SeeDs of Discovery
Lead Research Organisation:
National Inst of Agricultural Botany
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
We propose to deploy a computing hardware and software platform and initiate the implementation of advanced analyses of wheat genotype and phenotype data generated by the Seeds of Discovery (SeeD) programme. The platform will integrate computing resources and expertise at TGAC, CIMMYT and NIAB with the purpose of facilitating data-intensive bioinformatics analyses to leverage data generated by SeeD and other initiatives such as the International Wheat Yield Partnership (IWYP) for the genetic improvement of wheat. This platform and the proposed research will enable the incorporation of the extensive wheat genotype and phenotype data, collected to date and in the future, with the emerging wheat reference genomes and other diversity information generated at TGAC and other international wheat research centres. These datasets will be made readily available to the community via current public and open resources such as the Wheat Information System and the Ensembl Plants browser. This will directly add value to the SeeD and IWYP programmes and enhance their benefits to the wheat breeding and scientific community.
This project will address some of the current constraints limiting the exchange and value addition from “big data” generated by SeeD, IWYP and other CIMMYT and broader wheat community projects.
This project will address some of the current constraints limiting the exchange and value addition from “big data” generated by SeeD, IWYP and other CIMMYT and broader wheat community projects.
Planned Impact
unavailable
Organisations
- National Inst of Agricultural Botany (Lead Research Organisation)
- Pontifical Xavierian University (Collaboration)
- University of Western Australia (Collaboration)
- University of Bristol (Collaboration)
- Monogram Network (Collaboration)
- Helmholtz Association of German Research Centres (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- University of California, Davis (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Rothamsted Research (Collaboration)
- DivSeek International (Collaboration)
- Cold Spring Harbor Laboratory (CSHL) (Collaboration)
Publications
Afgan E
(2018)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
in Nucleic Acids Research
Boden SA
(2023)
Updated guidelines for gene nomenclature in wheat.
in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Bohra A
(2022)
Reap the crop wild relatives for breeding future crops
in Trends in Biotechnology
Caccamo M
(2017)
Delving into diversity: computational key to the crops of the future
in Research Features Magazine
Carballo J
(2021)
Eragrostis curvula, a Model Species for Diplosporous Apomixis.
in Plants (Basel, Switzerland)
Carballo J
(2019)
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality.
in Scientific reports
Grüning B
(2018)
Bioconda: sustainable and comprehensive software distribution for the life sciences.
in Nature methods
Higgins J
(2021)
Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.
in Rice (New York, N.Y.)
Sansaloni C
(2020)
Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints.
in Nature communications
| Description | As part of the project we are developing a novel data analysis strategies to enable the incorporation of the extensive wheat genotype and phenotype data, collected to date and in the future, with the emerging wheat reference genomes and other diversity information generated by partners in the UK and other international wheat research centres. As a first step we will support the mapping and presentation of the genotype data in databases such as the Ensembl Plants scheme. This initial analysis will be key for the integration of the data with other wheat diversity data and the implementation of software that will allow for the identification and characterisation of haplotypes. We will then configure the datasets to support more sophisticated analysis such as genomic selection and GxE modelling. |
| Exploitation Route | We will make the data generated by this project available to the wider wheat genomics community. The data will be accessible via databases and integrated with other wheat resources. |
| Sectors | Agriculture Food and Drink |
| Description | The data generated by this project has supported the work at CIMMYT to improve their communication with farmers across the globe. The Seed of Discovery project implements a dedicated extension service to translate research outcomes to improve agronomical practices. We have contributed to these services by presenting at workshops and attending debates in events open to farmers (in particular in Mexico - e.g. event in August 2017). As part of the project we have also deployed an advanced computing hardware and software platform for the analysis of large genomics datasets for wheat varieties generated from the Seeds of Discovery (SeeD) project. The platform integrates computing resources and bioinformatics expertise at the Earlham Institute, NIAB and James Hutton Institute in the UK to enable crop geneticists at CIMMYT to implement sophisticated data analysis algorithms with the objective to improve the use of the genetic resources for wheat. The computing platform is distributed across the partners' sites with hardware deployed at CIMMYT in Mexico and the Earlham Institute in UK. This includes large capacity storage units, the support for links to transfer data across the sites and a high-performance computing (HPC) unit to support software pipelines. The HPC infrastructure is hosted at the Earlham Institute and is based on a Silicon Graphics (SGI) UV300 system, one the most advanced computers of its kind. This hardware has been configured to be accessed remotely by researchers at CIMMYT and eventually by other scientist across the globe. |
| First Year Of Impact | 2016 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Societal Economic |
| Description | Study gene expression using RNA sequencing technology in response to heat shock in a subset of a panel of 168 synthetic-derived lines selected for heat tolerance |
| Amount | $150,000 (USD) |
| Organisation | CGIAR |
| Sector | Charity/Non Profit |
| Country | France |
| Start | 01/2019 |
| End | 12/2020 |
| Title | Enhancements to JHI software stacks |
| Description | Several major changes and enhancements have been made to CurlyWhirly to help deal with the visualization of data related to this project. These include - but are not limited to - changes to the data format to support the ability to associate multiple URLs relating to each data point majorly extending the flexibility of CurlyWhirly's data integration with external websites and databases, improvements to the way points are detected when in multi-selection mode, and improvements to the default colour palette to better deal with this type of high density data and more readily handle large numbers of categories of datapoint. Major refactoring to the Flapjack codebase to modularise its analysis routines to allow these to be run on the command line in addition to the graphical user interface. This work was extended by wrapping the analysis routines for use in Galaxy; opening up the analysis routines for easy installation and use by bioinformaticians and biologists, while also providing a simple route for running these analysis routines on High Performance Computing (HPC) infrastructure. A prototype integration of our plant genetic resources database Germinate with Galaxy has been developed which establishes Germinate as a data source for Galaxy. This work enables Galaxy users to call out to Germinate, where they can use the rich - domain specific - search and filtering user interface of Germinate to browse data, for the ultimate goal of selection of a set of data to be returned to Galaxy, where the data can be analysed using a wide variety of analysis tools, including most standard bioinformatics analysis tools. Research and development on a new method of running our server side web services. This led to the development of a generic interface for jobs which need to be run on a server, allowing for the server back end to be either a standard server using a lightweight job scheduling system, or two of the main HPC job scheduling systems. The development of this API means that any of our software can be easily extended to exploit most HPC clusters to speed up large scale data analysis. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Several major changes and enhancements have been made to CurlyWhirly to help deal with the visualization of data related to this project. These include - but are not limited to - changes to the data format to support the ability to associate multiple URLs relating to each data point majorly extending the flexibility of CurlyWhirly's data integration with external websites and databases, improvements to the way points are detected when in multi-selection mode, and improvements to the default colour palette to better deal with this type of high density data and more readily handle large numbers of categories of datapoint. Major refactoring to the Flapjack codebase to modularise its analysis routines to allow these to be run on the command line in addition to the graphical user interface. This work was extended by wrapping the analysis routines for use in Galaxy; opening up the analysis routines for easy installation and use by bioinformaticians and biologists, while also providing a simple route for running these analysis routines on High Performance Computing (HPC) infrastructure. A prototype integration of our plant genetic resources database Germinate with Galaxy has been developed which establishes Germinate as a data source for Galaxy. This work enables Galaxy users to call out to Germinate, where they can use the rich - domain specific - search and filtering user interface of Germinate to browse data, for the ultimate goal of selection of a set of data to be returned to Galaxy, where the data can be analysed using a wide variety of analysis tools, including most standard bioinformatics analysis tools. Research and development on a new method of running our server side web services. This led to the development of a generic interface for jobs which need to be run on a server, allowing for the server back end to be either a standard server using a lightweight job scheduling system, or two of the main HPC job scheduling systems. The development of this API means that any of our software can be easily extended to exploit most HPC clusters to speed up large scale data analysis. |
| URL | https://ics.hutton.ac.uk/software |
| Title | Galaxy server for UK SeeD |
| Description | Galaxy ( https://galaxyproject.org ) is an open-source web framework for running bioinformatics tools and workflows in a reproducible and shareable way. We are leveraging Galaxy to make both the SeeD HPC hardware and its software tools easily accessible to users. Moreover, we are integrating the Galaxy server with the other SeeD resources and databases, allowing users to import datasets from them directly into Galaxy for subsequent analysis. Galaxy has been deployed to a virtual machine hosted at the Earlham Institute, which submits computing jobs to the SGI UV 300 platform. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Collaborators of the SeeD project are presently using the Galaxy server to test the Galaxy tools developed as part of the project. We are also extending the number of installed tools in order to have the service ready to be effectively used by a larger number of users in the coming months. |
| URL | http://galaxy.seed.earlham.ac.uk/ |
| 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 | DivSeek Partnership |
| Organisation | DivSeek International |
| Sector | Learned Society |
| PI Contribution | I bring infrastructure expertise to this partnership, influencing and impacting policy to provide computational and training capacity to other DivSeek partners. I promote the range of infrastructure projects that are developed in my group at EI, but also solutions developed at other centres that can contribute to the DivSeek consortium. Partners are exposed to EI projects such as COPO, Grassroots (Wheat Information System, CerealsDB, marker design), CyVerse UK and Galaxy, through working group communications and meetings at international conferences such as PAG and RDA. I lead the Data Standards for Interoperable Tools working group, and we aim to collate community-suggested standards and tools, and advise the partnership and their stakeholders in best practice for delivery of sustainable and interoperable infrastructure. |
| Collaborator Contribution | The DivSeek consortium contributes expertise and knowledge exchange in advances in crop diversity, improving our networking and understanding of challenges and potential solutions to social, structural, and biological problems. With over 66 global partners including EI, this is a powerful and highly respected group of research institutes that are working together to enable a step change in efficiency of interactions, leading to improved crop diversity research and data sharing. |
| Impact | EI is a founding partner of DivSeek, and Dr Davey leads one of the new working groups, "Data Standards for Interoperable Tools" (http://www.divseek.org/standards/) |
| Start Year | 2015 |
| Description | Proyecto Omicas / Omics project |
| Organisation | Pontifical Xavierian University |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | Participation as an associated collaborator. The research program optimization Multiscale In-silico Agricultural Crops Sustainable (omics) is the winner of the second round of Colombia Science in focus Food which seeks, through seven projects, develop and implement strategies science and technology to improve agricultural varieties with the aim of contributing to food security and sustainable production worldwide . |
| Collaborator Contribution | Omic is made up of researchers, undergraduate and graduate students , and support staff from 16 institutions, including institutions are higher education (IES) accredited, national and international, IES national non - accredited, international research centers in agriculture and domestic enterprises in the industrial sector, with the Pontificia Universidad Javeriana Cali anchor entity . |
| Impact | This is a multidisciplinary project that involves collaborators working on genetics, genomics, bioinformatics, agriculture, phenotyping and social sciences. The Colombian government is also directly engaging with the collaborators. |
| Start Year | 2019 |
| Description | RNA-Seq Heat-tolerance study |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | We are implementing the analysis of RNA-seq data generated from a number of samples and cultivars focused on heat tolerance. |
| Collaborator Contribution | CIMMYT contributed with the funding for the generation of the RNA-seq data as well as the field trials from which the samples were extracted. JIC contributes to the analysis of the data. |
| Impact | RNA-seq data from a large collection of samples of wheat grown in México. |
| Start Year | 2020 |
| 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 |
| Description | Genome Informatics 2018 - Genome Campus - Cambridge - September 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited speaker at the Genome Informatics meeting in 2018. This is the most prominent annual bioinformatics conference. The session on Complex Genomes was initiated with this presentation. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/genome-informatics-2018/ |
| Description | International Wheat Genetics Symposium - 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 | A poster presentation about the wheat profile and nomenclature effort (part of the Wheat Initiative and UK-SeeD project). |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://iwgs2017.boku.ac.at |
| Description | Invited Speaker at the 10-year celebration of the Centre of Excellence in Genomics (ICRISAT, India) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 10-year anniversary of the Centre of Excellence in Genomics. This event congregated researchers and industry stakeholders from across the globe working in crop genomics. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.icrisat.org/celebrating-a-decade-of-genomic-advances-in-agriculture/?utm_content=buffer55... |
| Description | Key Note Speaker at VIII Argentinian Bioinformatics and Computational Biology Congress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Key note speaker - meeting was followed by a number projects to apply for GCRF funding to work with researchers in Latin America |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://ufq.unq.edu.ar/8cab2c/ |
| Description | Kick off event of the Omics Project - key note speaker |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Key note speaker at the Omicas project kick-off workshop in Cali (Colombia) |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.omicas.co/noticias/recomendaciones-y-agenda-del-taller-anual-omicas |
| Description | Monogram Bioinformatics Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Workshop to present results of the SeeD/UK infrastructure project (including new data and bioinfomatics tools). |
| Year(s) Of Engagement Activity | 2018 |
| Description | NIAB Director's day |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented at the NIAB Director day - the focus of the presentation was on describing the application of new technologies to agriculture. I engaged with a diverse audience - explaining the advantages that new technologies could bring to agronomical practices. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation at GOBii Annual Meeting, August 2018, Philippines |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk covering James Hutton Institute tools & technologies to assist plant breeding |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at Monogram 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation was given covering a range of the software tools we have developed and their their use in the Seeds of Discovery project at the Monogram 2018 meeting in Norwich. This was to an audience of more than 100 plant geneticists and commercial plant breeders. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://ics.hutton.ac.uk/software |
| Description | Presentation at PAG 2018 - Connecting Crop Phenotype and Genotype Data Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Modern day genomics, genetics and plant breeding relies on high-throughput sequencing and phenotyping technologies, generating data sets that have been increasing over the last few years in terms of both size and complexity. Storage and analysis of these diverse data sets is only possible via a combination of utilizing data warehousing, HPC clusters (often via the parallelization of existing code sets), information visualization, and visual analytics technologies. At the James Hutton Institute we develop novel software tools, web applications, databases and information resources (https://ics.hutton.ac.uk/software) which allow users to explore and query their data in logical and intuitive ways - ultimately leading to improved solutions for scientific data management and information dissemination. Germinate 3 stores various diverse data types and acts as a hub for other tools: Flapjack is built around graphical genotyping enabling users to sort and manipulate lines based on their genotype or on observed or predicted phenotypes; CurlyWhirly is a 3D viewer for PCA/PCo data; Tablet provides 2nd-generation sequence assembly and alignment visualization; and Helium utilizes plant pedigrees as a visualization framework. These resources are used by many institutes, companies, and large international projects, including the Genomic & Open-source Breeding Informatics Initiative (GOBII), Seeds of Discovery (including UK Seed), Crop Wild Relatives, and the International Wheat Yield Partnership. We will describe our tools, and the benefits they offer, and show how they're evolving to embrace new technologies such as the Plant Breeding API (BrAPI) for connectivity with external tools and resources, and Galaxy for the pipelining of analyses/HPC utilization. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Visit and presentation to the Bioscience Division at UCL |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | This visit was focused on exploring potential collaborations between UCL and NIAB. We are currently discussing a joint appointment and pursuing PhD funding opportunities. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Visit to CIMMYT - UK/SeeD infrastructure - preparation of data analysis for manuscript - October 2018 |
| 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 | Meeting at CIMMYT to finalise the analysis for the UK/Seed project and support the writing of the manuscript. Meetings with researchers at CIMMYT with the view to apply for follow up funding. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Wheat Gene Nomenclature 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 workshop was held on 28 September 2020. It brought together wheat researchers and breeders from across the globe. The theme of the workshop was focused on the continuous development of a wheat gene nomenclature. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Wheat Information System - Wheat Initiative - Gene Nomenclature Workshop - Berlin - July 2018 |
| 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 | Second workshop of the Gene Catalogue and Nomenclature Working groups. The meeting focused on the initiative to name genes in the wheat genome in a consistent manner and following the principles set out by the well-established Wheat Gene Catalogue. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://wheatis.org |
| Description | Wheat Initiative - Expert Working Groups meeting (Saskatoon) |
| 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 | As part of the activities of the Wheat Information System I presented and contributed to the annual meeting of the Wheat Initiative in Saskatoon (Canada) on 27 July 2019. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.wheatinitiative.org |
| Description | Wheat Initiative meeting - Expert Working Group chairs |
| 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 | Meeting held on 2 February organised by the Wheat Initiative. It was attended by the chairs and co-chairs of the Expert Working Groups. |
| Year(s) Of Engagement Activity | 2021 |