Decoding Biodiversity (DECODE): Development of Novel Experimental and Bioinformatic Tools for Genomic Diversity and Analysis
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
A work package of the grant Decoding Biodiversity (DECODE) this project will develop tools and techniques to investigate biodiversity. Specifically this includes developing methods for: comparing multiple genomes within and across species to identify structural changes; using multiple genomes to improve annotation of coding and regulatory regions in the genome; resolving complexity of bacteria communities and biological roles within those communities; the deployment of sequences as real-time sensors of environmental communities. With our partners IBM and Eagle genomics we will make the software and workflows developed are robust deployable and scalable.
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- Syngenta International AG (Collaboration)
- RAGT Seeds (Collaboration)
- James Hutton Institute (Collaboration)
- IBM (Collaboration)
- Murdoch University (Collaboration)
- Eagle Genomics Ltd (Collaboration)
- Elsoms Seeds (Collaboration)
- University of Saskatchewan (Collaboration)
- Tozer Seeds (Collaboration)
- University of Tennessee Health Science Center (Collaboration)
- Montana State University (Collaboration)
Publications
Ariaeenejad S
(2024)
Precision enzyme discovery through targeted mining of metagenomic data.
in Natural products and bioprospecting
Bell KL
(2023)
Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.
in Molecular ecology
Benoit G
(2024)
High-quality metagenome assembly from long accurate reads with metaMDBG.
in Nature biotechnology
Bloomfield S
(2025)
Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications
in Microbial Genomics
Boulton W
(2025)
Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.
in Scientific data
Böhne A
(2024)
Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection.
in npj biodiversity
Cai YM
(2023)
Tuning Plant Promoters Using a Simple Split Luciferase Method to Assess Transcription Factor-DNA Interactions.
in ACS synthetic biology
Cerk K
(2024)
Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.
in Microbial biotechnology
| Description | NATO Science & Technology Organisation Technical Team |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | BBSRC-NSF/BIO: Integrative analysis and Visualisation of Fly Cell Atlas datasets to enable cross-species comparisons |
| Amount | £340,861 (GBP) |
| Funding ID | BB/T014563/2 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 11/2025 |
| Description | BioFAIR - Digital Research Infrastructure |
| Amount | £34,000,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 07/2029 |
| Description | Connecting Research Culture Conference |
| Amount | £59,558 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 05/2025 |
| Description | DANIO-CODE - the next frontier: Decoding transcription regulation in regeneration by advanced genomics and computational tools |
| Amount | £241,097 (GBP) |
| Funding ID | EP/Z535400/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2024 |
| End | 10/2028 |
| Description | ELIXIR Co-ordination Office bridging award |
| Amount | £133,933 (GBP) |
| Funding ID | BB/X011100/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 03/2025 |
| Description | Interim BioFAIR award |
| Amount | £358,676 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 03/2025 |
| Description | Research Capability Funding: Rapid nanopore metagenomic sequencing of preterm microbiota and proinflammatory mediators/biomarkers in infection mediated preterm labour |
| Amount | £49,000 (GBP) |
| Organisation | Norfolk and Norwich University Hospital |
| Sector | Hospitals |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2024 |
| Description | The tree phyllosphere microbiome - an overlooked and important sink for carbon monoxide? |
| Amount | £645,350 (GBP) |
| Funding ID | NE/X001245/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2023 |
| End | 04/2026 |
| Title | Annotation of the genome assembly of hexaploid wheat cultivar 'Paragon' |
| Description | Annotation of the hexaploid wheat cultivar 'Paragon', https://plants.ensembl.org/Triticum_aestivum_paragon/Info/Index |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Paragon is an important UK spring wheat cultivar. Academic impact Key parent for existing Wheat Genetic Improvement Network (WGIN) resources. Lots of genetic resources in the Paragon background including deletion lines and QTL populations. This Annotation will contribute towards the "International Initiative on PanGenome and Haplotype Catalogues in Wheat" in collaboration with Rajeev Varshney. Industrial impact This genome annotation serves as a bridge between wheat research and breeding companies including Elsoms, RAGT, KWS, Limagrain. |
| URL | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-60/gff3/triticum_aestivum_paragon/ |
| Title | Fusarium Pan-Annotations: improved individual and collective genome annotations |
| Description | A 'pan-annotation' of genomes from 77 taxa (83 accessions) across the genus Fusarium, delivered as part of the Earlham Institute Strategic Programme Grant 'Decoding Biodiversity' (BBSRC). Manuscript and annotation workflow tutorial in prep. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | -Establishment of effective 'pan-annotation' reannotation workflow -Improved annotation quality both individually and collectively for Fusarium genomes -Detection of different rates of alternative splicing across Fusarium species complexes |
| URL | https://zenodo.org/doi/10.5281/zenodo.13829922 |
| Title | Genome Annotation Workshop 2024 - Test data |
| Description | Test datasets for the Genome Annotation Workshop 2024 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The dataset was used for the Genome Annotation Workshop 2024, providing users with hands-on experience with annotation tools, including those developed at the Earlham Institute (Mikado, Portcullis, REAT, Minos). The course had both national and international attendees, who attended virtually. 100% of attendees who provided feedback would recommend the course and rated the trainers, overall quality of the event, and training materials as excellent or very good. |
| URL | https://zenodo.org/doi/10.5281/zenodo.11221191 |
| Title | Low coverage genome sequencing data to uncover tilapia genetic diversity in the Lake Victoria Basin |
| Description | Low coverage genome sequencing data to uncover tilapia genetic diversity in the Lake Victoria Basin |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | na |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB75650 |
| Title | Sequence reads and genome assembly of hexaploid wheat cultivar 'Cadenza' |
| Description | PacBio HiFi reads representing 34x coverage of the hexaploid wheat cultivar 'Cadenza' and genome assembly. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Cadenza is an important UK wheat cultivar, tolerant to frost. Academic impact A TILLING population of 1,200 Cadenza M2 plants which can be re-analysed using this genome assembly. This genome will contribute towards the "International Initiative on PanGenome and Haplotype Catalogues in Wheat" in collaboration with Rajeev Varshney. Industrial impact This genome assembly serves as a bridge between UK wheat research and breeding companies including Elsoms, RAGT, KWS, Limagrain. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB85527 |
| Title | Sequence reads and genome assembly of hexaploid wheat cultivar 'Paragon' |
| Description | PacBio HiFi reads representing 31x coverage of the hexaploid wheat cultivar 'Paragon' and genome assembly. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Paragon is an important UK spring wheat cultivar. Academic impact Key parent for existing Wheat Genetic Improvement Network (WGIN) resources. Lots of genetic resources in the Paragon background including deletion lines and QTL populations. This genome will contribute towards the "International Initiative on PanGenome and Haplotype Catalogues in Wheat" in collaboration with Rajeev Varshney. Industrial impact This genome assembly serves as a bridge between wheat research and breeding companies including Elsoms, RAGT, KWS, Limagrain. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB59244 |
| Description | Collaboration with Eagle Genomics |
| Organisation | Eagle Genomics Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Eagle Genomics is one of the partners in DECODE ISP. DECODE ISP will be developing valuable datasets and bioinformatics tools that Eagle Genomics would be interested in hosting on their E-Datascientist platform. Series of meetings with researchers and ISP leads with Eagle Genomics bioinformaticians and heads of innovation and product. |
| Collaborator Contribution | Providing insights into type of tools and datasets needed to generate impact to address key challenges faced in agriculture, food nutrition, and biotech. Assessing Earlham's new bioinformatics tools and providing feedback on deploying them on Eagle Genomics platform Assisting with on-boarding datasets on the Eagle Genomics e[datascientist] platform Providing guidance on how to productionise and package bioinformatics tools Providing opportunities to realise the socio-economic impact from tools and datasets through Eagle Genomics clients. |
| Impact | Letter of Support and Memorandum of Understanding about the collaboration. |
| Start Year | 2022 |
| Description | Collaboration with Elsoms Group (CASE - CD) - Understanding variation in flowering-related traits among commercially important Apiaceae herb species. |
| Organisation | Elsoms Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Expertise and Know-How in marker discovery for plant breeding. Expertise and Know-How in identification of genetic diversity across large biological collections. Expertise and Know-How in sequencing and bioinformatics analysis of plant genomes. Knowledge and expertise in genebanks and genotyping orphan crops. Computational and bioinformatics expertise and best practice. |
| Collaborator Contribution | Plant material and breeding knowhow for Apiaceae herb species |
| Impact | CASE Studentship agreement. |
| Start Year | 2022 |
| Description | Collaboration with IBM Research, STFC, and RAGT - HNCDI Excelerate |
| Organisation | IBM |
| Department | IBM Research in the UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Earlham is contributing by genomic data for 27 UK wheat varieties and wheat pan-transcriptome data. |
| Collaborator Contribution | IBM will design, develop, and test the bioinformatic workflow to enable processing of genomic and developing statistical and ML predictions of potential useful genetic variation and markers for valuable agricultural traits. RAGT brings expertise in plan breeding. STFC Hartree Centre brings expertise in supercomputing, data science and artificial intelligence (AI) technologies for enhanced productivity, smarter innovation and economic growth. |
| Impact | No outputs or outcomes yet. |
| Start Year | 2023 |
| Description | Collaboration with IBM Research, STFC, and RAGT - HNCDI Excelerate |
| Organisation | RAGT Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Earlham is contributing by genomic data for 27 UK wheat varieties and wheat pan-transcriptome data. |
| Collaborator Contribution | IBM will design, develop, and test the bioinformatic workflow to enable processing of genomic and developing statistical and ML predictions of potential useful genetic variation and markers for valuable agricultural traits. RAGT brings expertise in plan breeding. STFC Hartree Centre brings expertise in supercomputing, data science and artificial intelligence (AI) technologies for enhanced productivity, smarter innovation and economic growth. |
| Impact | No outputs or outcomes yet. |
| Start Year | 2023 |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | IBM |
| Department | IBM Research in the UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | RAGT Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | University of Tennessee Health Science Center |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | International Initiative on PanGenome and Haplotype Catalogues in Wheat |
| Organisation | Murdoch University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | EI are providing our Paragon, Cadenza and Watkins genomes for including in the International Initiative on PanGenome and Haplotype Catalogues in Wheat being put together by Rajeev Varshney, Director of the Centre for Crop & Food Innovation, Murdock University, Australia. |
| Collaborator Contribution | Wheat research groups from around the world are contributing wheat cultivars for inclusion into this group. |
| Impact | None yet. |
| Start Year | 2025 |
| Description | International Initiative on PanGenome and Haplotype Catalogues in Wheat |
| Organisation | University of Saskatchewan |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | EI are providing our Paragon, Cadenza and Watkins genomes for including in the International Initiative on PanGenome and Haplotype Catalogues in Wheat being put together by Rajeev Varshney, Director of the Centre for Crop & Food Innovation, Murdock University, Australia. |
| Collaborator Contribution | Wheat research groups from around the world are contributing wheat cultivars for inclusion into this group. |
| Impact | None yet. |
| Start Year | 2025 |
| Description | MetaBodger Compare: Highly Scalable Pangenomic Variant Finding |
| Organisation | James Hutton Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I developed the concepts, algorithms and software for MetaBodger compare. Montana State University initially provided expert guidance and funding. Earlham Institute now provides funding, expert guidance on implementation and support across multiple teams. The James Hutton institute are also providing expert guidance on testing and implementation. |
| Collaborator Contribution | Graph algorithm guidance provided by Dr. Brendan Mummy, MSU. Guidance on implementation in plant genomes provided Dr. Jennifer Lachowiec, MSU. Guidance and support for the implementation in complex crop pan genome provided by Dr. Micha Bayer, James Hutton Institute. Guidance, support and software testing for various pan genomes is being supplied by various groups across the Earlham Institute headed by PIs Dr. Anthony Hall, Dr. Wilfired Haerty, Dr. Neil Hall. Support and guidance for software testing provided by Dr. David Swarbreck. |
| Impact | The collaboration is multi-disciplinary encompassing groups with various research interests across biological and computational sciences. |
| Start Year | 2024 |
| Description | MetaBodger Compare: Highly Scalable Pangenomic Variant Finding |
| Organisation | Montana State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I developed the concepts, algorithms and software for MetaBodger compare. Montana State University initially provided expert guidance and funding. Earlham Institute now provides funding, expert guidance on implementation and support across multiple teams. The James Hutton institute are also providing expert guidance on testing and implementation. |
| Collaborator Contribution | Graph algorithm guidance provided by Dr. Brendan Mummy, MSU. Guidance on implementation in plant genomes provided Dr. Jennifer Lachowiec, MSU. Guidance and support for the implementation in complex crop pan genome provided by Dr. Micha Bayer, James Hutton Institute. Guidance, support and software testing for various pan genomes is being supplied by various groups across the Earlham Institute headed by PIs Dr. Anthony Hall, Dr. Wilfired Haerty, Dr. Neil Hall. Support and guidance for software testing provided by Dr. David Swarbreck. |
| Impact | The collaboration is multi-disciplinary encompassing groups with various research interests across biological and computational sciences. |
| Start Year | 2024 |
| Description | Syngenta collaboration |
| Organisation | Syngenta International AG |
| Country | Switzerland |
| Sector | Private |
| PI Contribution | Facilitating regular meetings between EI and Syngenta researchers to develop 2 new collaborative projects. |
| Collaborator Contribution | Attended industry Seminar. Arranged introduction to further teams at Syngenta. |
| Impact | None yet. |
| Start Year | 2023 |
| Description | Tozer Seeds Knowledge Transfer Partnership |
| Organisation | Tozer Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Develop a project idea for a Knowledge Transfer Partnership (KTP) with Tozer Seeds, management of the application process and negotiation of IP and terms. The KTP will help Tozer to develop internal capacity to analyse genomic data for accelerated breeding. This collaboration began as a service provided by NBRI1 and JV in 2022, after which the BDI team assisted in developing it further into the KTP. |
| Collaborator Contribution | Tozer co-applied for KTP with EI and will be providing funding and in-kind support. |
| Impact | Application for a KTP submitted in November 2023. Earlham Institute gaining status as a KTN Knowledge Base. KTP was funded and started in July 2024 and will run till December 2026 (30 months) |
| Start Year | 2022 |
| Title | European national patent application for the Method and apparatus for detecting pathogens PCT/GB2023/050022 |
| Description | entered the regional phase at the European Patent Office on 26 June 2024 |
| IP Reference | PCT/GB2023/050022 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2024 |
| Licensed | No |
| Impact | no impacts yet |
| Title | European national patent application for the Methods for extraction and sequencing of nucleic acid for the PCT/GB2023/051992 |
| Description | Methods for extraction and sequencing of nucleic acid |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2025 |
| Licensed | No |
| Title | METHOD AND APPARATUS FOR DETECTING PATHOGENS |
| Description | We describe a method and system for detecting pathogens in a sample, particularly an air sample. The method is designed to run in real-time alongside sequencing processing of the sample so that results are quickly available to a user. Each input sequence read in the plurality of sequence reads is compared using a first classification algorithm and assigned to a taxon. An input sequence is classified as potentially pathogenic when the taxon to which the input sequence read is assigned corresponds to a pathogen taxon. Each input sequence read classified as potentially pathogenic is compared using a second classification algorithm to a plurality of target sequences in a second database which is selected based on the pathogen taxon. A confidence score is used as part of the decision-making process to decide if an individual read represents a genuine match to a pathogen. |
| IP Reference | WO2023131795 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2023 |
| Licensed | No |
| Impact | We are in the process of developing a spinout company that will license this IP and realise impact. |
| Title | PCT application based on GB2400934.2 - Sequencing methods |
| Description | confidential |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2025 |
| Licensed | No |
| Title | PCT application related to GB2210963.1 - Methods for extraction and sequencing of nucleic acid |
| Description | Methods for extraction and sequencing of nucleic acid |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2023 |
| Licensed | No |
| Title | Priority application GB2200151.5 - Method and apparatus for detecting pathogens |
| Description | Method and system for detecting pathogens in a sample, particularly an air sample. |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2022 |
| Licensed | No |
| Title | Priority application GB2210963.1 - Methods for extraction and sequencing of nucleic acid |
| Description | Methods for extraction and sequencing of nucleic acid |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2022 |
| Licensed | No |
| Title | Priority application GB2400934.2 - Sequencing methods |
| Description | confidential |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2024 |
| Licensed | No |
| Title | US national phase patent application Method and apparatus for detecting pathogens |
| Description | pending |
| IP Reference | US18/727,087 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2024 |
| Licensed | No |
| Impact | No impact yet |
| Title | (Software) Bug Fixes | COPO Project |
| Description | In the Collaborative OPen Omics (COPO) website application, software bugs usually emerge upon observations from end-users or from a project team member's maintenance checks. A software bug is an error, flaw or fault in the design, development, or operation of COPO that causes it to produce an incorrect or unexpected result, or to behave in unintended ways. Debugging is the process used to try find, correct and reproduce or pinpoint the cause of the bug. Bug fixes are crucial interventions to safeguard against software failures, inaccuracies, economic losses and avoid repercussions from poor software quality. The bug fixes and a brief description of it are recorded in COPO GitHub repository. Some examples of bug fixes in COPO are: - Enable the COPO Accessions Dashboard web page which can be accessed at https://copo-project.org/copo/copo_accessions/dashboard, to be viewed by end-users who are not logged into COPO - Corrected the data structure and results displayed when the audit Application Programming Interface (API) methods are queried - Grammatical, typographical and syntax error fixes - Ensuring that a default value is set or an appropriate error message is displayed when a code exception occurs The COPO project team aims to focus on precision and endeavours to perform bug fixes in a timely manner in order to deliver a metadata broker website platform that is robust, reliable and economically viable. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Notable impacts of bug fixes include: - Bugs fixes reflect the Collaborative OPen Omics (COPO) project team's commitment to support the research community by providing a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results - Bug fixes are a catalyst for operational efficiency, enhances end-users' experience and navigation of the COPO web application and prevents bugs to be raised by end-users (once they are discovered by the project team before the end-users) - Future COPO project team developers and members of the research community having the GitHub open-source/commit history can use it to relate to individual lines of code in the COPO project back to the original thought processes and reasoning behind why that code had been changed - Bug fixes prevent the inaccurate display of information on the COPO web application and improves the quality of the metadata broker service that COPO provides to the research community since the more bugs that are fixed, the more reliable the COPO project becomes - The quality and reliability of COPO are upheld once bugs are resolved and this results in COPO being a more robust and trustworthy metadata broker service to the research community - Fixing bugs in a timely manner can lead to the discovery of another bug which may not be apparent until the initial bug(s) have been fixed or the new discovered bug can be more severe than the initial bug(s) - Prevent end-users from incidentally creating duplicated samples when the 'Submit' button or 'Confirm' button is clicked by disabling the button which is still displayed during the processing period after the end-users have made metadata submissions/updates in COPO |
| URL | https://github.com/collaborative-open-plant-omics/COPO-production |
| Title | Applicaiton support |
| Description | Provide application support to user and also do performance tunning to COPO |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | Help user to use COPO, solve COPO bug and do enhenancement based on user's requirement |
| URL | https://copo-project.org |
| Title | Audit Log | COPO Project New Feature |
| Description | In the Collaborative OPen Omics (COPO), the audit log provides a record of all update actions that have been performed on samples by sample providers, system (members of the COPO development team) and sample managers. Actions that trigger an update of samples are but not limited to: - When a sample manager accepts or rejects samples - When a sample provider reuploads/resubmits an amended manifest in COPO - When a sample request is made to the COPO project team to update samples (in accordance with the sample project guidelines and the sample manger's affirmation) |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts include: - The audit Application Programming Interface (API) methods on the COPO API web page and audit records provide a tracking of the history of changes made to samples. The audit log increases stakeholders' awareness of sample changes, makes sample data more reliable and improves data quality. - The API methods are useful for querying as well as verifying sample updates and their integrity. Each audit log can be downloaded in a Comma-separated values (CSV) format or viewed in a json format via the API methods. - The audit API methods allows the scientific community to easily reference, access and fetch the open-source data from COPO without developing their own specialised methods. The results can reduce metadata duplication, avoid inconsistency between data held amongst various metadata brokers and can be used in analysis as well as publications. - The sample update log and Audit API methods include but are not limited to the following. Sample updates can be queried by the following using the Audit API methods: - The date and time of the update action - The user who performed the update - The update type of the action (e.g. user or system) - The field on which the value was changed - The outdated and new values of the sample fields that were updated - The identification (ID) and type of the sample that was updated |
| URL | https://copo-project.org/static/swagger/apidocs_index.html#/Audit |
| Title | Creation of API Method to Retrieve Sample Records by Sequencing Centre | COPO Project New Feature |
| Description | An Application Programming Interface (API) method was created to retrieve sample records in the Collaborative OPen Omics (COPO) project by sequencing centre. A dropdown list of available sequencing centres are provided to choose from in the API method. API methods were created to query COPO records by sample and manifest |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2024 |
| Impact | Sample managers, sample providers and any individual in the scientific community can analyse and be informed of the number sample records based on the centre where the samples have been sequenced. The results, which are produced in both csv format and json format, can be shared and incorporated in various publications, third parties and API methods for further analyses etc.. |
| URL | https://copo-project.org/static/swagger/apidocs_index.html#/Sample/get_sample_sequencing_centre |
| Title | ERGA Permits Deposition to B2DROP | COPO Project New Feature |
| Description | In the Collaborative OPen Omics (COPO) project, code was integrated to allow permits related to the European Reference Genome Atlas (ERGA) Tree of Life (ToL) project be deposited to a third party storage known as B2DROP. The permits are deposited to B2DROP after the samples that the permits are associated to have been accepted by sample manager. Each permit is deposited in a correlated taxonomy identification directory. B2DROP is a secure and trusted data exchange service for researchers and scientists to keep their research data synchronised and up-to-date and to exchange with other researchers. Permits pdf files provided by sample or manifest providers in COPO alongside a sample manifest to guarantee that the sample(s) in question can be legally transferred to the sequencing centre indicated, can be vouched at the indicated collection(s) and has been sampled in compliance with all applicable rules. The types of permits that can be submitted in COPO available are Ethics, Sampling and Nagoya. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | The integration of depositing European Reference Genome Atlas (ERGA) permits in COPO on B2DROP faciliates the following: - Submitted permits can be viewed after they have been submitted - Storage and sharing of permits submitted by sample submitters with members of the the ERGA Tree of Life (ToL) project group - A centralised location for permits according to their taxonomy identification since each permit is stored in a correlated taxonomy identification (taxon ID) directory |
| Title | ERGA_SATELLITES Associated Project/Subproject Integration | COPO Project New Feature |
| Description | The European Reference Genome Atlas (ERGA) Satellites (ERGA_SATELLITES) project is one of the primary biogenome projects for the European Reference Genome Atlas (ERGA) project sample manifest. Its data is brokered and validated in COPO then, deposited to European Nucleotide Archive (ENA) and National Centre for Biotechnology Information (NCBI) via Collaborative OPen Omics (COPO). In COPO, ERGA_SATELLITES samples are realised when "ERGA-SATELLITIES" is set as the value for the "PRIMARY_BIOGENOME_PROJECT" field for samples within a manifest and "ERGA-SATELLITIES" is set as the associated project type for a work profile created in COPO. This work profile is created by sample providers and it is the same profile that the samples/manifest will be submitted under. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts include enabling Collaborative OPen Omics (COPO) to support the submission and validation of ERGA manifests that relate to the European Reference Genome Atlas (ERGA) Satellites (ERGA_SATELLITES) subproject |
| URL | https://github.com/collaborative-open-plant-omics/COPO-production/commit/535c25d5b55b941cdc14f6b07bc... |
| Title | Enhancements and Fixes for API Performance, Data Retrieval, and Compliance | COPO Project |
| Description | This development effort involved multiple enhancements and fixes to the API, including performance improvements, error resolution, and restructuring of key methods. Several API methods were refactored for better data retrieval, including those related to specimens, bioimages, and project associations. Additional properties and compliance adjustments were made to align with data standards, including RO-Crate and Darwin Core (DWC). |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | • Improved API Performance: Optimised retrieval logic for faster data access. • Increased Data Accuracy: Fixed missing/incorrect values, ensuring accurate API responses. • Enhanced Usability: Added new API methods for better data querying, such as retrieving samples linked to images and projects. • Stronger Compliance: Updated schema to include required compliance fields and standard terms. • Better Maintainability: Refactored key API methods, making the system more robust and scalable. |
| URL | https://copo-project.org/api |
| Title | Enhancements for Data Mapping, Standards Integration, and API Fixes | COPO Project |
| Description | This update focused on improving the handling of standards in the API, particularly in the context of Darwin Core (DWC) mapping and manifest-based data retrieval. A new CSV return format was implemented to support standard-based exports, and fixes were applied to ensure proper retrieval of fields based on manifest versions and selected standards. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Notable impacts: • Improved Standards Compliance: Enhanced tol_dwc mapping and retrieval logic to align with established data standards. • Flexible Data Export: Added CSV output format to facilitate standard-based data sharing. • Better API Reliability: Fixed field retrieval issues, ensuring accurate data access based on manifest versions and standards. • Enhanced Interoperability: Updates support more seamless integration with external systems using standardized data structures. |
| URL | https://copo-project.org/api |
| Title | Improving System Robustness and Image Publishing with Continuous Testing | COPO |
| Description | It is a broker for life science data. It allows user to upload metadata and data for life science and publish them to the public repository |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | We continue to maintain, enhance and provide user support for COPO. Through COPO, users can upload the metadata in a spreadsheet format and have them published in public repository. What we have done in 2024: 1. refactor the "profile" application for easy creation and customisation 2. refactor the sample approval process for easy configuration and extension 3. integrate continuous testing before we do the deployment 4. publish images to bioimage archive 5. bug fixing 6. user support - sample update required by the data manager |
| URL | https://copo-project.org |
| Title | MARTi - Metagenomic Analysis in Real Time |
| Description | MARTi is an open- source software tool that enables real-time analysis and visualisation of metagenomic sequencing data, including taxonomic composition and antimicrobial resistance gene analysis. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | MARTi is routinely used for in-house metagenomic analysis. The tool is now publicly available for beta testing purposes and is being tested by other research groups. |
| URL | https://marti.readthedocs.io |
| Title | MARTi 0.9.18 (2024) |
| Description | Metagenomic Analysis in Real-time |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Training delivered on "Nanopore metagenomics" course, preprint published. |
| URL | https://marti.cyverseuk.org |
| Title | MARTi 0.9.22 (2025) |
| Description | Metagenomic Analysis in Real-time |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Training delivered on "Nanopore metagenomics" course, preprint published. |
| URL | https://marti.cyverseuk.org |
| Title | MetaMDBG |
| Description | MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Tool has already been used to generate complete genomes from complex environments such as soils and sediments. |
| URL | https://github.com/GaetanBenoitDev/metaMDBG |
| Title | MetaMDBG Analysis Scripts |
| Description | A collection of scripts and workflows of the manuscript "High-quality metagenome assembly from long accurate reads with metaMDBG" to assess HiFi metagenomics assembly quality |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Tool has already been used to generate complete genomes from complex environments such as soils and sediments. |
| URL | https://zenodo.org/record/8321179 |
| Title | Minos - a gene model consolidation pipeline for genome annotation projects |
| Description | Minos is a Python3/Snakemake - based pipeline that generates and utilises metrics derived from protein, transcript and expression data sets to consolidate gene models obtained from gene annotation workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The tool has bee used to deliver annotation for 9 wheat accessions as part of the 10+ Wheat Genomes Project (http://www.10wheatgenomes.com/) and is being used to support a variety of Earlham Institute annotation projects and featured as part of Biohackathon Europe 2023 https://doi.org/10.37044/osf.io/fy49g |
| URL | http://www.10wheatgenomes.com/ |
| Title | Minos - a gene model consolidation pipeline for genome annotation projects | 2024 Updates |
| Description | Minos is a Python3/Snakemake pipeline designed to consolidate gene models from gene annotation workflows by generating and utilising metrics derived from protein, transcript, and expression datasets. ** Main changes added to this release ** - Reordered the lookup to look at CPC models next if Mikado models are absent in the metrics_info.txt file to get the full list of models 3d9d22f - Introduced a configurable chunk size parameter within minos_config.yaml for BLAST and DIAMOND jobs, effectively mitigating HPC overhead. (8fed890) - Corrected threshold parameters for BLAST and DIAMOND BLASTP filtering, improving the accuracy of sequence similarity assessments. (c5b7d1f) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The Minos pipeline has been used to deliver diverse annotation projects at the Earlham Institute. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/minos |
| Title | Perform automatic test when user submit push the code changes for COPO to GITHUB |
| Description | We use CIRCLECI to activate the pipeline of automatic test when user push the codes changes to GITHUB. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | it is to ensure the code are tested before it it is released to production. |
| URL | https://copo-project.org |
| Title | Population Genomics Associated Project/Subproject Integration | COPO Project New Feature |
| Description | The Population Genomics (POP_GENOMICS) sample manifest adapts the European Reference Genome Atlas (ERGA) project sample manifest. Its data should be brokered and validated in COPO then, deposited to European Nucleotide Archive (ENA) via COPO. In COPO, a POP_GENOMICS samples are realised when: - "RESEQUENCING" is set as the value for the "PURPOSE_OF_SPECIMEN" field for all samples within a manifest and POP_GENOMICS - POP_GENOMICS and Biodiversity Genomics Europe (BGE) are set as associated project types for a work profile that is created in COPO. This profile is created by sample providers and it is the same profile that the samples/ manifest will be submitted under. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts include: - Enabling COPO to: - Support the submission and validation of ERGA manifests that relate to the Population Genomics (POP_GENOMICS) subproject - Accept manifests that have empty values for certain columns. COPO will then set a default value to the empty values according to the POP_GENOMICS Standard Operating Procedure (SOP) guidelines |
| Title | Project Development Team Documentation | COPO Project New Feature |
| Description | The Collaborative OPen Omics (COPO) project team documentation is hosted on the Earlham Institute's Confluence website and is accessible to only members of the COPO project team. It is a living document that will be updated as the COPO web application evolves. It is a guide to help new and existing members of the COPO project team understand the COPO system and understand how to use it so that they can continue the development of the COPO web application and provide a metadata broker service to the research community. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts of the COPO project team documentation include: - Limiting the need for extensive training and allows new project team members to get up to speed quickly and efficiently with the Collaborative OPen Omics (COPO) web application - Provides a consistent reference guide for all project team members - Allows for quick look up of information - Provides a guide on how to use the COPO system, solve notable bugs/user requests and how to navigate the system for the COPO users - The documentation reflects up-to-date procedures, methods and guidelines to navigate the COPO system from a project developer's perspective |
| Title | Provide Read submission / Assembly Submission / Seq Annotation Submission / Barcoding Submission in COPO |
| Description | Allow user to upload Files to ECS server and then use the files for different kind of submission to ENA. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | COPO user are able to submit Read / Assembly / Seq Annotation / Barcoding manifest to ENA |
| URL | https://copo-project.org |
| Title | REAT - Robust and Extendable eukaryotic Annotation Toolkit (2023 updates) |
| Description | REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Being used to support EI's annotation projects including the DToL Protist project Components of the toolkit were developed to support the annotation of wheat accessions as part of the 10+ Wheat Genome Project. Assessed as part of Biohackathon Europe 2023 https://doi.org/10.37044/osf.io/fy49g |
| Title | REAT - Robust and Extendable eukaryotic Annotation Toolkit | 2024 Updates |
| Description | REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. ** Main changes added to this release ** - Breaking update - REAT Homology Miniprot Integration - Harmonise conda dependencies and installation 7063181 - Updated REAT singularity definition file and updated software to make them compatible with rest of the tools 3494464 - Added new generic script create_mgc_groups_from_gff.py to create groups.txt file for multi genome compare from the alignments GFF file 1588ffe - Added new script to reformat miniprot GFF from mRNA->CDS to gene->mRNA>[exon|CDS] OR match->match_part format - miniprot2GFF3.py 24a3000 - Added new script to create alignment summary from multi_genome_compare --detailed tab output file - create_alignment_summary.py 7e69707 - Fixed missing '--source' to the spaln2gff output gff3 697aa21 - Changed default coverage and identity to '0' in spaln2gff script 5883703 - Round float to int before binning - create_alignment_summary.py 3857669 - Added checks to --spaln_extra_parameters to have -Q and -A parameters specified and not to include options -t, -K, -O, -Q, -M, -T, -d, -o, -yL ee874ca - Added spaln and miniprot specific options for running REAT homology WDL pipeline ee874ca - Renamed output 'all_avgF1.bin.txt' to 'Junction_precision_binning.tsv' ee874ca - Reorganised REAT homology outputs folder ee874ca - Added miniprot support to REAT Homology pipeline 3947259 - Updated splan command to incorporate new pass through parameters 3947259 - Added a common 'task_attr' to manage HPC resource for additional workflow tasks 3947259 - Refactored task 'ScoreSummary' by incorporating create_alignment_summary.py script 3947259 - Changed rt_struct.wdl to common/rt_struct.wdl 3947259 - Changed task 'PrepareAnnotations' min_exon_len to 10 from 203947259 - Changed task 'PrepareAlignmentsSpaln' min_filter_exon_len to 10 from 20 3947259 - Removed recursion_level option from splan alignments tasks 3947259 - Updated list of software_available to the latest versions used for installation 5e1850b - Added new option --spaln_extra_parameters to pass on extra parameters for SPALN alignment, where user must include the -Q and -A parameters 5e1850b - Fixed incorrect parameter from --alignment_min_exon_len to --alignment_max_intron_length 5e1850b - Added new minimum intron length, alignment parameter (spaln) --alignment_min_intron_length 5e1850b - remove SPALN's Q value parameter --alignment_recursion_level, indicating the level of recursion for the Hirschberg algorithm, which is now part of the --spaln_extra_parameters 5e1850b - Changed --filter_min_exon default value from 20 to 10 5e1850b - Updated help docs to make it more clearer 5e1850b - Updated help docs - xspecies_cleanup 64a5d9e - Updated help docs - filter_GFF3_terminals.py e2721f7 - Added additional WDL's to package_data - setup.py 059d1b7 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The REAT pipeline has been used to deliver diverse annotation projects at the Earlham Institute. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/reat |
| Title | Refactoring COPO backend system |
| Description | It is to refactor the existing COPO project which is a big python django application. Python libraries updated, obsolete code removed and cleaned and the whole django application was separated into various modulized django applications for easy maintenance. We also upgraded the VM to ubuntu 20.04 from 16.04 and upgraded the mongodb, postgress db, nginx to the latest version. Use cluster version of mongodb such that we can do the audit trail of collection update. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | It is easy to maintain and less security issue due to the upgrade on OS, python lib, DB and proxy server. |
| URL | https://copo-project.org |
| Title | Refactoring the deployment procedure for COPO |
| Description | We use docker container to run COPO. Previously there was no script to do the deployment and the containers were run by executing docker command one by one. We need to remember the commands and the environment variables for the container. Now we use docker stack to the deployment. All the configuration including the environment variables, volumn mapping, secrets, cpu/memory resources etc for the containers are written to a docker compose file. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | It is easy to maintain and easy to do deployment. From the compose file, we can always know the container configuration |
| Title | Sequencing Centres' & BGE Automatic Email Notification When ERGA Samples Are Accepted | COPO Project New Feature |
| Description | After European Reference Genome Atlas (ERGA) manifests have been submitted by end-users in the Collaborative OPen Omics (COPO) web application, they are accepted by sample managers and/ Biodiversity Genomics Europe (BGE) checkers once the samples are compliant to the guidelines outlined in the project's Standard Operating Procedure (SOP). My task was to integrate/trigger an automatic email notification in COPO to the Biodiversity Genomics Europe (BGE) partners, sequencing centre personnel, ERGA group personnel as well as to the manifest submitter when samples have been accepted by sample managers. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts include: - Increasing awareness and confirmation to the ERGA group personnel, sequencing centre contact points and sample providers that submitted ERGA samples have been accepted - Affirmation to the sample submitters that the submitted samples can be shipped now that they have been accepted - Affirmation to the sample submitters that the Material Transfer Agreement (MTAs) documents should be signed and sent to the ERGA point of contacts |
| Title | Upgraded ToL Projects to Higher Versions | COPO Major Feature |
| Description | Upgraded the Collaborative OPen Omics (COPO) website application code, metadata validation rules and manifest metadata json schemas to manifest versions - 2.4.2, 2.4.3 and ultimately, manifest version 2.5 (which is the current manifest version to date). The upgrade was done to be compliant with the latest changes and requirements by the main Tree of Life (ToL) projects that are brokered through COPO. These projects are Aquatic Symbiosis Genomics (ASG), Darwin Tree of Life (DTOL) and European Reference Genome Atlas (ERGA). |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Impact | Notable impacts include: - Withdrawl of the 'SHORT_READ_SEQUENCING' term from manifests in manifest version 2.5 upgrade - NOT_COLLECTED being an option for the 'DECIMAL_LATITUTE' and 'DECIMAL_LONGITUDE' columns in manifests in manifest version 2.5 in upgrade - Addition of 'ETHICS_PERMITS_FILENAME' field, 'SAMPLING_PERMITS_FILENAME' field and 'NAGOYA_PERMITS_FILENAME' to columns to manifests in manifest version 2.3 upgrade - Addition of 'LATITUDE_START' field, 'LONGITUDE_START' field, 'LATITUDE_END' field, 'LONGITUDE_END' field in manifest version 2.4.2 in upgrade - Addition of 'PROXY_TISSUE_VOUCHER_ID_FOR_BIOBANKING' field in manifest version 2.4.2 in upgrade - Withdrawal of the field, 'GRID_REFERENCE', because its information is captured in the fields - 'DECIMAL_LATITUDE' and 'DECIMAL_LONGITUDE' in manifest version 2.4.2 in upgrade - Added 'DNA barcoding to be performed by GAL' as an option for the field, 'BARCODING_STATUS' in manifest version 2.4.2 in upgrade |
| URL | https://github.com/collaborative-open-plant-omics/COPO-production |
| Title | User Documentation | COPO Project |
| Description | The Collaborative OPen Omics (COPO) documentation was created using the Sphinx reStructuredText (reST) markup language and hosted on Read the Docs. Read the Docs is a popular platform for hosting documentation, and it is used by many open-source projects whereas Sphinx is a powerful tool that makes it easy to create professional documentation. This version of the COPO documentation replaces the previous version which was last updated in 2021. In addition, the Help section of the COPO web application was omitted and included in this version of the COPO documentation. The latest version of the COPO documentation comprises the following sections: - Getting Started This section provides an overview of the COPO web application. It includes information on how to create an account, log in, and navigate to the COPO web application. - COPO Profile This describes the types of work profiles that can be created in COPO as well as how to create and manage them. - COPO Data Submission This describes the various ways by which metadata can be uploaded and submitted to COPO. - COPO Data Updates This describes how submitted metadata can be updated in COPO and what metadata cannot be updated - COPO Data Discovery & Retrieval - This describes how to search for metadata in COPO and how to retrieve metadata from COPO - Advanced This describes how to set up the COPO project locally with Docker and with PyCharm or Visual Code Code (VSCode) - Polices This describes the policies that govern the use of COPO - Help This section describes the glossary of terms used in COPO web application, how to contact the COPO team regarding issues or enquiries and frequently asked questions (FAQs) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The new version of the COPO documentation provides users with a comprehensive and updated guide to using the COPO web application and the COPO API. It comprises the following sections: - Getting Started - COPO Profile - COPO Data Submission - COPO Data Updates - COPO Data Discovery & Retrieval - Advanced - Polices - Help |
| URL | http://copo-docs.readthedocs.io |
| Title | User Support | COPO Project |
| Description | As a User Support Specialist for the Collaborative OPen Omics (COPO) web application, my tasks involve but are not limited to the following: - Investigating, resolving and responding to enquiries and issues raised by end-users of the COPO web application and the Tree of Life (ToL) project group personnel in a timely manner - Granting sample metadata providers and sample metadata managers access to requested ToL project groups - Liaising with COPO's European Nucleotide Archive (ENA) point of contact to suppress duplicated and invalid samples - Recommending and/or performing minor actions (code-wise) to correct issues or bugs raised by COPO end-users - Adding child projects/subprojects to parent projects upon request in ENA - Updating Aquatic Symbiosis Genomics (ASG), Darwin Tree of Life (DTOL) and European Reference Genome Atlas (ERGA) sample records - Liasing with Wellcome Sanger Institute point of contacts to update DTOL records |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | Notable impacts include: - Maintaining collaboration with the research community to utilise COPO to make metadata submissions - Enhancing sample providers' productivity and ability to proceed with manifest submissions when for example, samples are updated upon user request by COPO - Timely code bug fix, communication and response to COPO sample providers/submitters' enquiries enable the sample providers to meet their deadline in submitting sample metadata - Fixing issues and bugs in COPO increases user experience and productivity as well as the quality and reliability of the COPO web application - Updating sample metadata values upon request ensures that accurate metadata is provided and available in the wider research community - Granting users access to requested Tree of Life (ToL) project groups allows them to proceed with sample manifest submissions - Liaising with European Nucleotide Archive (ENA) point of contact to suppress samples that were redundant in COPO and should be permanently or temporarily removed - Provided a linkage to parent projects after having associated the subprojects to the parent/main projects in ENA |
| Title | clusterMAGs |
| Description | C++ program to cluster MAGs into de novo species clusters. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Central part of the MATAFILER pipeline developed in the Hildebrand group, this software allows for completely automated species definitions in metagenomes. |
| URL | https://github.com/hildebra/clusterMAGs |
| Title | ehancement to TOL project function on COPO |
| Description | 1. Allow user to submit images to Bioimage Archive 2. Upgrade the API version to connect to ENA. We use v2 ENA api which is asychnorous. 3. Send email to notify user and data manager when the sample is rejected by ENA 4. Allows sample user / manager to download the most update-to-date manifest from COPO. and then they can update the manifest and upload it again to COPO. In such a way, the samples are updated. Previously, we had to update the sample manually per user's request. 5. Identify and solve the duplicated submission to ENA 6. Capture the exception stack trace log to log file such that it is easy to trace the error 7. Add BGE-checker for ERGA BGE profile. If the sample is to Sanger Sequence Centre, once it is approved by BGE checker, it will be direct to Sanger user for approval before submitting to ENA. For other samples, once BGE checker approves, they will be submitted to ENA immediatedly. 8. Allow the sample managers to search the profile based on the keywords on samples. i.e. they can now search the profile by using sample's scientific name. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | make COPO more reliable and easy to use |
| URL | https://copo-project.org |
| Description | AI in the Biosciences UK Network (AIBIO UK) kick-off event |
| 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 | Virtually attended kick-off event for AIBIO-UK. A BBSRC-funded network to support and enhance engagement between the Bioscience and AI communities in the UK. Took part in online discussions. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://aibio.ac.uk/ |
| Description | Advancing Biodiversity Research: The Evolution of Collaborative OPen Omics (COPO) Project | Earlham Institute Seminar | April 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | The seminar explored the evolution of the Collaborative OPen Omics (COPO) project as an open-source metadata broker in biodiversity research. With its capability to broker different data seamlessly, COPO has revolutionised the way by which researchers collaborate and share information. An integral part of COPO's development involves standardising as well as enriching metadata and enabling the integration of diverse datasets for publication to the European Nucleotide Archive (ENA) which facilitates public dissemination. Additionally, COPO's user-friendly API empowers users to query sample data efficiently, further enhancing accessibility and interoperability in biodiversity studies. Through its continuous evolution, COPO continues to drive innovation and collaboration in the field of bioscience research. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://raw.githubusercontent.com/collaborative-open-plant-omics/Documentation/main/assets/files/pre... |
| Description | Agri-Tech E REAP conference 2023 (09/11/2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Attended Agri-Tech E's annual event REAP and took researchers from the DECODE and CELLGEN ISPs. Set up an EI exhibition stand, assisted JA with his talk and assisting with networking on the day. The exhibition stand was comprised of talking points to showcase the EI researchers and their work attending Agri-Tech E. This included: - a lego sequencer to demonstrate the genomics work being undertaken in clonal crops in DECODE and forage crops in CELLGEN, and how sequencing is carried out by NBRI1 - a basket of clonal crops being researched in DECODE - wheat seedlings from lines being researched in DECODE - a short presentation to compliment JA's talk, demonstrating how image analysis is used to determine diversity of seed packets |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.agri-tech-e.co.uk/microsite-page/reap-2023/ |
| Description | Agri-TechE Digging Deep (16/05/2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Showcase of the range of technologies and emerging research available to better understand, monitor and manage the range of activities happening beneath our feet that have an impact on farming and land management. Participants included: - Farmers and land-owners interested in soil health monitoring - Researchers wanting to share their work in this area and understand commercial applications - Tech developers with a solution for measuring and managing soils - Individuals with a general interest in soils and associated micro-organisms |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.agri-tech-e.co.uk/civicrm/event/info/?reset=1&id=27270 |
| Description | BAYER Innovation Scout visit to NRP (22/05/2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Innovation Scout from BAYER visited NRP. Colleagues from EI attended a lunch with the scout to discuss relevant research. A member from each NBI gave an introductory talk to the scout on the opportunities to collaborate at their institute. EI is now talking with BAYER on how best to collaborate as part of the CELLGEN ISP. |
| Year(s) Of Engagement Activity | 2024 |
| Description | BBSRC Pioneer panel membership |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Membership of the BBSRC pioneer awards panel 2023 |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ukri.org/opportunity/pioneer-awards-early-stage-frontier-bioscience-research/ |
| Description | BBSRC sLoLa Outlines panel |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Membership of the BBSRC strategic LoLa Committee. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ukri.org/opportunity/strategic-longer-and-larger-slola-grants-frontier-bioscience-2023-t... |
| Description | DBT Agri-Tech Investment Specialist visit to Norwich Research Park (06/02/2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | A member from each NBI gave an introductory talk to the specialist on agri-tech development at their institute, to give the specialist an understanding of the research ongoing on the park. |
| Year(s) Of Engagement Activity | 2024 |
| Description | DSW Annual Meeting |
| 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 | Coordinated a science showcase entitled 'Cutting-edge wheat and pathogen (pan) genomics' at the annual DSW all-hands meeting. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Darwin Tree of Life (DToL) All-Hands Meeting | London (2024) |
| 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 | Engaged in discussions related to the Darwin Tree of Life (DToL) project which is brokered through Collaborative OPen Project (COPO) These discussions revolved around the following: - progress and achievements, - samples - sequencing - assembly - curation - annotation - addressing and being aware of the challenges in sequencing DToL genomes - being aware of the current landscape of activity for science using DToL genomes - promoting DToL through effective communication and visibility |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://docs.google.com/document/d/1Jh_3Uf2Nw9FaTohKJD508hlJlVHF0nAlxnyofwneQ8E/edit |
| Description | Digital Twins in bioscience, environmental and medical science |
| 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 | Digital twins (DT) and their application are an area of growing interest within the bioscience, environmental and medical science research and innovation community. BBSRC, NERC, MRC and DTNet+ jointly ran a hybrid community workshop focussed on digital twins in bioscience, environmental and medical science on Wednesday 18 September 2024 at Rothamsted Conference Centre. The event aimed to create a better shared understanding of the DT landscape as it relates to the bioscience, environmental and medical science research and innovation communities, including better insights into the discipline-specific opportunities and challenges together with opportunities to network as a community. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://engagementhub.ukri.org/bbsrc-research-strategy-and-programmes/digital-twins-workshop/ |
| Description | EI Innovate annual stakeholder engagement event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. EI Innovate events foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. In 2023, we showcased our two new strategic programmes of research - Cellular Genomics and Decoding Biodiversity - and two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry. The programme included talks about Earlham expertise and capabilities, examples of collaborations, panel discussions, Innovation Showcase, exhibition, tours of the two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry, and networking. |
| Year(s) Of Engagement Activity | 2019,2020,2021,2022,2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | EPSRC AMR focused One Health - Trusted Research Environment (OH-TRE) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This project is a part of the EPSRC-funded Digital Health Hub for Antimicrobial Resistance (AMR) which focuses on bringing together outstanding interdisciplinary teams across academia, government, the NHS, industry, and charities to harness emerging digital technologies to transform antimicrobial stewardship and one-health surveillance. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Eastern Promise event at the Royal Norfolk Show (27/06/2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Panel discussion on current research in the Norwich Food Science Supercluster and networking opportunity. Interest in collaboration from one organisation following the event related to DECODE. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Elected to Royal Norfolk Agricultural Agricultural Association Council |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | The RNAA Council is a volunteer body and has supervisory control over both the property and the general policy of the Association. It provides a useful check and balance to the strategic direction of the Association. Council comprises up to 48 elected members and meets twice a year, usually in the Spring and Autumn. Council members are expected to take an active interest in the development of the Association. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Equitable Practise in Evolution Training - Applying the Equity Compass |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This course helped me to reflect on and develop equitable and inclusive practice. It involved two in-person sessions (13 February 2024 & 13 March 2024) at the Earlham Institute to introduce The Equity Compass, a tool to address ongoing inequalities in STEM communication. These sessions were supported by a three-week online/self-motivated course via FutureLearn. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Excelerate technical kick-off meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Planning and technical discussion meeting with collaborators on HNCDI Excelerate project at IBM London: IBM Research (Laura Gardiner, James Strudwick, Tim Donovan), STFC (Sophie Houston, Megan Yates, Robin Kennedy-Reid, William Davies, Jayalakshmi Vijayan), RAGT (Chris Burt, John Baison, Heidi Town), EI (Liliya Serazetdinova, Anthony Hall, RLRP). |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Crucible |
| 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 | An interdisciplinary, cross-sector event that fosters collaborations between researchers and innovators on the Pathways FLF Development Network program. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Crucible in Cardiff 21-22 March 2024 |
| 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 | An interdisciplinary, cross-sector event that fosters collaborations between researchers and innovators on the Pathways FLF Development Network program. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Leadership Retreat |
| 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 | A Pathways FLF Development event to give insights into navigating the process of leading research and innovation programmes, and managing teams. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Flash Talk: WP1: Objective 1.2: Genome Annotation Improvement |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a 1 minute flash talk on research plants for work package 1, objective 1.2: Genome Annotation Improvement. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Genome Annotation Workshop (May 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | In this three-day, virtual course participants gained an overview of Next Generation Sequencing technologies relevant to genome annotation, gaining the benefits of each platform, including the use of a number of tools developed at EI to support high-quality annotation (Mikado and Portcullis, PMIDs 30052957 and 30418570 respectively). Through a programme of talks, demonstrations and hands-on sessions all lead by EI faculty, topic covered were: • Understanding what to look for in a sample that will pass quality control and that will likely succeed in producing viable sequencing data, including how to assess the quality of RNA-Seq data. • Learn about reference guided transcriptome assembly and steps for processing short and long read data. • Learn about alternative approaches for annotating protein coding genes in eukaryotic species utilizing transcriptome and homology data, via projection and evidence guided gene prediction. Discuss the challenges of annotation in different contexts. • Hands on experience of annotation tools including tools and pipelines developed at the Earlham Institute. You will build gene models, explore the use of combiners/choosers for integrating alternative gene predictions (EVM / MINOS) and assess the accuracy of different annotation tools. The course had 25 attendees, with 88% from academia. International attendees made up 40% of the cohort, attending virtually from Australia, Austria, Belgium, France, Germany, Netherlands, Philippines, Taiwan and United States. 100% of attendees that provided feedback would recommend the course, and rated the Trainers, Overall Quality of the event and Training Materials as Excellent or Very Good. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/genome-annotation-workshop-2024 |
| Description | IBERS visit |
| 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 | A group of EI staff visited IBERS in Aberystwyth from 19-21 July 2023 (Jose De Vega, Anthony Hall, Seanna McTaggart, Camilla Ryan, Christine Fosker) to discuss the DECODE ISP, find opportunties for collaboration and tour IBERS and the biorefinery. |
| Year(s) Of Engagement Activity | 2023 |
| Description | ISP all hands meetings FTMA4 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | ISP all hands meeting allow the interaction amongst all the work package members. In addition to project and impact progress updates, workshops are held to drive discussion in areas such as IDEA, policy impact, futher funding opportunities and more. |
| Year(s) Of Engagement Activity | 2023,2024 |
| Description | Invited talk - Brown & Co ABC Tour (28 Sep 2023) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Invited speaker at Brown & Co "ABC Training Tour" at the Centrum, Norwich. Title of talk "Natural biodiversity, in-field metagenomics and environmental surveillance" |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited talk Syngenta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation of work on Pangenomes and work within DECODE Title:Why one genome just isn't enough: How multiple wheat genomes are changing our understanding of plant evolution. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited talk at DTRA Tech Watch meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited to present at the online DTRA Tech Watch seminar series. Invite list for this series is around 500 people linked to defence research. Title of talk "Air-seq: Rapid automated identification of airborne pathogens". |
| Year(s) Of Engagement Activity | 2024 |
| Description | Invited to participate in Royal Society 'Transforming Our Future' workshop, 'Innovating Agriculture' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This meeting explored the agricultural science and innovation that is transforming the future of food and farming to meet rising production and environmental demands. The agricultural sector needs to meet the challenge of producing more food to meet rising demand whilst also achieving environmental targets. This two-day conference examined the science and innovation aiming to transform the future of food and farming. The event brought together stakeholders from across industry, academia, government and the wider agricultural community to address three key areas: increasing sustainable yields, improving input efficiency and developing novel food production systems. Panel discussions considered how best to support and fund innovation in food and agriculture, and how to accelerate translation and take-up of new ideas. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://royalsociety.org/science-events-and-lectures/2024/06/agriculture-tof/?gad_source=1&gclid=Cjw... |
| Description | KTN Plant Sector Board meeting, 25 May 2023 |
| 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 | LS is a member of the Knowledge Transfer Network meeting of the Plant Sector Advisory Board. LS attended the meeting on 25th May 2023 and invited RRP of the AH Group gave a talk on using multi-omics approaches to accelerate plant breeding. The purpose was to inform the PSAB members about the advances in pangenomics and multi-omics to advance crop breeding. PSAB members are representatives from industry and academia, senior leaders in their organisations who are interested in accessing latest innovations. The intended outcomes are new collaborations between the Earlham Institute and other organisations utilising these technological approaches (wheat pangenomics). |
| Year(s) Of Engagement Activity | 2023 |
| Description | Maximizing Subgenomic Assemblies; K-mer composition guided subgenome classification of "Un" contigs - Machine Learning Seminar -03-07-24 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | This seminar present work that was originally developed during my PhD, but is being reengineered to support activities within EI (most notably rapid subgenomic/chromosomal assignment of sequenced/assembled molecules). As a result of this talk, a number of colleagues have requested to meet to see if the tools and/or concepts discussed can be used for work they are interested in. |
| Year(s) Of Engagement Activity | 2024 |
| Description | MetaBodger Compare: Highly Scalable Pangenomic Variant Finding |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation for Delivering sustainable wheat annual presentation |
| Year(s) Of Engagement Activity | 2025 |
| Description | Metagraph & Metabodger - EI Plant Genomics Seminar - 31/05/24 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a talk on research initially developed during my PhD but which has continued development post-PhD and now during my time here at EI. Several groups have expressed interest in using it for their research and this talk was to disseminate information about the methods behind MetaBodger as well as the pros and cons of implementation. Audience members mostly featured EI staff, but also national and international collaborators. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Methods to detect hidden diversity research project page |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Published a research project page detailing aims and activity from WP1 of the Decoding Biodiversity ISP - methods to detect hidden diversity. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.earlham.ac.uk/research-project/methods-detect-hidden-diversity |
| Description | Multigenome Brassica Project (MGBP) Steering Committee Meeting |
| 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 | Attended Annual MGBP Steering Committee meeting at PAG30 to discuss future opportunities to work together. |
| Year(s) Of Engagement Activity | 2023 |
| Description | NBI Summer school teaching session 12-07-24 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Around 15 students took park in a "Phylogenetics for conservation" session, which featured a lecture on conservation, a lecture on phylogenetic and a practical conservation phylogenetics workshop. Students also had the opportunity to ask scientific as well as general questions about working in science. Students were very engaged and provided verbal feedback that they found the session informative and enjoyable. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Nanopore Metagenomics: from sample to analysis 18-19 July 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The goal of this course is to provide an overview of lab and in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. This course will cover theory of experimental methods and sample collection, plus theory and hands-on experience of DNA extraction and library preparation. The second part of the course will cover data analysis and visualisation providing hands-on opportunities including the use of QC tools, EI's MARTi software and tools for Metagenome Assembled Genomes (MAGs), all delivered via virtual machines. You will also have the opportunity to discuss and apply lessons to your own projects with EI's experts during an optional Q&A session. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/nanopore-metagenomics-2023-sample-analysis |
| Description | Nanopore Metagenomics: from sample to analysis 31 Oct - 1 Nov 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The goal of this course is to provide an overview of lab and in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. This course will cover theory of experimental methods and sample collection, plus theory and hands-on experience of DNA extraction and library preparation. The second part of the course will cover data analysis and visualisation providing hands-on opportunities including the use of QC tools, EI's MARTi software and tools for Metagenome Assembled Genomes (MAGs), all delivered via virtual machines. You will also have the opportunity to discuss and apply lessons to your own projects with EI's experts during an optional Q&A session. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Nanopore metagenomics: from sample to analysis 2024 |
| 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 | Training course. The goal of this course is to provide an overview of lab and in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/nanopore-metagenomics-sample-analysis-2024 |
| Description | Norfolk Rural Economic Strategy visit to Norwich Research Park (29/03/2023) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Anglia Innovation Partnership hosted the Norfolk Rural Economic Strategy Steering Group (agenda and strategic policy attached) on 28th March at Centrum. BN presented AirSeq and MARTi to the steering group. The steering group reports to Norfolk County Council with member stakeholders advocating on the challenges and opportunities for rural Norfolk. Their recommendations have led to large initiatives being funded and delivered with partners. The aim of the event was for organisations to become more aware of how issues, plans, funding and decisions can be influenced, and how Norwich Research Park organisations can work with these agencies. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Notre Dame Science Workshop 13-06-24 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Science workshop to educate young children (Nursery, pre-year 1) about the importance of biodiversity for food. This included a discussion about the importance of caring for the environment with a particular emphasis on fruit/vegetable farms. This was followed by a workshop where adults cut open tomatoes, the children then extracted and planted seeds. Children were then given opportunities to ask questions about our activity or any science-related questions. The teachers have reported an increased interest in the topics discussed and a return next year has been discussed. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Nuffield student hosting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | I hosted a Nuffield student for 2 weeks. The research project was "Genomic analysis of fungal species to identify causal genes of ecologically-critical phenotypes.". The outcomes of this work have made it into a publication which is under review. |
| Year(s) Of Engagement Activity | 2024 |
| Description | PAG Talk 2024- Wheat Genomics to Breeding session |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sequencing, assembling and annotating key cultivars and representatives of 7 wheat sub-populations Wheat diversity can be split into 7 subpopulations. Here I will give an update on work as part of the Design Sustainable Wheat programme to sequencing, assembly and annotating these. How these and other data sets can be added to improve the utility of existing data. |
| Year(s) Of Engagement Activity | 2024 |
| Description | PAG2024 Trticeae Genetics and Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Title: Using pangenomes in Anger to Reduce reference bias in transcriptomic experiments |
| Year(s) Of Engagement Activity | 2024 |
| Description | Pan-Pooideae Meeting at PAG32 |
| 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 | Workshop at PAG32 to discuss the international Pan-Pooideae network. Overview of current research proposals and plans for next meeting. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Plant Pangenome Working Group |
| 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 aim of this group is to bring together a small group of researchers with overlapping expertise in wheat genomics and pangenome architecture to identify possible strategies and approaches that will enable a high resolution pangenome reference for the wheat community. We held an initial meeting at PAG32 in SanDiego, Jan 2025 to gauge interest, exchange experiences and plan further virtual meetings. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Poster: "NATO Technical Activity: Sequencing for Environmental Aerosol Background Monitoring" (Richard Leggett, Aerosols & Microbiology, 4-6 June 2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster at Aerosols and Microbiology conference, 4th - 6th June 2024. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://microbiologysociety.org/event/society-events-and-meetings/aerosols-and-microbiology.html |
| Description | Poster: Rapid surveillance of the urban air microbiome (Richard Leggett, Aerosols & Microbiology, 4-6 June 2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Richard Leggett presented poster at Aerosols and Microbiology conference, 4th - 6th June 2024. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://microbiologysociety.org/event/society-events-and-meetings/aerosols-and-microbiology.html |
| Description | Presentation to John Innes Foundation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presented 'Data driven plant science' to John Innes Foundation Science subcommittee. This has helped secure continued funding for PGRs. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Quarterly Institution Strategic Programme Work package meetings |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | ISP work package meetings are hybrid and open to and involve all participants in the ISPs, including partners. The meetings include 1-3 oral presentations showcasing ongoing work and roundtable discussions on successes, barriers, and opportunities. |
| Year(s) Of Engagement Activity | 2023,2024,2025 |
| Description | Research group retreat |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | The whole research group participated in a retreat where each member gave an oral presentation that explored possible future research directions. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Royal Norfolk Agricultural Show - Stewarding |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Assistant Head Steward helping RNAA coordinate STEMM village, AgriTechE and new machinery/innovations area at the Royal Norfolk Show, over 2days. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.royalnorfolkshow.co.uk/ |
| Description | Science Fair Judging 05-07-24 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | This event involved myself, and other visiting scientists, to judge pupil-led science projects at Neatherd high school, Dereham. This involved interaction with more than 20 groups of children who had conducted a range of research projects to learn more about their research interests, aims and processes involved in their projects. Ultimately we had to decide a winner and 2 runners up, along with a "Most creative" award and "Honourable mention". The pupils were highly engaged and seemed genuinely excited to meet scientists from a range of backgrounds. The winning project was so well done I brought to their attention that they may wish to explore high school science journal publication. The school expressed interest in our return next year. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Svevo Pangenome Meeting |
| 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 | Researchers from the U of Bologna organised a Svevo pangenome meeting at PAG32 in San Diego (Jan 2025), to discuss research and publication plans with international collaborators. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Talk at 2023 EI Innovate workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a talk entitled "Advancing wheat genomics through multiple genome assemblies" in session 2 "High-quality genomes and pangenomes for plant and animal breeders" to showcase EI's ability to generate high-quality wheat genomes. This was followed by a panel discussion involving speakers from the session. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | Talk at PacBio Roadshow, Wellcome Trust, London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented a talk on how PacBio sequencing was enabling our wheat research. I had a few questions afterwards and many people talked to me about wheat genome assembly afterwards. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://events.pacb.com/discoveries-roadshow-2023/page/2569888/london-new |
| Description | Talk to International Undergraduate Summer School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | Gave a talk introducing the Earlham Institute, including the span of our research interests. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk: "Air-Seq: Using DNA sequencing to detect airborne strawberry pathogens" (Mia Berelson, Aerosols & Microbiology, 5 June 2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mia Berelson gave a talk at the Aerosols & Microbiology conference, Bristol, 4-6 June 2024 |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://microbiologysociety.org/event/society-events-and-meetings/aerosols-and-microbiology.html |
| Description | Talk: "Real-time and in situ metagenomics" (Richard Leggett, Norwich Nanopores Day) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Norwich Nanopores Day, 19 Sep 24 |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk: "Tools for real-time and in situ metagenomics using nanopore sequencing" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited keynote talk at TSL Summer Conference in Plant-Microbe Interactions. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.tsl.ac.uk/tsl-summer-conf-15th-26th-july-2024 |
| Description | Teaching Assistant for Data Carpentry Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Attendees required either set-up assistance or assistance when issues emerged for the Data Carpentry topics - Data Organisation in Spreadsheets and Data management with SQL. The topics taught the fundamental data skills needed for anyone that deals with data and datasets. Ultimately, the attendees should be able to more effectively manage and analyse data as well as apply the tools and approaches directly to their ongoing research. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/data-carpentry-workshop-2024 |
| Description | Teaching Assistant for Software Carpentry Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Periods of being a Software Carpentry teaching assistant: 12th December, 2023 - 14th December, 2023 (URL: https://www.earlham.ac.uk/events/software-carpentry-workshop-dec23) 7th February, 2023 - 10th February, 2023 (URL: https://www.earlham.ac.uk/events/software-carpentry-workshop-2023) Attendees required either set-up assistance or assistance when issues emerged for the Software Carpentry topics - The Unix Shell, Version Control with Git and Programming with Python. The topics enabled attendes to use the shell to do more in less time, write structured programs and use Git to manage and share information. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/software-carpentry-workshop-dec23 |
| Description | The fish, the fungus, the grass, the bee - and the brassica |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on Earlham Institute's membership of ERGA, gaining positive feedback and shares from external organisations. As we live through the planet's sixth mass extinction event, the Earlham Institute has joined the European Reference Genome Atlas (ERGA), a ground-breaking network of researchers across Europe documenting our vanishing lifeforms. ERGA is a continent-wide response to the threat to diversity, collecting and sequencing the genomes of all European eukaryotes to better understand them for the future. It is part of the wider Earth Biogenome Project. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/fish-fungus-grass-bee-and-brassica |
| Description | UK plant breeders to benefit from online research tools |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | News story on the collaboration between EI, IBM Research, STFC and RAGT Seeds to develop pan-genomic resources for the plant breeding industry. Thanks to the partners involved the piece was very well engaged with online. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/uk-plant-breeders-benefit-online-research-tools |
| Description | UK-LATAM Agri-Tech Innovation Through Smart Farms Project Visit to Norwich Research Park (20/02/2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A member from each NBI gave an introductory talk to the LATAM delegates on the opportunities to collaborate at their institute. There was interest from one organisation to collaborate on DECODE. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Workshop UK:BalticWheat workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk at the workshop "Why multiple wheat genomes are important" |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop between Earlham and Eagle Genomics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A visit 7 Earlham colleagues to Eagle Genomics in London to build a collaborative framework between Eagle and Earlham, as part of collaborations with DECODE and CELLGEN ISPs. Key areas of the framework include IP management, software licensing; terms of access to EI tools and data; standardisation of tools and data to enable commercialisation; and areas of joint research interests resulting in publications (animal health and probiotics, soil health). This visit was funded through the BBSRC FTMA4. |
| Year(s) Of Engagement Activity | 2023 |
| Description | https://www.earlham.ac.uk/news/earlham-institute-BBSRC-funding-award-2023 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We issued a press release to mark the 5-year funding award from BBSRC, which supports the Earlham Institute, ISPs, and NBRIs. We secured widespread regional media coverage, including BBC Look East and online, ITV Anglia, and the EDP. The feedback from BBSRC on this coverage was very positive, particularly due to competing stories on life science funding. The launch campaign received around 28.5k impressions and 1,000 engagements across social media platforms, with the launch tweet achieving 330 engagements on its own. The majority of ISP partners engaged either by sharing ours posts or publishing their own messages, which included Kew Science, UK CEH, Eagle Genomics, and PacBio. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-BBSRC-funding-award-2023 |
| Description | k-mer sketching for subgenome identification and comparison - IBERS-EI genomics taskgroup - 12/03/24 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A number of professionals from EI and IBERS (Aberystwyth University) attended this talk. This research was developed during my PhD but has since been applied to research destined for publication within EI. |
| Year(s) Of Engagement Activity | 2024 |