undertake bioinformatics analysis. 
Type Of Technology Grid Application 
Year Produced 2019 
Impact We have produced a robust and secure cloud framework within CyVerse UK to allow DFW researchers to access DFW and public data to analyse, as well as upload their own. We have already completed two successful pilot projects with external collaborators, and are now making the services available to all DFW researchers. 
URL http://cyverseuk.org/about/collaborations/designing-future-wheat/
 
Title DavRods Tools Update 
Description This update to mod_davrods includes the ability to add, edit and delete metadata entries from within a web browser, pull the metadata on demand into the web page using AJAX calls rather than on the initial loading of the page, as well as other user interface enhancements such as location breadcrumbs. It also allows the downloading of all of the metadata for a given iRODS data object or collection in a variety of different formats. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software underpins data sharing infrastructure used by DFW 
URL https://github.com/billyfish/eirods-dav/releases/tag/1.4.1
 
Title EIRods-DAV 
Description Eirods-dav provides access to iRODS servers using the WebDAV protocol and has a complete REST API for accessing and manipulating metadata from within a web browser. It adds a substantial amount of functionality to the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Eirods-dav leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact The software is now used to host the Designing Future Wheat data portal. 
URL https://opendata.earlham.ac.uk/wheat
 
Title Eirods-dav 
Description Eirods-dav provides access to iRODS servers using the WebDAV protocol and exposes a REST API for accessing and manipulating metadata from within a web browser. It adds a substantial amount of functionality to the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Davrods leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Eirods-dav is used to allow web-based access to a selection of files and research data released to the public by the Earlham Institute such as the Triticum Aestivum assemblies. It is used by the Grassroots Infrastructure to allow access to data produced by the Designing Future Wheat project. The Eirods-dav application runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/data/
 
Title Ensembl Plant Release 35 
Description Genome browser and associated analysis tools for plants including Wheat 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This resource is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Ensembl Plant Release 36 
Description General plant genomes browser and associated analysis software 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Software and data in the browser is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Ensembl Plants Release 37 
Description General genome browser for plants including wheat. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Software and data content is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Grassroots Tools Website 
Description This is the website for the Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Too soon to record impact 
URL https://grassroots.tools/
 
Title Knetminer Builder Update 
Description This is a software tool that is used to automatically construct knetminer instances and is being applied to all crop instances including wheat. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This enables regular updates to the knetminer instances when new component datasets are released. 
URL https://github.com/Rothamsted/ondex-knet-builder/releases/tag/v1.2
 
Title Leaf-GP Software Distribution 
Description Leaf-GP software is published with the software paper entitled "Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat" in Plant Methods in last December. The software is distributed under the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The software is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. It presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact The Leaf-GP paper generated 18169 downloads within a month and received an attention score of 21 (https://biomedcentral.altmetric.com/details/30811558#score), No.1 amongst all Plant Methods papers (48 in total) published from October 2017 and the attention scoring of the paper is higher than 91% of its contemporaries published from October 2017, worldwide. 
URL https://github.com/Crop-Phenomics-Group/Leaf-GP/releases
 
Title OWL Ontology for Bioknowledge Networks 
Description This ontology is used as part of a suite of tools to represent knetminer knowledge networks using RDF 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Making knetminer systems shared through semantic web technology will facilitate sharing and access to the data from other tools. 
URL https://github.com/Rothamsted/bioknet-onto
 
Title Ondex to RDF Exporter 
Description Ondex components and applications that are necessary for building genome-scale knowledge networks used in projects like KnetMiner. It includes the Ondex base, CLI, workflow engine and a set of plugins (parsers, mappers, transformers, filters and exporters) that are relevant for building genome-scale knowledge networks 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact It is part of a suite of tools that help knetminer networks, including those developed for wheat, be shared through linked open data methods. 
URL https://github.com/Rothamsted/ondex-knet-builder/tree/master/modules/rdf-export-2
 
Title Parental Genotype Service 
Description The Parental Genotype Service works with data from various cross-parental breeding lines with associated genotypic markers along with which parent is responsible for their presence in the child line. It can accept various queries across this data, 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact As part of a collaboration with Paul Wilkinson at the University of Bristol and Luzie Wingen at the John Innes Centre, it is used as part of a QTL web service available from the CerealsDB website. 
URL http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/select_QTL.php
 
Title The Grassroots Infrastructure 
Description The Grassroots software is an open source "as-a-Service" stack that powers a number of data dissemination and analysis activities at EI, and other sites such as CerealsDB at the University of Bristol. We have continued to develop the functionality within the software stack to share crop-related datasets. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Grassroots has previously been used to host the Field Pathogenomics project website and Yellow Rust map, the EI wheat BLAST service, the CerealsDB federation project, and the multi-scale improvements to the Polymarker marker design software. Recently, Grassroots has been put forward as the main data repository and metadata catalogue for the Designing Future Wheat project, and has started to host data from this project, the Open Wild Wheat Consortium, and 5 new wheat genomes from EI. The Grassroots service runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/
 
Title iRODS filename completion tool for BASH 
Description This is a tool to allow the iRODS client icommands to have auto-complete functionality within Bash as is the case with normal mounted filesystems. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact For people using the iRODS client icommands, it allows time to be saved as instead of having to type out the full paths which is error-prone and time-consuming, they can simply press the tab key to get all current matching filenames taking into account any characters that they may have already entered. 
 
Description 10 plus wheat genome project workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was to provide a consortium update on the 10 plus wheat genome project
Year(s) Of Engagement Activity 2018
URL http://www.10wheatgenomes.com
 
Description AI in life sciences - Presentation at the Royal Institute of Great Britain, organised by Royal Society of Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Artificial Intelligence - Can AI save the world? Dr Ji Zhou, Phenomics Project Leader at the Earlham Institute. Discussions regarding the inclusion of self-learning algorithms into systems that underpin modern life could help us address many of the global challenges society faces. But they also carry risks that may have devastating results. Can AI truly save the world, or is it too risky to depend on machine learning to solve our problems?

This event is presented in partnership with the Royal Society of Biology, the Biochemical Society and the British Pharmacological Society for Biology Week 2018.

Biology Week 2018 is from 6th-14th October and showcases the important and amazing world of the biosciences, getting everyone from children to professional biologists involved in fun and interesting life science activities.
Year(s) Of Engagement Activity 2018
URL https://www.rsb.org.uk/get-involved/biologyweek/royal-institution-debate
 
Description BMGF CIMMYT - UK Wheat Research Workshop - August 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A workshop was organised by the Bill and Melinda Gates Foundation between key CIMMYT investigators and Designing Future Wheat Investigators to explore areas of common interest to help network links and to identify areas of common interest. Possibilities of future collaborative projects were explored.
Year(s) Of Engagement Activity 2017
 
Description Bioinformatics for Breeding 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The practical course featured a collection of methods and bioinformatics tools fundamental for modern breeding, especially for crops. Next generation sequencing (NGS) has made large collections of open-source diversity genomic data possible, such as SNPs, that can be used as molecular markers for breeding. Combined with phenotypes, genome-wide association studies provide breeders with an understanding of the molecular basis of complex traits. Content: SNP calling/discovery and SNPs effects and context; NGS techniques for genotyping; Genetic markers, linkage analysis, and genetic maps; High-throughput phenotyping and image analysis; Association mapping (GWAS); Genome-wide predictions, modelling and simulations; Genomic selection.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/bioinformatics-breeding
 
Description CerealsDB Workshop for end users 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Academics and breeders attended to get overviews and tutorials of the tools available within CerealsDB, Grassroots and Ensembl Plants. This gave them an opportunity to discover how these tools might be useful for them as well as giving feedback to us, as the developers of these platforms, to help plan useful future work.
Year(s) Of Engagement Activity 2018
 
Description Challenges and Opportunities in Plant Science Data Management (Workshop, PAG 2019) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Davey organised the PAG 2019 workshop Challenges and Opportunities in Plant Science Data Management alongside Carolyn Lawrence-Dill from Iowa State University, USA.
Year(s) Of Engagement Activity 2019
URL https://www.intlpag.org/2019/
 
Description Conference organiser of PAG San Diego attracting 3800 plant and animal researchers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I am on the organising committee of the largest plant and animal ag genomics conference attracting some 3800 researchers, policy makers, industry etc
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
 
Description Covers workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Anthony Hall and David Swabrick from the Earlham Institute provided an 'Introduction to Transcriptomics' and as a 'Guide to Annotating Eukaryotic Genomes'. You can download this PDF on the tab to the right.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/cyverse-uk-rnaseq-workshop-2018
 
Description CyVerse Workshop (University of York) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Contributed to a CyVerse UK workshop (20-21 March 2017), delivering a session on RNAseq analysis. Workshop participants were guided in real-time through an established analysis pipeline in a cloud computing environment.
Year(s) Of Engagement Activity 2017
 
Description CyVerse Workshop (University of York) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Contributed to a CyVerse UK workshop (20-21 March 2017), delivering a session on RNAseq analysis. Workshop participants were guided in real-time through an established analysis pipeline in a cloud computing environment.
Year(s) Of Engagement Activity 2017
 
Description DFW Presentation to DEFRA chief science advisor 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact A discussion of the outcomes and impact of WISP and DFW programmes
Year(s) Of Engagement Activity 2019
 
Description Data Brokering for Plant Scientists (DivSeek partner's meeting, PAG 2018, San Diego) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Delivered a lightning talk to promote the COPO data brokering platform at the annual DivSeek partner's meeting at PAG.
Year(s) Of Engagement Activity 2018
 
Description Data, Data, Data Everywhere (Pint of Science talk, Norwich) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Davey delivered a talk as part of the Norwich 2017 Pint of Science series about the challenges and solutions for modern data management in the life sciences, including recent data developments, high-performance computing, and software tools.
Year(s) Of Engagement Activity 2017
URL https://pintofscience.co.uk/event/crops-crystals-and-computers-technology-for-food-security
 
Description DivSeek Partner's Meeting (PAG 2019) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Davey attended the DivSeek Partner's Meeting in the Courtyard Marriott hotel at PAG 2019.
Year(s) Of Engagement Activity 2019
 
Description Down The Tubes! Talk at the Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Davey gave a talk on the internet and data science entitled "Down The Tubes!" at the 2018 Norwich Science Festival.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/down-the-tubes/
 
Description EMPHASIS 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact EMPHASIS is a project to develop a European Science Infrastructure (ESFRI) for plant phenotyping. A community workshop was held at Rothamsted in 2018. An important component of the activities of EMPHASIS is the management and sharing of data following agreed national/international standards.
Year(s) Of Engagement Activity 2018
URL https://emphasis.plant-phenotyping.eu/
 
Description Elixir Authentication Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A workshop on how to integrate the Elixir authentication & authorisation protocols within the Grassroots infrastructure.
Year(s) Of Engagement Activity 2018
 
Description Engagement with Industry - KWS UK Ltd 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Mr Bian and Miss Minotto showed EI CyVerse infrastructure and Grassroots Infrastructure's features, including data sharing to the staffs from KWS UK Ltd: Ed Byrne, Janina Dordel, Andreas Menze and Vipul Patel.
Year(s) Of Engagement Activity 2018
 
Description Genome 10K and Genome Science Conference - Video 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Follow up video of the Genome 10k Genome Science conference held at NRP. View son Youtube - 70
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=25Dtu6ay7Is
 
Description Genome 10K and Genome Science social media engagement 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Social media campaign and press releases to promote the Genome10K and Genome Science event at NRP August 2017. We ran several campaigns from January to August to help promote registration for the event and gain interest from industry. SOCIAL MEDIA - Engagement 1920 Impressions 2084245. This has been our biggest campaign to date garnering engagement with International delegates in science and industry. The comms team also supported with design for promotional material such as posters, sponsor brochures and conference programmes.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Grassroots Infrastructure and the Wheat Information System (Genome 10K & Genome Science 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mr Bian and Dr Tyrrell presented a poster at Genome 10K & Genome Science 2017 conference.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Grassroots Infrastructure and the Wheat Information System (RDA Interest Group on Agricultural Data (IGAD), Barcelona) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Davey delivered a talk about the Grassroots software infrastructure for the dissemination of wheat data through federation and integration of storage and compute e-infrastructure.
Year(s) Of Engagement Activity 2017
URL https://www.rd-alliance.org/rda-interest-group-agricultural-data-igad-pre-plenary-meeting-3-4-april-...
 
Description Hosting a PhD student from CIMMYT (Mexico) for training 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Hall lab group hosted a Phd student supervised by Dr Matthew Reynolds (CIMMYT) and Dr John Faulkes (University of Nottingham) for training in crop genetics.

Over a period of 3 days we introduced her to concepts surrounding phenotype - genotype association analysis culminating in the successful application of GWAS to her data.

This lead to a very well recieved poster presentation at the Plant and Animal Genomes conference in 2019:

https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006

Strategies for achieving genetic gains in yield potential must combine enhanced above-ground dry matter as well partitioning to the grain (harvest index). The present study aligned with NIFA-IWYP (International Wheat Yield Partnership) project N-IWYP700* aimed to identify grain partitioning traits that help maximize grain yield in high biomass backgrounds.
A High Biomass Association Panel (HiBAP) comprised of 150 spring wheat elite genotypes was phenotyped in 2015-16 and 2016-17 at CIMMYT experimental station Norman E. Borlaug located in NW Mexico. Physiological traits measured included biomass, plant length (height, spike, awns, peduncle, internode 2 & 3), organ DM partitioning (spike, leaf lamina, true stem and leaf sheath) and fruiting efficiency (# of grain set per unit spike dry weight) at anthesis (GS65) + 7 days and at harvest, biomass, grain yield, yield components and harvest index was measured. BLUEs (Best Linear Unbiased Estimators) from the cross-year analysis and molecular markers generated using the 35K Wheat Breeders Axiom array were used to carry out a genome-wide association study (GWAS).

Novel marker-trait associations for the grain partitioning traits were identified mainly in chromosomes 5B and 6A; resulting in 13 at anthesis (e.g. LamPI, spike length) and 9 at harvest (e.g. HI, FE_GSP). More detailed results will be presented and their potential application in breeding programs in marker-assisted selection discussed.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006
 
Description Industry Seminar - Chris Burt, RAGT 'Bridging the valley of death: Molecular breeding in cereals'. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Second of our Industry seminar series. Chris Burt of the RAGT group spoke about the challenges associated with molecular breeding in cereals. A meeting with the Senior Management Team was organised along with a networking lunch with students.
Year(s) Of Engagement Activity 2017
 
Description Industry Seminar - R&D Facilitator, AB Agri 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Firts of the EI Industry Seminars programme, provides an opportunity for companies to visit EI and discuss the challenges they face in industry and how EI's research could help.
Mike Salter (AB Agri) was the first speaker and delivered a talk on challenges on monetising the microbiome. In addition to the talk, Mike met with members of the Senior Management Team, joined a networking lunch with students, post-docs and other EI staff and had met with researchers and EI director.
Key Figures:
Talk attendance= ~45
Networking Lunch attendance = 7
Meetings = 3 (members of SMT, Ji Zhou, Neil Hall)
Year(s) Of Engagement Activity 2017
 
Description Integrative Bioinformatics 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Gave a workshop about the Grassroots Infrastructure and COPO to end users.
Year(s) Of Engagement Activity 2018
 
Description JRS Biodiversity R workshop, Nairobi 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr Davey travelled to Nairobi, Kenya, as part of a JRS Biodiversity funded programme to teach a day R workshop to 23 representatives from the African Conservation Centre, Kenya Wetlands Biodiversity Reseach Centre, National Museums of Kenya, University of Nairobi, and the Jomo Kenyatta University.
Year(s) Of Engagement Activity 2019
 
Description John Innes Centre open day to the public 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact To show the general public plant science research in practise.
Year(s) Of Engagement Activity 2017
 
Description KTN Agri-tech mission in Colombia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Attended and contributed to Agri-tech Catalyst Colombia organised by the agri tech KTN and innovate UK. Talked and participated in workshops across Colombia
Year(s) Of Engagement Activity 2018
 
Description Meeting for collaborators on the Field Pathogenomics project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact As part of the Field Pathogenomics project, a meeting with the industrial collaborators to discuss what features they would like added to the web-based tool that we created for users to access the data.
Year(s) Of Engagement Activity 2016
URL https://grassroots.tools/yellowrust-map/
 
Description Member of the board of the G20 wheat initative 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I am a board member of the G20 wheat initiative set up by the G20 agricultural ministers to facilitate coordination of wheat research in the G20 countries. We organise working group to facilitate such coordination, and to identify priorities for funding by funding agencies within the G20 countries
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description Member of the management board of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A management board member of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description Monogram Grain Conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation of GWAS of 150 spring wheat lines associating agronomic, yield and biomass related traits to SNP markers for use in the CIMMYT (Mexico) pre-preeding marker trait assisted breeding program. This work is now published here: https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13052 and was carried out as part of the International Wheat Yield Partnership to provide essential marker trait associations to wheat breeders at CIMMT for tracking high biomass and radiation use efficiency, both which are thought to be a current bottleneck in genetic gains in their populations.

The poster was well received and gained a lot of attention during the poster session. A link made during this yielded an on going collaboration with scientists at Rothamsted Research (Mathew Paul).
Year(s) Of Engagement Activity 2018
URL http://www.monogram.ac.uk/MgNW2018.php
 
Description Norfolk forum Science festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact To provide the general public with an insight into plant science research
Year(s) Of Engagement Activity 2017
 
Description Oral Presentation The Rank Prize meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was run as an invitational meeting run by the "The Rank Prize Fund" and was named "The shape of wheat to come". The meeting was attended by 30 early career scientists and around 20 more seasoned scientists with the aim of introduction of early career scientists to long established members of the wheat community (including breeding companies). A participant was invited from the most influential groups studying wheat mainly from the UK and France. Each participant was required to
A brief description below:

The Trustees' Advisory Committee on Nutrition is arranging a series of symposia on topics that are of current interest. In 2018 we intend to organise a mini-symposium on The Shape of Wheat to Come which will be held at The Wordsworth Hotel, Grasmere, Cumbria, England, from 19th to 22nd March 2018.

The aim of the meeting is to provide a forum in which leading scientists and young research workers can meet and interact, in order to stimulate discussion and to advance the development of the subject. Attendance is by invitation only and will be limited to about 30 participants. The main speakers will have about 40 minutes for their talk and related discussion and the young scientists will be allocated 20 minutes to give an account of their work. The value of these symposia lies in their small, fully interactive nature, not only during the presentations and discussion, but at other times over meals, in the hotel bar and during recreational periods.
Year(s) Of Engagement Activity 2018
 
Description Oral presentation and poster presentation at the Plant and Animal genome conference (PAG) San Diego 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave a talk entitled "Exploring epigenetic diversity in polyploid wheat" to an audience of scientists including; PIs, postdocs, students, industrial partners and breeders. This highlighted the findings of our epigenetic diversity study.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4886
 
Description Oral presentation at conference: Training on Durum Wheat Genomics and Breeding, University of Bologna, Italy 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at training conference to educate and train breeders, farmers and students in bioinformatic techniques for the analysis of wheat genomics data
Year(s) Of Engagement Activity 2017
URL http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding
 
Description Oral presentation at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended and presented work at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel. This built links with researchers in Italy, France and Israel for future collaboration and sparked their interest in epigenetic research.
Year(s) Of Engagement Activity 2017
 
Description Oral presentation: Agilent User group meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact I presented my work analysing the methylation of wheat to many of the users of Agilent technology in the UK since I implemented Agilent technology for the study. Many PI's and postdoctoral researchers were present and were interested in how they could use this methodology for their own analyses.
Year(s) Of Engagement Activity 2018
URL https://www.chem.agilent.com/edm/2017/06/Uk_Seminar_2017/Documents/GenUGM/Agenda_GUGM.pdf
 
Description Organisation a day workshop at Eucarpia meeting , Clermont_Ferrand Paris, with INRA (French) and Proweizen (German ) and CIMMYT researchers 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The worship was to discuss possible collaborations which could lead to bids into the EU for funding
Year(s) Of Engagement Activity 2018
 
Description Organising and hosting: Genome 10K and Genome Science Parallel Conferences 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Earlham Institute hosted two conferences in parallel - The biannual Genome 10K conference and the annual Genome Science meeting from 29 August - 1 September 2017 (http://www.earlham.ac.uk/genome-10k-and-genome-science-conference). The conference attracted over 350 delegates, including sponsors and local council representatives in addition to the target attendees of PhD students, Postdocs and PIs from around the World. We received fantastic support from Greater Norwich Partnership, which comprises several local councils, including fantastic opportunities to showcase the city as well as entertain delegates with an exclusive tour of the castle. A joint press release was made with the councils, which was picked up by local media, resulting in a news article, and a lengthy (~15 minute) in-studio interview with our Director of Science, Federica Di Palma, raising awareness of the institute, our research and the wider goals of projects associated to the conference e.g. Genome 10K Project. Feedback from the delegates was fantastic with many delegates providing verbal feedback at the conference itself, including praise around gender balance of speakers, logistics and organisation of the conference, catering and entertainment. As part of our commitment to supporting early career researchers, we offered, at no additional registration cost, limited spaces on training and careers development workshops (de novo assembly course, RNAseq using Galaxy course, science communication workshop, CV skills workshops, and a session on career paths). Delegates enjoyed the location of the conference, for many it was their first visit to the area, and hosting these two conferences not only raised the profile of the institute and it's location, but also the fantastic research that we are engaged in, and elicited promises of return visits through anticipated collaborations, plus an appreciation for our skills in wider activities such as training and events.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/genome-10k-and-genome-science-conference-2017-gallery
 
Description PAG 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave talk at the Plant and Animal genome conference:
Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency
Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions.
Year(s) Of Engagement Activity 2019
 
Description Paul Bailey talk at PAG at Cyverse workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As more genomes are sequenced it is becoming apparent that gene duplication and deletion are important drivers in evolution, with rapidly expanding gene families often a signature of their role in an organism's adaptation to the environment. To identify these events, we are building a gene family analysis toolkit which will be deployed on the Cyverse cloud infrastructure for use by the scientific community. Central to its purpose will be the ability to distinguish evolutionary relationships between genes within gene families for currently and newly sequenced species, both at the intra- and inter-species level.
As a pilot study, we are using a collection of landrace bread wheats (the Watkins collection) which have been sequenced by exome capture to explore the diversity of the large Nucleotide Binding Leucine Rich Repeat (NLR) family of plant resistance genes in the collection. Illumina read data from each wheat line have been assembled using various tools. The resulting contigs have been aligned to their corresponding subgroups within the NLR family. Looking at subgroups that are expanded relative to other monocot species, we can demonstrate that further novel gene duplication events have occurred in specific lines of the Watkins collection. The next step will be to understand whether specific genes in the family are under positive selection and therefore which genes have particular functional significance. The assembly and downstream procedures will be placed into a Docker container for use on Cyverse as a tool for exploring the diversity of any gene family in any species with sequence data.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29841
 
Description PhenoHarmonIS Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk was given about the tools and data available within the Grassroots Infrastructure and how it uses standards to describe crop-based experimental data
Year(s) Of Engagement Activity 2018
URL https://sites.google.com/a/cgxchange.org/cropontologycommunity/2018-phenoharmonis
 
Description Phenotyping Data Standards Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop was convened to discuss the use of an emerging international standard for describing phenotyping datasets - MIAPPE withing the Designing Future Wheat programme. Most of the participants were collaborators in the the project, but a major contributor came from INRA.
Year(s) Of Engagement Activity 2018
 
Description Plant and Animal genomes conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attendance to plant and animal genomes conference 2019- including 2 x poster presentations. One poster contained work carried out and reported in a recent publication ( 10.1111/pbi.13052). This poster recieved a lot of attention and we were approached multiple times by scientists working in wheat barley and rice along with making contact with a member of the breeding community (KWS) who was interested in the marker trait associations (MTAs) we had discovered and presented in the poster. The second poster featured collaborative work we have carried out with Dr John Faulkes from the University of Nottingham, which also gain wide interest as it denotes the first identifiaction of markers relating to various stem and spike partitioning indices.

These presentations also have lead to further discussions with scientists from NIAB about the use of a capture probe set we have designed as part of Designing Future Wheat ISP and our International Wheat Yield partnership grant.
Year(s) Of Engagement Activity 2019
URL https://www.intlpag.org/2019/
 
Description Presentation - Characterization of functional noncoding RNAs: From prediction to experimental validation. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Evolution in the 21st Century: The Inaugural Conference of the Milner Centre for Evolution. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Convergent evolution of immunity in aquatic plants 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Presentation at The Sainsbury Laboratory retreat. The audience included group leaders, postdoctoral researchers and graduate students
Year(s) Of Engagement Activity 2018
 
Description Presentation - GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the 2018 Galaxy Community Conference (GCC2018), Portland, OR, USA, 25-30/06/2018. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industry representatives
Year(s) Of Engagement Activity 2018
 
Description Presentation - Aequatus: An open-source homology browser 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the 13th International Conference on Genomics (ICG13) Shenzhen, China. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industrial representatives.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Genomics applications for conservation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presentation as part of a training course for the use of genomic resources for species identification delivered to law enforcement officers in Cali, Colombia. The audience included university lecturers, graduate and undergraduate students, conservation organizations, law officers, representatives of the ministry of environment, ministry of justice,
Year(s) Of Engagement Activity 2018
 
Description Presentation - Poster - Characterization of Functional ncRNA in Plants 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Bioinformatics for Plant Biology Course, EMBL-EBI Hinxton
Year(s) Of Engagement Activity 2018
 
Description Presentation - RCUK GROW Colombia Natural Diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Presentation as part of FIMA 2018 in Bogota, Colombia. The audience included general public, conservation organization, schools, law officers
Year(s) Of Engagement Activity 2018
 
Description Presentation - What can we learn form a high Koala-ty genome? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation as part of the Norwich Science Festival. The audience included general public and schools
Year(s) Of Engagement Activity 2018
 
Description Presentation on DFW at the DEFRA stakeholders WGIN meeting at RRES 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Request for more information on the programme
Year(s) Of Engagement Activity 2017
 
Description Presentation on WISP/DFW to ACC1 Cereals and Grains conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The presentation was to inform the cereal grain (rice, maize and wheat) processes community on the step change which has occurred in wheat research and the involvement of WISP/DFW in the step change
Year(s) Of Engagement Activity 2018
 
Description Presentation on WISP/DFW to the BBSRC legume community 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The presentation was to describe how the UK coordinated wheat programme was put together, and the impact the programme has had on the step change which has occurred in wheat research
Year(s) Of Engagement Activity 2018
 
Description Presentation on WISP/DFW to the BBSRC rice community 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation described how the coordinated WISP/DFW UK wheat programme was put together, and the impact the programme has had on the step change which has occurred in wheat research
Year(s) Of Engagement Activity 2018
 
Description Press Release - Spectre 'catch of the day: a net full of trees' 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Press release on SPECTRE, a new open-source software package that simplifies the complex business of creating phylogenetic networks and trees. Sarah Bastkowski and Dan Mapleson. -SOCIAL MEDIA- Engagenments x 135, Impressions x78755
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/catch-day-net-full-trees
 
Description Royal Norfolk Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Stewarded the Innovation Hub at the Royal Norfolk Show. The Innovation Hub aims to showcase agricultural related technologies and developments and communicate them to the general public, farmers and growers. This two day event attracted around 80,000 visitors from around the county and across the UK.
Year(s) Of Engagement Activity 2017
 
Description Royal Norfolk Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Stewarded the Innovation Hub at the Royal Norfolk Show. The Innovation Hub aims to showcase agricultural related technologies and developments and communicate them to the general public, farmers and growers. This two day event attracted around 80,000 visitors from around the county and across the UK.
Year(s) Of Engagement Activity 2017
 
Description Susan Duncan PAG talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact San Diego, PAG XXVII - Plant & Animal Genome Conference, January 12-16th 2019

Talk entitled: Insights into Arabidopsis Gene Regulation and Wheat Nuclear Organisation using Single Molecule RNA FISH
Year(s) Of Engagement Activity 2019
 
Description Talk and discussion with Elsoms seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders.
Year(s) Of Engagement Activity 2018
 
Description The Breeding API (BrAPI) community meeting about Genotyping APIs at the Plant and Animal Genome conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Breeding API (BrAPI) Project is an effort to create a RESTful specification to enable interoperability among plant breeding databases. The discussion was focused on genotyping APIs.
Year(s) Of Engagement Activity 2019
 
Description Training - Single-Cell RNAseq Training Course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training delivered as part of the Single-Cell RNAseq Training Course at EI. The audience included postdoctoral researchers and graduate students
Year(s) Of Engagement Activity 2018
 
Description Training course delivery: BecA-ILRI Hub 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Myself and Laura Jayne Gardiner were approached to deliver a 1 week training session at the BecA-ILRI Hub, Nairobi, Kenya. The course was a 3 month training program ran by the Alliance for Accelerated Crop Improvement in Africa. Our contribution to the program was training in the background of NGS technologies and their use in crop development along with teaching applied bioinformatics fundamentals to the group of students. The students on the course were from >15 countries in Africa and returned to their host institutes with a fantastic base knowledge of bioinformatics which they will apply for crop/livestock improvement throughout Africa.
Year(s) Of Engagement Activity 2018
URL https://acaciaafrica.org/bioinformatics-community-practice/members-and-management/
 
Description UKRI Darwin Tree of Life Project meeting, London 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Dr Davey travelled to London with other EI staff to discuss strategy for an SPF bid to UKRI for the UK Darwin Tree of Life Project.
Year(s) Of Engagement Activity 2018
 
Description Visit from Collaborator from University of Bristol; Paul Wilkinson 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Visit from Collaborator from University of Bristol; Paul Wilkinson
Year(s) Of Engagement Activity 2018
 
Description Visit from Collaborators from University of Melbourne; Andrew Lonie, Glen Mooney and Rhys Francis 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Visit from Collaborators from University of Melbourne; Andrew Lonie, Glen Mooney and Rhys Francis
Year(s) Of Engagement Activity 2018
 
Description Web Article - Day in the life of... a wheat bioinformatician on her own research path - 18.07.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/day-life-%E2%80%A6-wheat-bioinformatician-her-own-research-path
 
Description Web article - A celebration of science in Norwich - 27.08.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

Promoting our engagement in the Noriwch Science festival beyond our region.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/celebration-science-norwich
 
Description Wheat Initiative group discussion at Plant and Animal Genome conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion of the latest research activities from the Wheat Initiative members.
Year(s) Of Engagement Activity 2019
 
Description WheatIS Expert Working Grop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The expert working group for the Wheat Information System is developing standards and tools to enable the global wheat science community to share data effectively.
Year(s) Of Engagement Activity 2014,2015,2016,2017,2018
URL http://wheatis.org/
 
Description iRODS functionality within the Grassroots Infrastructure (iRODS User Group Meeting 2017, Utrecht, The Netherlands) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Tyrrell presented work on the development of the eirods-dav software package for the Grassroots data dissemination platform.
Year(s) Of Engagement Activity 2017
URL https://irods.org/ugm2017/