Data access and analysis

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

The large-scale genomic, phenotypic and regulatory datasets emerging from the Designing Future Wheat BBSRC Strategic Programme (DFW), will be annotated, integrated and disseminated to generate critical reference resources supporting interpretation and driving new avenues of investigation. These activities will comprise the UK contribution to the international Wheat Information System (WheatIS), a unified global infrastructure for wheat biology being developed under the auspices of the G20 International Wheat Initiative. Wheat resources and information generated within the DFW programme will be presented in an easily accessible form, allowing ready access for UK and international plant researchers not directly working on wheat.
 
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 We have analysed breakpoints across 13 RIL hexaploid bread wheat populations using existing genotyping data. We established a breakpoint frequency of 40.8-51.9 breakpoints per RIL across the 13 populations. Analysed genomic position, how different parental cross affected breakpoint sites and hotspot positions, identified potential recombination QTL.

We have developed a new DNA capture platform based on IWGSC RefSeq 1.0 for the re-sequencing of wheat. This includes the entire genic portion and 2KB of promoter sequence. We have tested this with Chinese spring. We have generated a data set combining capture with 10x genomics technology to assemble genic islands. We are now analysing this to evaluate whether this offers a method for investigating genome rearrangement.

We have shown that the diverse data types already existing within DFW require a wide range of platforms to maximise the utilisation of the data in the wider research and commercial community. The activities of the WP4 Data Coordination Task Force have been establishing linkages between these platforms and putting measures in place to bring datasets together. We plan to use COPO to broker data for entry into public data repositories. The objective will be to bring the user to germplasm of interest through the DFW landrace pillar website and SeedStor which is the way users can search the Germplasm Resource Unit.

We have developed ChIP-Seq laboratory protocols tailored to bread wheat enabling the investigation of chromatin states and gene expression regulation. We have developed a protocol to analyse DNA methylation for large scale analysis of DNA methylation data and are currently in the process of testing this on sample datasets.

We have improved the efficiency of bulk segregant analysis tools to bring gene identification time down to around 1 week after sequencing. The tools are now available via CyVerse UK.

We have completed reanalysis of wheat TILLING data and integrated EMS / TILLING mutation data in Ensembl Plants release 35 (April 2017). We have also integrated l variant data (> 10 million polymorphisms), linking Ensembl Plants to CerealsDB. We have additionally been working on annotating the new IWGSC RefSeq 1.0 Chinese Spring assembly.

We have developed and deployed the prototype instance of the DFW project-specific data portal, and deposited initial DFW data within. We have added support for both ENA and MIAPPE v1 standards within COPO, and used the platform to deposit sequence data into suitable public repositories, as well as published open access publications on our scientific outputs based on these data.

New features and data are now available in KnetMiner for wheat. New features include improved search of gene lists, interactive filtering of search results and improved compatibility of KnetMiner with Cytoscape Desktop. New datasets include wheat gene expression studies from EBI and GWAS data from The Triticeae Toolbox. Wheat specific publications were added to the knowledge graph and abstracts were scanned for gene-phenotype information.
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 started to produce a project website, as well as an open data portal, for sharing DFW outputs with this community. We are actively interacting with the wheat community through the organisation of DFW stakeholder workshops to demonstrate and train users in our resources.

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

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

 
Description The main outputs of this award to date are focused on providing software and data for the wheat community, comprising biologists, bioinformaticians, breeders, and external stakeholders. We have started to produce 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. Our new sequencing protocols have been used to efficiently carry out the work against our genomics landscape objectives within DFW, and we will be publishing these in an open access journal for others to reuse. The new DNA capture platform will be provide a tool for the UK and international wheat community via Nimblegen. The capture design will be made open access. We have received over 1200 unique users to the Grassroots infrastructure data portal since April 2017 (the new service went live in November 2017), with approximately 80 requests for data downloads since the first large Toronto-licensed datasets were released in January 2018. The Grassroots BLAST service, comprising analysis capability over TCAGv1 CS42, 5 other elite varieties assembled with the w2rap software, and a wide array of other wheat genome databases, has received over 2000 unique users since April 2017, with 20456 BLAST jobs being processed during this time. With our new infrastructure, we are hosting not only the raw read data for these 5 new EI wheat assemblies, but also data from the Gardiner et al wheat exome capture (1.4TB) and sequencing data from the Open Wild Wheat Consortium (OWWC, 6.2TB), all available openly under the Toronto agreement. Similarly, the TGACv1 data held at the Ensembl Plants resource at the EMBL-EBI has seen widespread use, with over 20000 unique users comprising 1.3m page views (1st Aug '16 - 12th Mar '18). The wheat BLAST service running at the EBI also saw a large user base engaging with the data, providing 83695 BLAST searches for over 5600 users (Jan '17 - Dec '17, inclusive). Clear and accessible representation of these complex datasets has been used by wheat breeders and the research community. Examples include: Extracting gene content of key loci from the genome sequence of Chinese Spring in Ensembl Plants; downloading high density genotypic data on modern varieties compared to DFW germplasm in CerealsDB; Searching the genomes of modern UK varieties like Paragon, Robigus and Claire in Grassroots genomics; studying the pedigree and graphical genotype of the Breeders Toolkit on the DFW website; quickly and efficiently requesting seed from the Germplasm Resource Unit using Seedstor. We have jointly published and submitted 5 articles on crop phenotyping, and hosted 14 industrial visits to set up industrial collaborations with Syngenta, Bayer Crop Sciences, Limagrain and ADAS. The engagement with Bayer Crop Science was awarded a Bayer G4T focused project in 2017. We filed and published an Agri-Tech patent for the CropQuant technology (CropQuant - data processing of crop images, UKIPO, GB1709756.9, 2018), and showcased these innovations in REAP 2017 and KTN/Newton national Agri-Tech innovation conferences. Finally, we were invited to present our crop phenotyping technology work in DFW in six international conferences in the UK, China, Netherlands, and Japan. KnetMiner had over 1500 unique users since April 2017 (+200% compared to previous year) with most coming from the UK (30%), followed by US (24%) and including users from developing countries such as Malaysia (4%), Philippines (2%) and India (2%). The average session duration lasted 5:22 minutes (-35% indication for users can get information faster). We have run a training course to wheat researchers and breeders at the Wheat Bioinformatics Workshop in Bologna and since have started a collaboration with the Tuberosa group to rank genes in wheat QTLs using KnetMiner and our new Neo4j graph database. We were invited to present KnetMiner at PAG2018 and had follow-up interactions with the Quesneville group at INRA to add KnetMiner to the federated WheatIS index.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)
Impact Types Cultural,Societal,Economic

 
Description A member of the Science Board of the G20 wheat initiative set up by the G20 agricultural ministers to coordinate wheat research across the G20 countries
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact By coordinating wheat research to address food security issues across the G20 countries, it makes more effect use of the funding by G20 government agencies
 
Description BEIS/UKRI/RCUK Cloud Workshop, London, 24-10-2017
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description 16ALERT
Amount £283,383 (GBP)
Funding ID BB/R000662/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 08/2017 
End 08/2018
 
Description Bayer Grants4Traits
Amount £20,661 (GBP)
Organisation Bayer 
Department Bayer CropScience Ltd
Sector Private
Country United Kingdom of Great Britain & Northern Ireland (UK)
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 £30,429 (GBP)
Funding ID BB/R021376/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2018 
End 03/2021
 
Description IPA Industrial Partnering Award - China Partnering Awards - Forge a long-term UK-China relationship in phenotyping, Agri-Tech innovation and crop research for Rice and Wheat
Amount £30,429 (GBP)
Funding ID BB/R021376/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2018 
End 03/2021
 
Description John Innes Centre Institute Strategy Funding - The elucidation of transcription factor networks underling internode extension in wheat
Amount £13,911 (GBP)
Organisation John Innes Centre 
Sector Charity/Non Profit
Country United Kingdom of Great Britain & Northern Ireland (UK)
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 of Great Britain & Northern Ireland (UK)
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 of Great Britain & Northern Ireland (UK)
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 of Great Britain & Northern Ireland (UK)
Start 08/2017 
End 07/2018
 
Description UK-China Newton Network+ Round 1 - AirSurf for automated image analysis and UAV-deployed remote sensors
Amount £30,000 (GBP)
Funding ID Newton Network+ SM003 
Organisation Newton Fund 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 03/2018 
End 07/2018
 
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 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/
 
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, United Mexican States 
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 Wheat Information System (WheatIS) 
Organisation Cold Spring Harbor Laboratory (CSHL)
Country United States of America 
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 of Great Britain & Northern Ireland (UK) 
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, French Republic 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Zentrum Munchen
Country Germany, Federal Republic of 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico, United Mexican 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 Rothamsted Research
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of America 
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 of Great Britain & Northern Ireland (UK) 
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 of America 
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, Commonwealth of 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Title CropQuant - data processing of crop images 
Description Field of the invention: the present invention relates to data processing of images of a crop, in particular a cereal crop such as wheat, maize or rice, for use in image-based field phenotyping. The method comprises retrieving a series of images of a crop captured over a period of time and identifying, in an image (or "initial image") selected from the series of images to be used as a reference image, a reference system against which other images can be compared, the reference system including an extent of a crop plot and/or one or more reference points. The method also comprises, for each of at least one other image in the series of images, calibrating or adjusting the image using the reference system, and determining a height of a canopy of the crop in the image, a main orientation of the crop and/or a value indicative of vegetative greenness (for example, a normalised green value in an RGB colour space and/or excessive greenness). This can afford greater flexibility when monitoring a crop, particularly large numbers of crops, over periods of months. For example, the method can be used to process images of a crop which have been captured in the field and, thus, subject to vagaries of weather. Moreover, the method can be used for each crop and, thus, allow large data to be processed for large numbers of crops. 
IP Reference UKIPO, GB1709756.9 (application ref: PJP/81353GB1) 
Protection Patent application published
Year Protection Granted 2018
Licensed Commercial In Confidence
Impact CropQuant technology has been reported by UK national and EU media over a dozen of times since 2016. It has been featured as a stand-out example of UK-based Agri-Tech innovations and was presented BBSRC's Harvest 2050 and other industry-related activities. Recently, our bespoke farming robot CropQuant Sheila was invited to exhibit at REAP 2017, an event organised by Agri-Tech East, KTN and Innovate UK.
 
Title 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 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 exposes a REST API for accessing and manipulating metadata from within a web browser. It adds a substantial amount of functionality to the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Davrods leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Eirods-dav is used to allow web-based access to a selection of files and research data released to the public by the Earlham Institute such as the Triticum Aestivum assemblies. It is used by the Grassroots Infrastructure to allow access to data produced by the Designing Future Wheat project. The Eirods-dav application runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/data/
 
Title Ensembl Plant Release 35 
Description Genome browser and associated analysis tools for plants including Wheat 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This resource is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Ensembl Plant Release 36 
Description General plant genomes browser and associated analysis software 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Software and data in the browser is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Ensembl Plants Release 37 
Description General genome browser for plants including wheat. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Software and data content is used by academic and commercial users 
URL http://plants.ensembl.org/index.html
 
Title Grassroots Tools Website 
Description This is the website for the Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Too soon to record impact 
URL https://grassroots.tools/
 
Title Knetminer Builder Update 
Description This is a software tool that is used to automatically construct knetminer instances and is being applied to all crop instances including wheat. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This enables regular updates to the knetminer instances when new component datasets are released. 
URL https://github.com/Rothamsted/ondex-knet-builder/releases/tag/v1.2
 
Title Leaf-GP Software Distribution 
Description Leaf-GP software is published with the software paper entitled "Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat" in Plant Methods in last December. The software is distributed under the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The software is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. It presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact The Leaf-GP paper generated 18169 downloads within a month and received an attention score of 21 (https://biomedcentral.altmetric.com/details/30811558#score), No.1 amongst all Plant Methods papers (48 in total) published from October 2017 and the attention scoring of the paper is higher than 91% of its contemporaries published from October 2017, worldwide. 
URL https://github.com/Crop-Phenomics-Group/Leaf-GP/releases
 
Title OWL Ontology for Bioknowledge Networks 
Description This ontology is used as part of a suite of tools to represent knetminer knowledge networks using RDF 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Making knetminer systems shared through semantic web technology will facilitate sharing and access to the data from other tools. 
URL https://github.com/Rothamsted/bioknet-onto
 
Title Ondex to RDF Exporter 
Description Ondex components and applications that are necessary for building genome-scale knowledge networks used in projects like KnetMiner. It includes the Ondex base, CLI, workflow engine and a set of plugins (parsers, mappers, transformers, filters and exporters) that are relevant for building genome-scale knowledge networks 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact It is part of a suite of tools that help knetminer networks, including those developed for wheat, be shared through linked open data methods. 
URL https://github.com/Rothamsted/ondex-knet-builder/tree/master/modules/rdf-export-2
 
Title 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/
 
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 Conference organiser of PAG San Diego attracting 3800 plant and animal researchers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I am on the organising committee of the largest plant and animal ag genomics conference attracting some 3800 researchers, policy makers, industry etc
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
 
Description 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 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 Engagement with Industry - KWS UK Ltd 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Mr Bian and Miss Minotto showed EI CyVerse infrastructure and Grassroots Infrastructure's features, including data sharing to the staffs from KWS UK Ltd: Ed Byrne, Janina Dordel, Andreas Menze and Vipul Patel.
Year(s) Of Engagement Activity 2018
 
Description Genome 10K and Genome Science Conference - Video 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Follow up video of the Genome 10k Genome Science conference held at NRP. View son Youtube - 70
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=25Dtu6ay7Is
 
Description Genome 10K and Genome Science social media engagement 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Social media campaign and press releases to promote the Genome10K and Genome Science event at NRP August 2017. We ran several campaigns from January to August to help promote registration for the event and gain interest from industry. SOCIAL MEDIA - Engagement 1920 Impressions 2084245. This has been our biggest campaign to date garnering engagement with International delegates in science and industry. The comms team also supported with design for promotional material such as posters, sponsor brochures and conference programmes.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Grassroots Infrastructure and the Wheat Information System (Genome 10K & Genome Science 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mr Bian and Dr Tyrrell presented a poster at Genome 10K & Genome Science 2017 conference.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Grassroots Infrastructure and the Wheat Information System (RDA Interest Group on Agricultural Data (IGAD), Barcelona) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Davey delivered a talk about the Grassroots software infrastructure for the dissemination of wheat data through federation and integration of storage and compute e-infrastructure.
Year(s) Of Engagement Activity 2017
URL https://www.rd-alliance.org/rda-interest-group-agricultural-data-igad-pre-plenary-meeting-3-4-april-...
 
Description 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 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 Meeting for collaborators on the Field Pathogenomics project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact As part of the Field Pathogenomics project, a meeting with the industrial collaborators to discuss what features they would like added to the web-based tool that we created for users to access the data.
Year(s) Of Engagement Activity 2016
URL https://grassroots.tools/yellowrust-map/
 
Description Member of the board of the G20 wheat initative 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I am a board member of the G20 wheat initiative set up by the G20 agricultural ministers to facilitate coordination of wheat research in the G20 countries. We organise working group to facilitate such coordination, and to identify priorities for funding by funding agencies within the G20 countries
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description Member of the management board of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A management board member of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description 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 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 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 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 WheatIS Expert Working Grop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The expert working group for the Wheat Information System is developing standards and tools to enable the global wheat science community to share data effectively.
Year(s) Of Engagement Activity 2014,2015,2016,2017,2018
URL http://wheatis.org/
 
Description iRODS functionality within the Grassroots Infrastructure (iRODS User Group Meeting 2017, Utrecht, The Netherlands) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Tyrrell presented work on the development of the eirods-dav software package for the Grassroots data dissemination platform.
Year(s) Of Engagement Activity 2017
URL https://irods.org/ugm2017/