Data access and analysis
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
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.
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- University of Paris-Saclay (Collaboration)
- IBM (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- OXFORD NANOPORE TECHNOLOGIES (Collaboration)
- Monogram Network (Collaboration)
- Nanjing Agricultural University (Collaboration)
- Helmholtz Association of German Research Centres (Collaboration)
- Intel (United States) (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- ELIXIR (Collaboration)
- Rothamsted Research (Collaboration)
- John Innes Centre (Collaboration)
- Huazhong Agricultural University (Collaboration)
- BASF (Collaboration)
- University of Bristol (Collaboration)
- RAGT Seeds (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- University of Western Australia (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- University of East Anglia (Collaboration)
- University of California, Davis (Collaboration)
- Syngenta International AG (Collaboration)
- KWS UK (Collaboration)
- Kansas State University (Collaboration)
- Cold Spring Harbor Laboratory (CSHL) (Collaboration)
- Hewlett Packard Enterprise (HPE) (Collaboration)
Publications
Akay A
(2019)
Identification of functional long non-coding RNAs in C. elegans
in BMC Biology
Alkhudaydi T
(2019)
An Exploration of Deep-Learning Based Phenotypic Analysis to Detect Spike Regions in Field Conditions for UK Bread Wheat.
in Plant phenomics (Washington, D.C.)
Backhaus AE
(2022)
High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat.
in Plant physiology
Baggs E
(2017)
NLR diversity, helpers and integrated domains: making sense of the NLR IDentity.
in Current opinion in plant biology
Bailey PC
(2018)
Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.
in Genome biology
Bailey PC
(2018)
Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.
in Genome biology
| 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 | Since 2017, we have endeavoured to bring together researchers from across the programme and beyond into the industrial and breeding sectors, to deliver a cohesive and faceted set of data science objectives. We have met all our objectives within the reporting period, demonstrating the key impacts of dedicated funding and effort put forward to solve issues in data management, analysis, sharing and reuse according to the FAIR principles. EI has continued our development of the Grassroots data platform, which has been aided by close collaboration between the EI data infrastructure members and data generators at JIC and Rothamsted. The Grassroots Field Trials system has had a major upgrade in the last year with the system now taking into account a datatype of values for the phenotypic data e.g. numeric, text, dates, etc. With this, we are now able to do statistical analysis for all of the numeric phenotypic data and produce user-friendly ways of displaying this data such as interactive heatmaps. The options for exporting the data have increased too. As well as the existing Frictionless Data Packages, the application now automatically generates PDF reports for each study that users can download as well offering CSV downloads of the plot data. Alongside these features, working closely with the users and curators, many new metadata fields have been added to the system too. The number of studies in the system has grown to 143 with 65 having full plot data. We organised a workshop "Designing Future Wheat in Practice" (November 2022) to introduce data generators and curators to the process of submitting data into the system. The Haerty group has continued to work on the GeneSeqToFamily workflow. Following the improvement of GeneSeqToFamily to be able to handle large collections of genes (>1.4 million CDS) and identification of 208,510 gene families across 10 wheat varieties, we have developed web services to make the data available, but most importantly searchable, to the community on Grassroots. This will include the possibility to retrieve gene families, associated trees and alignments from a given gene name or BLAST search. We are collaborating with JIC to link with the Wheat Expression Browser. We have started to make all families identified, including alignments and associated trees, publicly available. The data and analyses are fully available here: http://wheatgenefamilies.cyverseuk.org/. We engaged with Rothamsted Research to make our data available to knetminer. We released our pipelines on the EI Github repository (https://github.com/TGAC/GSTF_snakemake). A manuscript focusing on the pipeline development will be submitted by the end of Q2 2023. We developed a pipeline to annotate long noncoding RNAs across 10 heat varieties and to compare their expression. We identified 48,854 lncRNAs across all strains and characterise their expression. Although 17,411 appears to be cultivar specific, the remaining are found across at least two cultivars, with nearly 4000 reproducibly expressed across all cultivars. We also identified lncRNA triads. We made our code available on the Earlham github repository (https://github.com/TGAC/lncRNA-analysis). A manuscript focusing on the annotation and regulation of these loci will be submitted for publication in Q3 2023. This work led to a collaboration with Dr Laura Dixon (Leeds University) to annotate and characterise the expression of lncRNAs associated with flowering in wheat. We modified protocols for very low input RNA-Seq developed first for mammalian systems and applied those to investigate gene expression along the axis in the developing spikelet. This work was performed in collaboration with Dr Iain Macaulay (EI, NC1), Prof Cristobal Uauy (John Innes Centre), Prof Richard Morris (John Innes Centre). We demonstrate significant changes in expression in thin slices across the axis, identifying MADS-box transcription factors, including VRT-A2, as highly expressed at the base of the spikelets, and associated with increased numbers of rudimentary basal spikelets (10.1093/plphys/kiac156). In DFW WP2.2, in collaboration with Kim Hammond-Kosack (RRes) we used the long term grassland experiment to harvest a diverse set of ~80 wild grass root fungal species. From this collection we identified fungal species important to drive understanding of the adaptation of the Take-all pathogen (Gaeumannomyces tritici) to wheat, as well as other species able to colonise wheat roots with novel biocontrol properties. To this set we added known wheat infecting Take-all and biocontrol isolates. Interacting with DToL Fungi, we spearheaded advances in high molecular weight DNA extraction and also extracted RNA for 17 isolates. In collaboration with David Swarbreck (Core Bioinformatics Group, EI) we have produced de novo genome assemblies for all strains and annotated gene models using a novel iterative approach which consolidates evidence from multiple strains sequenced in the same pipeline. Following the generation of a long read assembly and annotation of Amblyopyrum muticum in collaboration with John Feller at Kansas state University and University Nottingham DFW partners, the Hall group has continued work on the de novo annotations of the 10+ wheat genomes which are now live on Ensembl plants (http://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core). We published a paper on chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines in collaboration with Nottingham (Plant Genomes, https://doi.org/10.1002/tpg2.20193). A second collaborative paper has been published with Nottingham, and we have also submitted a paper to the Plant Biotechnology Journal on whole genome sequencing to uncover the structural and transcriptomic landscape of hexaploid wheat/Am.muticum introgression lines (https://doi.org/10.1111/pbi.13859). In addition to these synthetic hybrids we have also used the same methods in collaboration with CIMMYT to identify an natural introgression linked to increased heat tolerance (https://doi.org/10.1038/s42003-022-04325-5). We have published: a gene mapping framework for wheat combining Mapping by Sequencing and traditional markers demonstrated using the Yr7 yellow rust resistance gene (https://doi.org/10.1371/journal.pone.0231157); a paper as part of the 10 plus wheat genome international collaboration including EI's contribution of 4 elite UK cultivar two critical to DFW - Paragon and Cadenza and a collaboration including PIs from EI and JIC (https://doi.org/10.1038/s41586-020-2961-x) about multiple wheat genomes revealing global variation, important to power modern breeding. All data is uploaded to Ensembl Plants by the Ensembl team at EBI, and the raw datasets are publicly available on the DFW Grassroots data portal. We have now generated a Hi-Fi assembly for Paragon generating a a high quality assembly for this key UK cultivar (PRJEB59244) . In collaboration between researchers in Paris, EI and JIC we have published a paper (https://doi.org/10.1186/s13059-020-01998-1) about how wheat chromatin architecture is organised in genome territories and transcription factories; We have identified significant variation in gene expression along the developing spikelet axis in Paragon, including transcription factors, and established a computational pipeline to identify long non-coding RNAs in wheat and application to the 12+ pan transcriptomes. In collaboration with EI and JIC we are finalising the analyses on the transcriptomic data generated from sections of the developing spike. Our work highlights differential gene expression along the axis, identifying genes among differentially expressed genes. Those MADS-box genes were previously found to be associated with spike development. We aim to submit a manuscript in the coming months. We are currently looking at further extending this work to a much finer resolution through the application of spatial transcriptomic using the 10X Genomics Visium platform. Anil Thanki and Nicola Soranzo have continued to improve the GeneSeqToFamily pipeline to enable large annotation sets (over 4 million genes across 10 wheat accessions) to be analysed. Anil Thanki has performed the preliminary annotation of the long non-coding RNA across the pan-transcripome lines, and is now investigating the pattern of expression of these non-coding genes across lines and tissues. This work is complementing the ongoing work on protein coding genes performed by Rachel Rushmore and Benjamen White in Anthony Hall's group. As with every year, we have continued to provide 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. DCTF meetings have been held every month since project start, despite COVID. This has meant we have increased our rate of data sharing for key data types, including field trials, omics and variation datasets, and publications. |
| 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. As a result of this, for example, field managers at Rothamsted Research are using our the DFW Grassroots infrastructure to house WGIN datasets. 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, Kronos, Cadenza, 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 and using a new API to quickly gain access to the germplasm information 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) |
| URL | https://designingfuturewheat.org.uk/resources/ |
| Description | Our analyses undertaken and tools developed across WP4 have provided exceptional levels of open data access, completely fulfilling to the remit of our original goals. This has been noted by the community as a dramatic step change in how wheat data and knowledge is shared with the international wheat research and breeding efforts. We have continued to develop the Grassroots infrastructure system at EI, which underpins the DFW Data Portal and field trial information systems. This field trial resource is vital for users to access fundamental accession, location, phenotyping and associated image data for DFW trials in a standardised form. This has provided JIC and RRes with consistent and fit-for-purpose mechanisms to standardise field trial information across the programme. Due to this success, trials from previous programmes (e.g. WGIN) have also been added into the system to provide consistent information from year to year. Within our DFW Data Portal we are also able to house all data types from small granular information to very large datasets and present them with rich metadata to the community. We now house 28TB of wheat datasets that have been accessed by over 6000 researchers from over 70 countries, and have transferred over 30TB of data to our users. Our DFW-wide Field Trial database and search service has seen good uptake, with researchers from JIC and Rothamsted providing more field trial data into the system. The level of access to open wheat data has been highlighted as a key strength of the DFW project. In terms of genomic impact, we have generated a long read assembly of Muticum in collaboration with Nottingham and Kansas state University. We also finished the work to identify introgressions with 25 lines submitted to the wheat Breeders Toolkit, providing this useful resource directly to the community. We developed a pipeline to generate high quality SNPs for designing KASP assays to distinguish between wheat and Muticum wheat and Thinopyrum, which we have released to the community. The wheat pangenome paper including the de novo assemblies of 4 UK elite cultivars Robigus, Clare, Paragon and Cadenza was published, and the paper included 9 DFW authors from both the JIC and EI. These genomes will power the new future of rapid and precise wheat breeding. Arbor have now launched wheat promoter capture bait products based on our DFW design (https://doi.org/10.1093/gigascience/giz018). We have now generated a HiFi assembly for Paragon (PRJEB59244) 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. 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). Our OpenNebula virtualisation management platform is working well, and we have provided compute and storage resources within the CyVerse UK cloud to DFW researchers, e.g. the KnetMiner SPARQL query endpoint (RRes), and the AutoCloner website (Bristol). Additional datasets have been added to the DFW data portal and the total size of these hosted datasets has grown to over 30TB. In terms of the amount of traffic, 1135 unique visitors have downloaded nearly 200,000 files and the amount of data downloaded has been 17TB. The functionality of search service has also also been expanded with more metadata being indexed and searchable along with new facets. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software) |
| Impact Types | Cultural Societal Economic Policy & public services |
| 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 | Interview with Environment Adviser from the UK Parliamentary Office of Science and Technology |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | Contacted by UK Parliament to contribute to a POSTnote (short document to advise ministers on a given topic) on genebanks and Digital Sequence Information as a result of my recent election to the DivSeek Board of Directors. I was interviewed to provide information around current international policies on DSI and how future UK involvement might be shaped around open licencing/MTAs of DSI datasets. |
| URL | https://www.parliament.uk/postnotes |
| 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 | 07/2017 |
| 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 | BB/S020942/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2021 |
| Description | A proof of concept that RECQ 7 can be used as a tool to increase recombination |
| Amount | £137,389 (GBP) |
| Funding ID | BB/T011963/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 09/2022 |
| 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 | 09/2023 |
| Description | BBSRC NRPDTP iCASE Studentship - Using open data and machine learning approaches to decode the regulatory regions of wheat |
| Amount | £28,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2025 |
| 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 | 03/2018 |
| End | 03/2021 |
| Description | Exploiting night-time traits to improve wheat yield and water use efficiency in the warming climate of North-western Mexico |
| Amount | £541,033 (GBP) |
| Funding ID | BB/S012834/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 05/2022 |
| Description | Frictionless Data |
| Amount | £3,333 (GBP) |
| Organisation | Open Knowledge Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2020 |
| End | 12/2020 |
| 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 | 03/2018 |
| 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 | 08/2018 |
| 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 | Academic/University |
| 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 | 07/2017 |
| 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 | The National Institute of Food and Agriculture |
| Amount | $884,000 (USD) |
| Organisation | U.S. Department of Agriculture USDA |
| Sector | Public |
| Country | United States |
| Start | 07/2022 |
| End | 07/2025 |
| 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 |
| Description | Using Nvidia technologies to conduct deep-learning based wheat phenotypic analysis |
| Amount | $6,000 (USD) |
| Organisation | NVIDIA |
| Sector | Private |
| Country | Global |
| Start | 06/2018 |
| End | 07/2019 |
| Description | Using REC Q7 to drive increases in recombination in crop genomes |
| Amount | £9,677 (GBP) |
| Funding ID | BB/T010096/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 02/2020 |
| 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 | The DFW CKAN Digital Repository |
| Description | The CKAN digital repository has been set up as part of WP4 of Designing Future Wheat to hold all DFW publications alongside any supplementary datasets and information. This gives the public and researchers immediate access to DFW funded research through open access routes where available. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We have buit scripts to find and make available open access versions of all DFW published research, either as preprints or as journal articles. We also supply any supplementary information as appropriate to aid information dissemination. The DFW CKAN runs within Earlham Institute's CyVerse UK National Capability. |
| URL | https://ckan.grassroots.tools |
| Title | The Grassroots DFW Data Portal |
| Description | Continually updated large datasaet repository for the DFW project. Houses a variety of key wheat and associated datasets that are either under the Toronto licence or others as apprpriate for the level of open access. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | To date, we house 24TB of wheat datasets that have been accessed by over 4000 researchers from 64 countries. |
| URL | https://grassroots.tools/dfw |
| 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 | ACACIA Bioinformatics Community of Practice (BixCoP) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Members of EI delivered training throughout the year for the BixCoP fellowship programme. |
| Collaborator Contribution | The GCRF STARS project was led by JIC and hosted at BeCA-Hub ILRI in Nairobi. |
| Impact | The training programme trsulted in a group of Fellows ready to take their skills back into their home countries and communities, with some undertaking Carpentries instructor training so that they can lead their own training courses in those communities. |
| Start Year | 2018 |
| Description | ACACIA Bioinformatics Community of Practice (BixCoP) |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Members of EI delivered training throughout the year for the BixCoP fellowship programme. |
| Collaborator Contribution | The GCRF STARS project was led by JIC and hosted at BeCA-Hub ILRI in Nairobi. |
| Impact | The training programme trsulted in a group of Fellows ready to take their skills back into their home countries and communities, with some undertaking Carpentries instructor training so that they can lead their own training courses in those communities. |
| Start Year | 2018 |
| Description | BASF |
| Organisation | BASF |
| Country | Germany |
| Sector | Private |
| PI Contribution | We are using the the promoter capture platform developed in (https://doi.org/10.1093/gigascience/giz018) to sequence wheat cultivars |
| Collaborator Contribution | Paying for sequencing and capture |
| Impact | Funded ICASE studentship "Using open data and machine learning approaches to decode the regulatory regions of wheat" |
| Start Year | 2020 |
| 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 | Collaboration with Oxford Nanopore Technologies |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of the upcoming EI strategic programme we will be producing novel protocols for single cell long read RNA and DNA sequencing as well as novel approaches to detect DNA replication through base modification |
| Collaborator Contribution | ONT will contribute through providing expertise in machine learning models applications (base modification), technology solutions and protocols developments for single cell RNA / DNA seq |
| Impact | Engagement with ONT on March 7th to develop the collaboration as part of the upcoming ISPs |
| Start Year | 2022 |
| 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 | ELIXIR Biodiversity Working Group |
| Organisation | ELIXIR |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Drs Davey and Shaw attended the first ELIXIR Biodiversity working group meeting in Milan 2020. Davey gave a talk on UK efforts to track biodiversity data, for example with the COPO platform. |
| Collaborator Contribution | ELIXIR initiated this working group and invited member ELIXIR nodes to attend. |
| Impact | Main outcome is building the community with a view to submitting an implementation study around biodiversity data. |
| Start Year | 2020 |
| Description | ELIXIR Plants Community |
| Organisation | ELIXIR |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | By actively being part of the ELIXIR Plants Community it has opened up the possibilities for future projects. Including offering our services and tools (COPO, CyVerse, Grassroots etc) for use in ongoing and future implementation studies. |
| Collaborator Contribution | Other community members have incorporated our tools/services into their plans for future work |
| Impact | ELIXIR Plant Services Roadmap 2020-2023: doi 10.7490 |
| Start Year | 2020 |
| 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 | https://github.com/AHallLab/PredictingCircadianTime Joint grant with the Alan Turing Institute https://doi.org/10.1101/2021.02.04.429826 |
| 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 | Academic/University |
| 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 |
| Country | France |
| Sector | Academic/University |
| 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 | Private |
| 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 | 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 | Helmholtz Association of German Research Centres |
| Department | Helmholtz Zentrum Munchen |
| Country | Germany |
| 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 | 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 | Monogram Network |
| 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 | 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 | GB1709756.9 |
| 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 | CropQuant for cereal growth measures |
| Description | A method of processing (batch processing) images of a crop (pot, plot or field) comprising: retrieving a series of images of a crop (pot, plot or field) captured over a period of time; identifying, in an (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 a set of (key reference points, such as the plot region, the canopy space and) height markers ; and for each of at least one other image in the series of crop growth images. |
| IP Reference | |
| Protection | Trade Mark |
| Year Protection Granted | 2021 |
| Licensed | Commercial In Confidence |
| Impact | The hardware and software solutions developed by my lab, i.e. the IoT-based crop monitoring solution called CropQuant (UKIPO, GB1709756.9, international PCT Patent Application No. PCT/GB2018/050985) and derived AI-based Agri-Robot (CropQuant-R) have attracted much industrial interest. The East Asia licence is in the process of being sold to a research organisation in China for US$80,000 plus VAT, plus 5% royalty. |
| 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 | CSV data download |
| Description | This Python code creates a CSV file from the JSON file of any Grassroots study that stores plot data. it is now part of the Fieldtrial frontend page. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | This feature was requested by the frequent users of the platform. CSV is a popular format which is very simple and lightweight, and it is widely supported. Any users interested in a particular study is now able to download the data in this flexible format. The CSV file is automatically generated when a study is loaded, the link for downloading the file appears on the top of each plot page, e.g. https://grassroots.tools/fieldtrial/plots/6086b6d702700f0686246e25 |
| URL | https://grassroots.tools/fieldtrial/plots/6086b6d702700f0686246e25 |
| 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 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. It also automatically generates and exports the datasets as Frictionless Data Packages. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | The software is 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 | Frictionless Data for wheat |
| Description | A tool to automatically generate Frictionless data Packages (https://specs.frictionlessdata.io/data-package/) for data stored in an iRODS system and make it available across the web. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | Allowing data scientists access to a well-supported set of APIs to allow them to create tools and workflows using the research datasets on the DFW data portal. |
| URL | https://opendata.earlham.ac.uk/wheat/under_license/toronto/ |
| Title | Grassroots BrAPI web service |
| Description | This is a web service that uses the Grassroots Field Trial service and adds a Breeding API (BrAPI) layer on top to allow other BrAPI-compliant software to access the field trial data. We currently have complete support for approximately a third of BrAPI classes and calls with partial support for others. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | This allows other data scientists, software developers and applications to easily access the field trial data stored in our system using a standard nomenclature and REST API. |
| Title | Grassroots Field Trial service |
| Description | A web-based application for submitting and searching for various aspects of field trial experimental data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | A web-based application for submitting and searching for field trial data. |
| URL | https://grassroots.tools/beta/dynamic/fieldtrial_dynamic.html?type=AllFieldTrials |
| Title | Grassroots Field Trial service |
| Description | A web-based software tool to allow the submission, searching, viewing and analysis of the data and metadata associated with plant-based field trial experiments |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | An increased number of people submitting data alongside people using the search and visualization parts of the service |
| URL | https://grassroots.tools/fieldtrial/all |
| Title | Grassroots Field Trial service |
| Description | A web-based software tool to allow the submission, searching, viewing and analysis of the data and metadata associated with plant-based field trial experiments |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | An increased number of people submitting data alongside people using the search and visualization parts of the service |
| URL | https://grassroots.tools/fieldtrial/all |
| Title | Grassroots Field Trial service |
| Description | A web-based software tool to allow the submission, searching, viewing and analysis of the data and metadata associated with plant-based field trial experiments |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | An increased number of people submitting data alongside people using the search and visualization parts of the service |
| URL | https://grassroots.tools/fieldtrial/all |
| Title | Grassroots Field Trial service |
| Description | Continuous updating of our existing web-based application for submitting and searching for various aspects of field trial experimental data. Updates include adding images , treatment factors, research programmes and vastly expanded faceted search functionality. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | 112 studies have now been added into the system. |
| URL | https://grassroots.tools/fieldtrial/all |
| Title | Grassroots Field Trial service |
| Description | Continuous updating of our existing web-based application for submitting and searching for various aspects of field trial experimental data. Updates include adding images , treatment factors, research programmes and vastly expanded faceted search functionality. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | 60 studies have now been added into the system and the pace of input is increasing as, after working closely with partners in the DFW programme, they are looking to use it as their submission system for all of this year's studies whilst in the field. |
| URL | https://grassroots.tools/beta/dynamic/fieldtrial_dynamic.html?type=AllFieldTrials |
| Title | Grassroots Field trial frontend |
| Description | Ongoing work for expanding and improving the Django web framework which display and organises the all the Field Trial studies submitted to Grassroots. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | We have added new features, improved performance, added more fields to capture extra information and reorganised the layout of tables, based on the feedback and suggestions from the main data generators and users of the portal. |
| URL | https://grassroots.tools/fieldtrial/ |
| Title | Grassroots Frictionless Data Tool |
| Description | This is a command-line tool to extract the resources within a Frictionless Data Package into a variety of formats such as Markdown, HTML, CSV, etc. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Users able to download complete field trial data packages from the Grassroots Field Trials service. |
| Title | Grassroots Frictionless Data Tool |
| Description | This is a command-line tool to extract the resources within a Frictionless Data Package into a variety of formats such as Markdown, HTML, CSV, etc. It will be available for as many different platforms as possible. It uses the schemas for each resource within the Data Package to generate the reports. It has in-built support for tabular-data-resources and will download and parse any web-based schemas from the resource profiles and use these when they are specified. It will output a file for each Data Resource within the Data Package. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | It allows users to get their data as Frictionless Data Packages and export them into other formats as needed |
| Title | Grassroots Gene Trees Search service |
| Description | This is a search service querying and mapping clusters to genes for sequence data |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | This is used as the backend service for a user-friendly Gene Trees search service combined with BLAST searches |
| Title | Grassroots Gene Trees Search service |
| Description | This is a search service querying and mapping clusters to genes for sequence data |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | This is used as the backend service for a user-friendly Gene Trees search service combined with BLAST searches |
| URL | https://wheatgenefamilies.cyverseuk.org/ |
| Title | Grassroots MARTi service |
| Description | A Grassroots service to allow MARTi samples to be indexed and searchable within Grassroots. Results link directly to the relevant samples within the MARTi web portal. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | It allows interoperability between Grassroots and MARTi allowing users to move between the two systems.https://github.com/TGAC/grassroots-service-marti |
| Title | Grassroots Parental Genotype service. |
| Description | This software stores information regarding peak markers and parental genotype information for various QTL. It is part of a collaboration between the University of Bristol, the John Innes Centre and the Earlham Institute. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | This software is used by the CerealsDB web service to give users a simple way to browse between QTL, peak marker informations and the parental genotype information. |
| URL | http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/select_QTL.php |
| Title | Grassroots Search Service |
| Description | A service to search against the services and data within a Grassroots infrastructure to find items of interest |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Allows users quicker and easier discovery of the data and services available |
| URL | https://grassroots.tools/service/search |
| Title | Grassroots Search Service |
| Description | A service to search against the services and data within a Grassroots infrastructure to find items of interest |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Allows users quicker and easier discovery of the data and services available |
| URL | https://grassroots.tools/service/search |
| Title | Grassroots Search service |
| Description | The Grassroots free-text search engine, based upon Lucene, allows us to give ranked, faceted results for various types of research data such as field trial information, research datasets, sequence data, etc. These data items are all faceted and each facet automatically weights searches for its specific fields. For example, queries that match study names get ranked higher than those that match queries in their description field instead. This is used for general searches as well as a specific faceted search applications such as the one we have for Measured Variables to denote phenotypic data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | This has allowed users to search across all of our data within the EI Grassroots infrastructure and allowed users to get to both services and data more quickly. |
| URL | https://grassroots.tools/public/service/search |
| 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 | Grassroots core infrarstructure code |
| Description | A set of libraries that are the foundation for all of the Grassroots services that are available for use |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Allowed more services to be developed and enhanced their common set of functionalities |
| URL | https://grassroots.tools/ |
| Title | Grassroots core infrarstructure code |
| Description | A set of libraries that are the foundation for all of the Grassroots services that are available for use |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Allowed more services to be developed and enhanced their common set of functionalities |
| URL | https://grassroots.tools/ |
| Title | Grassroots core infrarstructure code |
| Description | A set of libraries that are the foundation for all of the Grassroots services that are available for use |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Allowed more services to be developed and enhanced their common set of functionalities |
| URL | https://grassroots.tools/ |
| Title | Grassroots core infrastrructure |
| Description | 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. The Grassroots Infrastructure uses a controlled vocabulary of JSON messages to communicate, so any server or client that can understand JSON can be used to access and connect to the platform. We provide infrastructure to ensure that the scientific data remains the important factor, and not the worry about how to build a system to expose your data. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | The Grassroots Infrastructure has allowed researchers data scientists, breeders to perform a variety of data analyses such as sequence searching using BLAST, map-based interactive searches for field trial data, QTL parental genotype mapping, as well as custom bespoke software web services utilised by third parties such as the CerealsDB team at the University of Bristol as part of systems that they have developed for users. |
| URL | https://grassroots.tools |
| Title | Grassroots core infrastructure |
| Description | 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. The Grassroots Infrastructure uses a controlled vocabulary of JSON messages to communicate, so any server or client that can understand JSON can be used to access and connect to the platform. We provide infrastructure to ensure that the scientific data remains the important factor, and not the worry about how to build a system to expose your data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | The Grassroots Infrastructure has allowed researchers data scientists, breeders to perform a variety of data analyses such as sequence searching using BLAST, map-based interactive searches for field trial data, QTL parental genotype mapping, as well as custom bespoke software web services utilised by third parties such as the CerealsDB team at the University of Bristol as part of systems that they have developed for users. |
| URL | https://grassroots.tools |
| Title | Grassroots core server software |
| Description | 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. The Grassroots Infrastructure uses a controlled vocabulary of JSON messages to communicate, so any server or client that can understand JSON can be used to access and connect to the platform. We provide infrastructure to ensure that the scientific data remains the important factor, and not the worry about how to build a system to expose your data. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | The Grassroots Inftrastructure has allowed researchers data scientists, breeders to perform a variety of data analyses such as sequence searching using BLAST, map-based interactive searches for field pathogenomic data, field trial service as well as custom bespoke software web services utiliisd by third parties such as the CerealsDB team at the University of Bristol as part of systems that they have developed for users. |
| URL | https://grassroots.tools |
| Title | Grassroots free-text search engine |
| Description | The Grassroots free-text search engine, based upon Lucene, allows us to give ranked, faceted results for various types of field trial data. Each facet automatically weights searches for its specific fields. For example, queries that match study names get ranked higher than those that match queries in their description field instead. This is used for general searches as well as a specific faceted search applications such as the one we have for Measured Variables to denote phenotypic data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | This has allowed field trial data scientists to search across all of our data and allows them to search for the correct ontological terms to describe the phenotypic traits that have been measured within their trials. This has allowed researchers to be able to upload their data to our systems more quickly by allowing them to determine the correct ontological terms more easily. |
| URL | https://grassroots.tools/beta/public/SearchTreatment |
| Title | Heatmaps for field trials in Grassroots. |
| Description | This python code allows to display Grassroots studies that have plot data as interactive heatmaps, one per each phenotype observed in the study. It uses the Dash framework from the plotly library. The plots are embedded in the Field Trial frontend (https://grassroots.tools/fieldtrial/plots/603e3e9502700f7faf25dfb4) but the implementation is also running as a stand-alone web service (https://grassroots.tools/heatmaps.) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Heatmaps are ideal when you want to visualise a large dataset with many variables. A visual representation of a large study is useful to the users because it allows to identify patterns, clusters and trends in the data. These plots are interactive, which means that the measurements can be easily displayed by hovering over the plot of interest. |
| URL | https://grassroots.tools/heatmaps |
| 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 | Pipeline for long non coding RNA identification |
| Description | Pipeline enabling long non coding identification taking as input RNA-Seq data, genome sequence, and annotation. The pipeline handle the read mapping, de noo transcript assembly, comparison with existing annotations to identify novel intergenic transcript, assess the coding potential of the noevl transcripts report those identified as non coding and at least 200 nt long. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Long non codig RNAs are generally associated with gene expression regulation and previouly identified to have major roles in both animals and plant biology. The pipeline is organism agnostic, enabling the identification of lon non coding RNAs in any eukaryotic species. The aim is to make the pipeline available on Galaxy for the community to use. |
| URL | https://github.com/TGAC/lncRNA-analysis |
| 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. |
| Title | triad plot |
| Description | triad.expression is an R package used by the Hall group to do certain analyses of expression with so homoeologous copies of wheat genes |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | Using for scientists visualising gene expression data in complex polyploids |
| 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 | 5 ways EI is improving global food security |
| 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 | 5 ways EI is improving global food security |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/5-ways-earlham-institute-improving-global-food-security |
| Description | 600k machine learning collaboration to supercharge data driven science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 600k machine learning collaboration to supercharge data driven science |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/%C2%A3600k-machine-learning-collaboration-supercharge-data-driven... |
| Description | A PhD, is it worth it? Just ask our students |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A PhD, is it worth it? Just ask our students |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students |
| Description | A talk or presentation - Poster presentation - lncRNA identification and characterisation in wheat pan-transcriptome |
| 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 ISMBECCB 2021 - BOSC 2021 |
| Year(s) Of Engagement Activity | 2021 |
| Description | AI for Wheat workshop |
| 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 | The AI for Wheat workshop was a meeting of approximately 50 people from academia and industry to examine ways to use AI methods and algorithms on wheat-based data. |
| Year(s) Of Engagement Activity | 2020 |
| Description | AI for Wheat workshop 2020 |
| 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 | Attended the DFW AI for Wheat workshop at the Alan Turing Institute, where we discussed and planned the submission of proposals for collaborative Data Study Groups around the use of machine learning for wheat data analysis. |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Activity - DNA sequencer at Great Hockham Primary School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Activity at the Great Hockham Primary School |
| Year(s) Of Engagement Activity | 2019 |
| Description | Activity - Where have you BEEn? |
| 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 | Activity at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Affordable genome sequencing for pathogen analysis to help tackle global epidemics |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Blog post for the publication of the development of an affordable sequencing protocol applied to the sequencing of over 10,000 Salmonella isolates |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/newsroom/affordable-genome-sequencing-pathogen-analysis-help-tackle-global... |
| Description | Ai for Wheat Workshop |
| 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 | The Alan Turing Institute (ATI) hosted a workshop in partnership with the BBSRC-funded Designing Future Wheat research programme to explore the potential for innovative applications of data science and artificial intelligence to address problems relevant to the UK wheat community. This two day workshop will bring members of the UK wheat community and data science researchers together to identify suitable and exciting biological problems (with associated datasets) that could be further developed and made ready for a future wheat-focussed Data Study Group (DSG). DSGs are week-long intensive interdisciplinary workshops which explore a small number of topics in greater depth to seed longer-term collaborations which could lead to joint publications or research proposals. See here for more information https://www.turing.ac.uk/collaborate-turing/data-study-groups. We hope to encourage wide participation from data scientists and the UK wheat community, including stakeholders from industry and government. Problems considered within scope for the workshop include, but are not limited to: wheat genomics and genetics, phenotyping, breeding, GxExM interactions, agronomy, wheat pests and disease interactions, impacts of climate change, sustainability and wheat as part of a healthy diet. We particularly want to encourage participation from members of the wider data science community who consider that they have relevant skills or experience that could be brought to bear on the areas listed above and might be interested to be involved in future DSGs as a challenge owner (Early Career Researcher) or as a potential PI. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Attended and Presented a talk at the DFW All Hands 2020 |
| 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 | Rob Davey attended the DFW All Hands 2020 (DFW Annual Meeting) and presented a talk on the work being carried out in WP4 |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Blog about successful award application |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A blog describing our initial work on adding support for the Frictionless Data standard to our hosted data. This resulted in interest and feedback from new research groups about possible future work. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://frictionlessdata.io/blog/2020/08/17/frictionless-wheat/ |
| Description | Blog after completion of project |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A blog describing our fully-completed work on adding support for the Frictionless Data standard to our hosted data. This resulted in interest and feedback from new research groups about possible future work. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://frictionlessdata.io/blog/2021/03/05/frictionless-data-for-wheat/ |
| 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 Presentation - Genomics in Aquaculture - Evolutionn of chromatin accessibility in Nile tilapia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Genomics in Aquaculture |
| Year(s) Of Engagement Activity | 2022 |
| Description | Conference oral presentation - Monogram 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the results from hyperspectral reflectance and GWAS analysis in spring Wheat |
| Year(s) Of Engagement Activity | 2020 |
| 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-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019 |
| 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 | Cyberinfrastructure and the Carpentries - Workshop in Bogota, Colombia 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | We delivered a Carpentries instructor training in Bogota, Colombia, as part of the GROW Colombia project. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://froggleston.github.io/2019-10-22-ttt-colombia/ |
| Description | DFW Hackathon |
| 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 | A workshop to discuss and implement potential collaborations to create tools to solve bioinformatic needs within the DFW community. |
| Year(s) Of Engagement Activity | 2019 |
| 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 | EI Innovate: a platform for collaboration and new ideas |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate: a platform for collaboration and new ideas |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/ei-innovate-platform-collaboration-and-new-ideas |
| 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 General Public: Royal Norfolk Show 2022 - Will Nash |
| 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 | Engagement activities with the general public as part of the Royal Norfolk Show 2022, demonstrating our activities focusing on the application of new technologies to characterise biodiversity |
| Year(s) Of Engagement Activity | 2022 |
| 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 | Event - DNA Detectives |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Activity at the Eden project |
| Year(s) Of Engagement Activity | 2019 |
| Description | Frictionless Data for Wheat - CSV Conf talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Gave a talk on Frictionless Data for Wheat as part of the Grassroots Infrastructure |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://csvconf.com/2021/ |
| Description | Frictionless Data for Wheat blog |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A blog to describe our work on tools for integrating Frictionless Data into the Grassroots Infrastructure as part of our successful grant application from the Frictionless community. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://frictionlessdata.io/blog/2021/03/05/frictionless-data-for-wheat/ |
| Description | Frictionless Data for Wheat talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the Frictionless Data Community Call series, we gave a talk on the Frictionless Data functionality that has been developed as part of the Grassroots Infrastructure |
| Year(s) Of Engagement Activity | 2021 |
| 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 Field Trial Workshop |
| 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 | 25 people attended a workshop on submitting data to and using the Grassroots Field Trial system |
| Year(s) Of Engagement Activity | 2022 |
| 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 | Grassroots: An infrastructure for sharing services & data |
| 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 at a conference on agricultural data to show the various applications available as part of the Grassroots Infrastructure for disseminating bioinformatics data. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Grassroots: Field Trials database presentation |
| 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 talk on the Grassroots Field Trial system as part of the annual DFW all-hands meeting |
| Year(s) Of Engagement Activity | 2021 |
| 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 | Image Processing with Python |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Approximately 10 people attended a 2-day workshop on how to use Python and the skimage library to do basic image processing. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://datacarpentry.org/image-processing/ |
| 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 | Laying the Foundations; Why are Semantics in Agriculture Difficult? - PAG 2020 talk in Plant Phenotypes workshop |
| 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 gave an invited talk to approx 90 attendees at the PAG 2020 workshop "Plant Phenotypes" |
| Year(s) Of Engagement Activity | 2020 |
| 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 | 2011,2012,2013,2014,2015,2016,2017,2018 |
| 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 | 2011,2012,2013,2014,2015,2016,2017,2018,2019 |
| 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 - Non-human genomes, why bother? |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Oral presentation at the EI Open Day |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Building gene Families and assessing gene structure |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation at the Genome Annotation Workshop 2021 |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral presentation - Detection of differential isoform expression and usage during cellular differentiation using long read RNA sequencing |
| 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 London Calling 2021 meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral presentation - Enter the Nanoporium |
| 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 | Oral presentation as part of the Pint of Science |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Taking the long (read) view of alternative splicing during cell differentiation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation at the EI Long Read Symposium, Earlham Institute (virtual) 15 - 17th June 2021 |
| Year(s) Of Engagement Activity | 2021 |
| 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 | Organisation and Attendance at the Alan Turing Institute for AI for Wheat Workshop |
| 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 | Rob Davey helped organise the Alan Turing Institute - AI For Wheat Workshop 9th & 10th March 2020 This two day workshop will bring members of the UK wheat community and data science researchers together to identify suitable and exciting biological problems (with associated datasets) that could be further developed and made ready for a future wheat-focussed Data Study Group (DSG). DSGs are week-long intensive interdisciplinary workshops which explore a small number of topics in greater depth to seed longer-term collaborations which could lead to joint publications or research proposals. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.rothamsted.ac.uk/events/ai-wheat-workshop |
| Description | Organiser of Challenges and Opportunities in Plant Science Data Management PAG 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 | Co-organiser of Challenges and Opportunities in Plant Science Data Management PAG workshop, which saw 6 international speakers deliver presentations on various aspects of data management in the plant sciences. Approx 50 attendees. |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Poster Presentation - Intelligent Systems for Molecular Biology - Scaling up GeneSeqToFamily to handle pan transcriptomes and million of genes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Intelligent Systems for Molecular Biology 2022 conference |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster Presentation - Characterisation of long non coding RNAs in T. aestivum strains |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Plant and Animal Genome (PAG2020) Conference |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the annual PopGroup meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Poster presentation - BIOINFORMATICS IN THE ERA OF GENOMICS IN AFRICA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the First Nigerian Bioinformatics Conference (FNBC) 2019 |
| Year(s) Of Engagement Activity | 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 - Lego sequencer at the Women of the Fututre event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Activity at the Women of the Fututre event |
| Year(s) Of Engagement Activity | 2019 |
| 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 at Research Data Alliance's 14th Plenary - Interest Group on Agricultural Data (IGAD) Pre-Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented Grassroots infrastructure at Research Data Alliance's 14th Plenary - Interest Group on Agricultural Data (IGAD) Pre-Meeting in Helsinki Finland. IGAD is a domain-oriented group working on all issues related to global agriculture data. It represents stakeholders in managing data for agricultural research and innovation, including producing, aggregating and consuming data. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://aims.fao.org/activity/blog/presentations-available-igad-meeting-during-rda-14th-plenary |
| Description | Presentation for the Designing Future Wheat in Practice workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This course was aimed for researchers and students with an interest in cereals research and crop breeding. Intended for entry level, it covered crop development and phenotyping, wheat genetics and genomics, wheat pathology, sources of genetic diversity in wheat and genomics data resources. Our presentation introduced the Grassroots platform, particularly focused in the Field trials. It included practical examples using a Jupyter notebook. We showed how to retrieve and manipulate plots data for generating static heatmaps. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://wisplandracepillar.jic.ac.uk/training.htm |
| 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 | Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation - GROW Colombia UK workshop 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 | Robert Davey gave a talk on the C3 Biodiversidad ConsortiumProject Coordination and Website |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Students need to up their bioinformatics game |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Interview of an undergraduate student doing a research placement at EI on the importance of developing bioinformatic skills |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/students-need-their-bioinformatics-game-why-i-am-learning-code-py... |
| Description | Support open science and FAIRness through an integrated collaborative platform for life science: CyVerse UK and hosted services |
| 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 Earlham Institute, an Elixir UK node, is home to CyVerse UK, a collaborative cyberinfrastructure for life science. CyVerse UK objectives align greatly with the Elixir vision, as it aims to ensure researchers have easy access to HTC resources while lowering the entry barrier to bioinformatics, thanks both to the easy of use of the platform and the trainings provided. Great focus is posed on data storage, management, and overall how to ensure FAIRness. The Cyverse Data Store and Data Commons come with attached metadata, in the latter case a bare minimum set is required. Data availability and reliable data transfer take advantage of iRODs. The CyVerse cyberinfrastructure also hosts COPO and Grassroots, which are of particular interest to the data ecosystem. COPO is a brokering service between scientists and public repositories, enabling management, aggregation and publication of research outputs. COPO eases the process of metadata attribution by presenting the same intuitive interface for different repositories, and a wizard to guide the user through the steps of adding metadata. The Grassroots Genomics project aims to facilitate consistent approaches to generating, processing and disseminating public wheat datasets so that research efforts can be translated into community valuable resources thanks to effective sharing and reuse of data. On the computational side, CyVerse UK offers a number of registered and versionised applications users can run both using an API or through the parent CyVerse US web interface. Our last report shows how researchers not only from the UK, but also from Europe, America, Africa and Asia benefited from these applications. The CyVerse UK pool also hosts a Galaxy instance reserved to collaborators at BeCA. The expansion of the infrastructure will allow us to offer on demand virtual machines to the research community to support them in development, training or with collaborative virtual laboratory. |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Talk at the Designing Future Wheat (DFW) in Practice : DFW 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 | The aim of this DFW course was to offer training in important methodologies employed by different groups within DFW. The participants gained the skills necessary to apply these methodologies in their own research. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://wisplandracepillar.jic.ac.uk/training.htm |
| Description | Talk delivered at the ELIXIR Biodiversity working group Inaugural meeting - Milan 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Organised as part of a new ELIXIR working group to address challenges in biodiversity data management and infrastructure. |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Training delivered - Single Cell RNA-Seq data analysis 2022 - Graham Etherington, David Wright, Yuxuan Lan, Wilfried Haerty, Iain Macaulay |
| 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 | Training delivered as part of the Single Cell RNA-Seq data analysis 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022 |
| Description | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/uk-cbcb-elixir-cross-disciplinary-collaboration-bioinformatics |
| Description | UK project underpins global effort to map genomes of all life on earth |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Blog post on the contributions of EI to the Earth Biogenome Project |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/newsroom/uk-project-underpins-global-effort-map-genomes-all-life-earth |
| 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 Bioinformatics III workshop, South Africa |
| 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 | 25 people from across the crop industrial and academic sectors were trained in Wheat Bioinformatics, the third in a series of workshops organised by Diane Saunders, Burkhard SteuerNagel and Rob Davey, funded by the UK High Commission in South Africa. This workshops are valuable for the attendees to learn the up-to-date computational and analytical techniques to make the most of their own and publicly available wheat data, feeding these skills directly into their breeding programmes. |
| Year(s) Of Engagement Activity | 2020 |
| 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 | Why bioinformatics is important |
| 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 | Blog post on the importance of bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-bioinformatics-important |
| Description | Why cloud computing is important for life science research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article to highlight services and opportunities arising from the use of cloud computing in life science research |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/why-cloud-computing-important-data-driven-bioscience-research |
| Description | Why statistics is important in a world of big data |
| 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 | Why statistics is important in a world of big data |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-statistics-important-world-big-data |
| Description | iRODS UGM 2021 Talk |
| 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 on our iRODS developments as part of our Grassroots Infrastructure |
| Year(s) Of Engagement Activity | 2021 |
| 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/ |
| Description | member of the G20 wheat Initiative Science board during 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 | The members of the science board discuss how to better coordinate the wheat research activities in the G20 countries |
| Year(s) Of Engagement Activity | 2019,2020 |
| Description | member of the management board of the CGIAR wheat programme (CIMMYT and ICARDA) 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 | I offer advice to the management team of the wheat CGIAR programme |
| Year(s) Of Engagement Activity | 2019,2020 |
| Description | member of the organising committee for PAG 2020 |
| 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 | Suggest plenary speakers for inviting to speak at PAG 2020 meeting attracting 3000 animal and plant researchers |
| Year(s) Of Engagement Activity | 2019 |
| Description | poster presentation - Characterising and visualising 10 plus wheat gene families within Galaxy using GeneSeqToFamily |
| 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 Monogram 2021 meeting |
| Year(s) Of Engagement Activity | 2021 |