Cellular Genomics (CELLGEN): Data Science for Cellular Genomics
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
As a work package of the grant Cellular Genomics (CELLGEN) we will develop a data science ecosystem to enable us and the wider scientific community to interpret share and integrate cellular genomics datasets
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- National Institute of Genetics (Collaboration)
- Tropic Biosciences Ltd (Collaboration)
- Andalusian Center for Development Biology (Collaboration)
- Google (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
- Oxford Nanopore Technologies (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- AstraZeneca (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- WorldFish (Collaboration)
- Tufts University (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- QUADRAM INSTITUTE BIOSCIENCE (Collaboration)
- James Cook University (Collaboration)
- Medical Research Council (MRC) (Collaboration)
Publications
Bell AM
(2023)
Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons.
in bioRxiv : the preprint server for biology
Cai YM
(2023)
Tuning Plant Promoters Using a Simple Split Luciferase Method to Assess Transcription Factor-DNA Interactions.
in ACS synthetic biology
Chau C
(2024)
Automated Purification of DNA Origami with SPRI Beads.
in Small (Weinheim an der Bergstrasse, Germany)
Chougule K
(2024)
Pan genome resources for grapevine
in Acta Horticulturae
Collí-Dulá RC
(2024)
Single-cell RNA sequencing offers opportunities to explore the depth of physiology, adaptation, and biochemistry in non-model organisms exposed to pollution.
in Comparative biochemistry and physiology. Part D, Genomics & proteomics
Etherington G
(2023)
Schizosaccharomyces versatilis represents a distinct evolutionary lineage
Etherington GJ
(2024)
Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast.
in Yeast (Chichester, England)
Felix Shaw
EI Single Cell Schemas
Feng S
(2024)
Alleviating batch effects in cell type deconvolution with SCCAF-D
in Nature Communications
| Description | Advocacy to the House of Lords Science and Technology Select Committee |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | As a result of EI's evidence, the Committee's report included policy recommendations aligned to the Earlham Institute's advocacy especially on investment and skills. Since the enquiry, the Government has endorsed the role of the UK's life science sector as one of the most strategically important areas for development in the Modern Industrial Strategy. This policy will generate subsequent regulatory and investment decisions that will impact our work significantly. |
| URL | https://publications.parliament.uk/pa/ld5901/ldselect/ldsctech/55/5502.htm |
| Description | Alice Macdonald MP and Jess Asato MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In December 2024 the newly elected MPs Alice Macdonald and Jess Asato visited the Earlham Institute and Norwich Research Park for an introduction to our research and advocacy. They met staff, saw inside our laboratories and heard about the wide range of research we do and our priority advocacy objectives for science policy. |
| Description | Ben Goldsborough MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In August 2024 the newly elected MP for South Norfolk, Ben Goldsborough, visited the Earlham Institute as part of his introduction to his new constituency and the Norwich Research Park. He met senior staff, heard about our policy advocacy priorities, listened to some case studies and saw colleagues working in our laboratories. Afterwards he posted on social media, praising the Norwich Research Park and saying his visit had been "life affirming" and "encouraging". Since his visit he has spoken about Norwich Research Park and the Earlham Institute in numerous parliamentary debates and policy conversations with ministers. |
| Description | EDESIA DTP board |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.uea.ac.uk/research/research-with-us/postgraduate-research/latest-phds-and-research-stude... |
| Description | EI response to Government consultation on engineering biology |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Government invited evidence from research community to inform future policy - including regulation and funding decisions - on engineering biology |
| Description | Letter to Chancellor to protect science budget and maintain core research funding |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | The letter helped to persuade HM Treasury of the link between economic growth and a strong science research sector to drive innovation and investment. The DSIT budget and core research budgets were maintained. |
| Description | Letter to DEFRA Minister advocating against delay to implementation of legislation |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | As a result from the advocacy pressure that this letter contributed to, the Government restated their intention to bring forward the secondary legislation in March 2025. |
| Description | Ministerial advocacy on science impact of immigration restrictions |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Peter Prinsley MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In September 2024 the newly elected MP Peter Prinsley, visited the Norwich Research Park. He met senior staff, heard about the Earlham Institute's policy advocacy priorities and listened to some case studies. He was particularly interested in the Norwich Research Park's advocacy on strategic investment in infrastructure and the strength of clusters in R&D place strategy. |
| Description | Steff Aquarone MP visit and introduction to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In September 2024 the newly elected Lib Dem MP for North Norfolk, Steff Aquarone, visited the Earlham Institute as part of an introductory visit to Norwich Research Park. He met senior staff and gave a speech about wanting to work closely with EI on science policy development and relevant legislation and regulation. |
| 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 | Cell type deconvolution of gene expression in disease data sets |
| Amount | £121,841 (GBP) |
| Organisation | The Wellcome Trust Sanger Institute |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 04/2026 |
| 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 | Creating standardized approaches for aquatic symbiosis cell atlases and a cell atlas database for the scientific community (Biodiversity Cell Atlas) |
| Amount | £151,875 (GBP) |
| Funding ID | 12189 |
| Organisation | Gordon and Betty Moore Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 05/2024 |
| End | 09/2026 |
| 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 | Early Career Researcher Bursary |
| Amount | £500 (GBP) |
| Organisation | British Phycological Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2025 |
| End | 01/2025 |
| Description | Engineering gene regulatory networks to design disease-resistant crops |
| Amount | £1,409,847 (GBP) |
| Funding ID | BB/Y007786/1 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 02/2026 |
| Description | FAIR Futures: Expanding COPO for Next-Gen Life Science Research and Collaboration |
| Amount | £199,556 (GBP) |
| Funding ID | APP53011 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 04/2025 |
| Description | FAIR Futures: Expanding COPO for Next-GenLife Science Research and Collaboration |
| Amount | £159,645 (GBP) |
| Funding ID | UKRI294 |
| Organisation | Science and Technologies Facilities Council (STFC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 03/2025 |
| Description | Next generation tools for genome-centric multimodal data integration in personalised cardiovascular medicine |
| Amount | £340,025 (GBP) |
| Funding ID | 10098097 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 12/2027 |
| Description | Single molecule analysis of Human DNA replication |
| Amount | £644,575 (GBP) |
| Funding ID | BB/Y00549X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 07/2027 |
| Title | CellxGene server |
| Description | Set up a CellxGene server for EI users to easily visualize single-cell data. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The CellxGene server at EI provides an intuitive and interactive platform for users to easily visualize and explore single-cell RNA-seq data, which enhances data accessibility and accelerates biological insights. This centralized resource supports collaboration and reproducibility. |
| URL | https://10.0.152.139/cellxgene |
| Title | EISCA - EI Single-Cell Analysis pipeline |
| Description | The pipeline EISCA is designed to cover all analysis stages, from quantification and clustering to tertiary analyses, for both 10x and Smart-seq data. Built using Nextflow, the pipeline consists of three analysis phases. The primary phase includes quality control of raw reads, mapping and quantification, and converting the count matrix into Anndata and Seurat objects. The secondary phase focuses on single-cell quality control, cell filtering, clustering analysis, and the merging or integration of samples. The tertiary phase involves cell type annotation, differential expression analysis, and future implementations of other downstream analyses. Users can run each analysis phase separately by specifying the relevant parameter (e.g., --analyses secondary). Additionally, The pipeline allows users to exclude specific analyses within a phase as needed. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The development of this single-cell RNA-seq pipeline has significantly streamlined the analysis of 10x and Smart-seq data, enabling researchers to efficiently process and interpret large-scale single-cell datasets. By integrating quality control, clustering, and advanced tertiary analyses into a modular and automated workflow, the pipeline enhances reproducibility and reduces the complexity of single-cell RNA-seq analysis. Its flexibility allows users to customize their analyses, facilitating tailored workflows for diverse research needs. Additionally, the implementation in Nextflow ensures scalability and portability, making it accessible for high-performance computing environments and cloud-based platforms. This tool accelerates biological discoveries by providing a standardized, efficient, and reproducible approach to single-cell transcriptomics. |
| URL | https://github.com/TGAC/eisca |
| Title | Single cell RNA seq (10x) of immune cell in liver upon Slamonella typhimurium infection |
| Description | Single cell RNA seq (10x) of immune cell in liver upon Slamonella typhimurium infection in mice fed control or low protein diet |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Transcriptomic shifts in liver immune cells exposed to Salmonella typhimurium infection in animals fed control or low protein diet |
| Title | Single-cell quality control pipeline |
| Description | This is a quality control pipeline for scRNA-seq data, starting with FASTQ files generated from a SmartSeq2 experiment and a sample sheet containing the relevant metadata. Transcript-level counts are generated, merged, and used to compute QC metrics. A QC report is produced for each plate, as well as for the entire experiment. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The development of this quality control pipeline for SmartSeq2 scRNA-seq data has had a notable impact on improving data reliability and reproducibility in single-cell transcriptomics. By automating the processing of FASTQ files, generating transcript-level counts, and producing detailed QC metrics, the pipeline enhances data consistency and reduces manual effort. The standardized QC reports facilitate early detection of technical artifacts and batch effects, ultimately improving downstream analyses. Additionally, by streamlining quality control across multiple plates and entire experiments, this tool supports large-scale studies and enables more accurate biological interpretations. |
| URL | https://github.com/EI-CoreBioinformatics/eisinglecellpap |
| Description | Astrazeneca |
| Organisation | AstraZeneca |
| Department | Research and Development AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Analysis of long read bulk RNA-Seq for the detection of splicing variation in human cell lines under different conditions Additional collaborations with other groups at Astra Zeneca; Astra Zeneca visit to Earlham as part of Industry Seminar. |
| Collaborator Contribution | Experimental data (cell exposed to different compounds), sequencing data |
| Impact | Multidisciplinary collaboration combining molecular biologists and computational biologists |
| Start Year | 2023 |
| Description | Collaboration - JS UEA |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration on the investigation of the implications of small RNAs during cardiomyocytes differentiation and implication of disruption We are analysing long read data from the iPSC, early differentiation, late differentiation |
| Collaborator Contribution | The collaborators provided cells for preparation of sequencing libraries and proteomic data |
| Impact | the collaboration is multidsiciplinary bringing together molecular biologists, cellular biologists, bioinformaticians |
| Start Year | 2024 |
| Description | Collaboration - WorldFish |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | As part of this collaboration we have been generating genomic resources and identifying the genetic bases of traits of interest |
| Collaborator Contribution | WorldFish has been providing samples for sequencing, genetic data |
| Impact | 10.1186/s12864-022-09065-8 |
| Start Year | 2020 |
| Description | Collaboration James Cook University |
| Organisation | James Cook University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Collaboration to analyse single cell data from Barramundi, investigating gene regulation in the skin of different morphs |
| Collaborator Contribution | The partners provide sequencing data and aquaculture knowldege |
| Impact | The collaboration in multidisciplinary bringing together expertise in fish and aquaculture genetics, molecular biology, and bioinformatics |
| Start Year | 2024 |
| Description | Collaboration King College London |
| Organisation | King's College London |
| Department | Maurice Wohl Clinical Neuroscience Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational analyses of long read bulk and single cell data from human IPSCs with engineered mutation for Amyotrophic lateral sclerosis and derived neurons, bulk long reads RNA-Seq from mouse brains with human mutations for Amyotrophic lateral sclerosis |
| Collaborator Contribution | Generation of IPSC lines with causative mutations, generation of the mice lines with human mutation |
| Impact | The work is highly collaborative including clinicians, clinical geneticists, molecular biologists, cellular biologists, computational biologists |
| Start Year | 2023 |
| Description | Collaboration Nucleic Acid Therapy Accelerator |
| Organisation | Medical Research Council (MRC) |
| Department | Nucleic Acids Therapeutics Accelerator (NATA) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | NATA will raise oligo against isoforms of potential therapeutic value to enable follow up validation experiments |
| Collaborator Contribution | NATA will provide means to knock out and knockdown isoforms of interest, we will be providing a list of isoforms of potential therapeutic value |
| Impact | The work is highly multidisciplinary combining molecular biology, cell biology, and bioinformatics |
| Start Year | 2024 |
| Description | Collaboration UEA Medical School |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational analyses of long read data to assess polyAdenylation sites usage during cardiomyocytes maturation, both in wild type background and in cell lines with mutations for cardiac disorders |
| Collaborator Contribution | IPSC generation, cardiomyocytes maturation |
| Impact | Computational analyses of differential polyadenylation usage during cardiomyocytes maturation |
| Start Year | 2024 |
| Description | Collaboration with Oxford Nanopore Technologies |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of the upcoming EI strategic programme we will be producing novel protocols for single cell long read RNA and DNA sequencing as well as novel approaches to detect DNA replication through base modification |
| Collaborator Contribution | ONT will contribute through providing expertise in machine learning models applications (base modification), technology solutions and protocols developments for single cell RNA / DNA seq |
| Impact | Engagement with ONT on March 7th to develop the collaboration as part of the upcoming ISPs |
| Start Year | 2022 |
| Description | Danio-ReCODE |
| Organisation | Andalusian Center for Development Biology |
| Country | Spain |
| Sector | Private |
| PI Contribution | cross-species analyses of single cell atlases in order to understand regeneration across evolution |
| Collaborator Contribution | a PhD student is about to start working in this consortium |
| Impact | DANIO-CODE - the next frontier: Decoding transcription regulation in regeneration by advanced genomics and computational tools Multidisciplinary collaboration through a Marie Curie Doctoral Network with partners across Europe |
| Start Year | 2024 |
| Description | Earlham-Freudenreich group (Tufts) |
| Organisation | Tufts University |
| Department | Department of Biology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Collaboration combining Nieduszynski (EI) expertise in single molecule analysis of DNA replication with Freudenreich group expertise in yeast short tandem repeat (STR) biology. Our team is applying our single molecule technology to study replication through STRs in yeast using strains shared by the Freudenreich group. |
| Collaborator Contribution | Freudenreich group have contributed yeast strains and technical expertise on how to work with these strains. |
| Impact | None |
| Start Year | 2024 |
| Description | Earlham-NIG, Japan |
| Organisation | National Institute of Genetics |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | Single molecule analysis of DNA replication in human cells using cell lines where PrimPol can be depleted. |
| Collaborator Contribution | Generation of human cell line where PrimPol can be depleted. |
| Impact | None |
| Start Year | 2024 |
| Description | Earlham-UEA (Akay) |
| Organisation | University of East Anglia |
| Department | School of Biological Sciences UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Single molecules sequencing for detection of base modifications. Sharing of yeast strains that express ectopic copy of Dam methylase. |
| Collaborator Contribution | Growth of yeast strains in different media types to differentially label DNA. |
| Impact | None |
| Start Year | 2024 |
| Description | Earlham-UEA (JJB group) |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Single molecule analysis of DNA replication |
| Collaborator Contribution | In vitro DNA replication using the Xenopus cell free system |
| Impact | None |
| Start Year | 2024 |
| Description | Google Cloud |
| Organisation | |
| Department | Google UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration we will make available high dimension data sets and pipelines for analyses |
| Collaborator Contribution | As part of the collaboration Google Cloud will facilitate access to data sets and online analyses |
| Impact | This collaboration contributed to the submission of the CELLGEN ISP |
| Start Year | 2022 |
| Description | Impact of low protein diet on liver function upon Salmonella infection |
| Organisation | Quadram Institute Bioscience |
| Department | Gut Health and Food Safety |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My team has performed FACS cell sorting and 10X analysis of immune cells in the liver. |
| Collaborator Contribution | Dr Beraza holds the project license enabling studies of the Salmonella infection and impact on liver function in M. musculus. Her team provided the expertise in immune cell isolation from the liver. |
| Impact | We have published the article: Low protein diet exerts protective effect on liver function upon Salmonella infection. Generated findings were a basis for a PhD project that will commence in October 2025 as a part of BBSRC DTP program. |
| Start Year | 2021 |
| Description | Isolation and in vitro differentiation of human megakaryocytes |
| Organisation | University of Cambridge |
| Department | Cambridge Stem Cell Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Prof Cedric Ghevaert |
| Collaborator Contribution | As a part of FTMA we have had reciprocal visits to gain experience in the isolation and differentiation of megakaryocytes from human aphaeresis cones. We have shared our expertise in the library construction and sequencing. |
| Impact | Knowledge exchange |
| Start Year | 2023 |
| Description | Panhematopoietic clonal and molecular analysis using RNA-barcoding approach |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I was performing FACS sorting of cells, isolated samples were included in published papers. |
| Collaborator Contribution | Dr Rushworth and his team provided wild type (C57Bl6, n=25) and PEPC Boy (n=20) mice and skills (intravenous injections). |
| Impact | Publications: 10.1172/JCI153157 10.1101/2022.05.16.491933 10.3389/fimmu.2022.1003006 10.1073/pnas.1913278116 10.1182/bloodadvances.2022007033 |
| Start Year | 2019 |
| Description | Tropic Biosciences |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration we will be sequencing materials from Tropic Bioscience to identify variants segregating in their stocks, we will develop novel protocols for early assessment of plant embryos |
| Collaborator Contribution | As part of the collaboration Tropic Bioscience is providing material (tissues, DNA) and expertise |
| Impact | The collaboration contributed to the submission of the CELLGEN ISP |
| Start Year | 2022 |
| Description | Wellcome Trust Sanger Institute |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Computational analyses of single cell long read data (PacBio, ONT) for human IPSC and differentiated neuronal lineages (astrocytes, motor neurons) |
| Collaborator Contribution | Cells (IPSCs, derived neuronal lineages), sequencing data |
| Impact | The work is multidisciplinary bringing together cellular biologists, molecular biologists, and computational biologists |
| Start Year | 2023 |
| 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 | FlowFI - Flow cytometry Feature Importance |
| Description | Flow cytometry is a tool for spectral analysis of biological cells (including bacteria, human animal and plant cells) used in both medical and experimental contexts. FlowFI (Flow cytometry Feature Importance) is a python-based, graphical interface to enable investigators to perform online data driven feature importance analysis of flow cytometry spectral and possibly also imaging features for gating, the selection of a subset of cells based on their features, for identification of pathological or otherwise interesting cell morphologies. The software uses efficient spectral methods for feature importance analysis with parallel processing to enable analysis of large numbers of live samples for refinement of the gating approach at the bench. The software is capable of analysing data from any generic .fcs file but was tested using data generated with the BD FACSDiscover™ S8 Cell Sorter from BD Biosciences that can provide a range of spectral and imaging features. FlowFI does not perform or suggest a gating strategy, but instead ranks features by how much of the variance in the samples they account for. This is performed using robust spectral methods based on Laplace scoring [1]. FlowFI allows for a subset of features (e.g. imaging vs specific red, violet or blue features) to be analysed, allowing for results to be iteratively refined based on the subset of interest. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | New imaging flow cytometry datasets of immunologically active, haematopoetic mouse cells is now being produced using this software. |
| URL | https://github.com/jameswilsenach/FlowFI |
| Title | Master spreadsheet for spatial transcriptomics and scRNA-Seq |
| Description | This document contains all the metadata fields, data types, regex and cardinality rules for singlecellschemas |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | This forms the basis of the standard, and is used to generate the website content, manifest and validation rules. |
| URL | https://github.com/TGAC/SingleCellSchemas |
| 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 | 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 | Single Cell Standards Website |
| Description | Interactive website for displaying the single cell standards produced in my group |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Further dissemination of these standards |
| URL | http://singlecellschemas.org |
| Title | Software Architectural Design of COPO |
| Description | I have been responsible for the overall design and delivery of many new features in COPO over the past 12 months. Please see recent software output entries for further details. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The overall growth of COPO as a service |
| 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 | 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 |
| Title | eisinglecellpap |
| Description | eisinglecellpap is a smart-seq2 quantification and quality control pipeline, developed for single-cell service at the Earlham Institute. Starting with the FASTQ files generated from the SmartSeq2 experiment and a sample sheet containing the appropriate metadata, transcript level counts are generated, merged and used to produce QC metrics. QC reports and data package for delivery are generated. The pipeline communicates and posts QC reports JIRA. The pipeline is written in Python, Snakemake, and Perl. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Impact | The pipeline has been used in CellGen ISP and fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eisinglecellpap/ |
| Title | enhance COPO for single cell schema handling |
| Description | When single cell schema is ready, we transfer it into a spreadsheet file. User can fill in the spreadsheet and then upload it to COPO. COPO will do the validation and storage for the single cell data. In future, COPO will submit the data to the public repository. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Allow user to upload / store / download single cell schema manifest |
| URL | https://copo-project.org |
| Title | scSQANTI |
| Description | https://github.com/ConesaLab/scSQANTI_devel |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | These developments enable users to assess data quality from single cell long read sequencing |
| URL | https://github.com/ConesaLab/scSQANTI_devel |
| Title | setup a website for singlecellschemas.org |
| Description | It is a website to hold the signcellschemas specification |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | It is the place where user can find the single cell schemas specification |
| URL | https://singlecellschemas.org/ |
| Description | 1st PCA manifest hackathon |
| 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 | Produced filled manifest using single cell standards |
| Year(s) Of Engagement Activity | 2025 |
| Description | 1st Spatial Transcriptomics manifest hackthon |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | 1st test manifest produced for spatial transcriptomics |
| Year(s) Of Engagement Activity | 2025 |
| Description | 2nd PCA manifest hackathon |
| 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 | produced second test manifest from single cell schemas |
| Year(s) Of Engagement Activity | 2025 |
| 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 | Analysing cell imaging data at scale with AI |
| 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 | As part of the CellGen WP2, we wrote an article showcasing the partnership with the Earlham Institute and The Alan Turing Institute. The article focused on research being carried out by Sonia Fonseca, in the Wojtowicz Group at EI, and James Wilsenach at ATI, using an AI tool - FlowFI - to speed up the processing and analyses of cellular image data, primarily megakaryocytes. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/analysing-cell-imaging-data-scale-ai |
| Description | Attendance at Biocuration 2023 |
| 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 conference to network and find out latest developments. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Attended Gordon Research Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Lightning talk and poster presentation at this conference. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Big Data Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Gave talk on data management to PhD students. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Biofair Roadshow EI |
| 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 | Contributed thoughts to fact finding workshop |
| Year(s) Of Engagement Activity | 2023 |
| Description | Biohackathon - AI Ready Datasets for Biology |
| 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 | This activity was part of an effort to bring together practitioners at the intersection of the biomedical and information sciences in order to design new pipelines for standardisation of biological data processing. A technical report and code base is expected to follow from this project. Results were presented at Semantic Web Applications for Health Care and Life Sciences 2025. |
| Year(s) Of Engagement Activity | 2025 |
| Description | COPO demo to PCA metadata and infrastructure steering committee |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | showed functionality of COPO and how this could be used for PCA purposes |
| Year(s) Of Engagement Activity | 2025 |
| Description | COPO/Annotare standards coordination |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I met with the developers of Annotare to discuss sharing of metadata standards. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Course co-organiser Single Cell Bioinformatics Course 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 | Course on data analysis generated in single cell RNA sequencing experiments, 16 participants gained understanding in data analysis, interpretation and future directions in the single cell fields. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-bioinformatics-2024 |
| 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 | Data Science for Cellular Genomics 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 webpage detailing the aims and activity from WP1 of the Cellular Genomics ISP - Data Science for Cellular Genomics. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.earlham.ac.uk/research-project/data-science-cellular-genomics |
| Description | Demonstration of How to Submit Reads and ERGA Sample Manifests in COPO | EI Single Cell Data Management Training Course Session 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | - Gave a presentation regarding European Reference Genome Atlas (ERGA) and reads manifest submissions on Mon 6th November, 2023 as part of the Single Cell Data Management Course Session in the Advanced Single-Cell RNAseq Data Analysis workshop that was hosted by the Earlham Institute (EI) Advanced Training department - Described how to share work profiles so that other persons in the scientific community can collaborate and make manifest submissions in Collaborative OPen Omics (COPO) platform - Illustrated invalid manfiest submissions and relevant error messages that can be displayed as means to guide how to make the necessary corrections |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/advanced-single-cell-rnaseq-data-analysis-2023 |
| Description | EI Innovate 2023 |
| Form Of Engagement Activity | A talk or presentation |
| 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. It provided plenty of networking opportunities and allowed us to gain insight into our ongoing collaborations, explain how our expertise and facilities can be accessed and discuss potential ideas for new collaborations. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| 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 | EI Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave EI seminar |
| Year(s) Of Engagement Activity | 2024 |
| Description | EI manifest hackathon |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Produced first test manifest for single cell rnaSeq standard developed at earlham |
| Year(s) Of Engagement Activity | 2024 |
| Description | ENA single cell checklist meeting |
| 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 | Meeting with ENA collaborators to discuss necessary changes for submitting single cell rnaseq data |
| Year(s) Of Engagement Activity | 2025 |
| Description | ERGA all-hands Thessolaniki |
| 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 | Annual meeting of ERGA project |
| Year(s) Of Engagement Activity | 2023 |
| Description | ERGA data management training (Poland) |
| 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 | Gave talk about data management and COPO along with reps from ENA at a workshop in Poland |
| Year(s) Of Engagement Activity | 2025 |
| Description | Elixir UK all hands - Norwich |
| 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 networking group discussions |
| Year(s) Of Engagement Activity | 2023 |
| Description | Elixir UK all-hands |
| 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 | Took part in various sessions and a poster session at this UK based meeting. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Elixir all-hands Dublin 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster, and had discussion regarding development of ROCrate which led to several hackathons. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Elixir all-hands Uppsalla |
| 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 | Presented 2 posters at all-hands meeting |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engaged the DEFRA Lead on Strategy and Implementation for Digital Sequence Information and Access and Benefit Sharing in advance of COP 16 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Earlham Institute researchers met the DEFRA team working on Digital Sequence Information and Access and Benefit Sharing policy in advance of COP16 in Colombia. We discussed synergies between EI's advocacy and the UK policy position and how our advocacy could help to influence the international discussion on this subject at COP16. We published an article on this on our website: https://www.earlham.ac.uk/news/value-dsi-global-genomics-research-must-be-heard-cop16. The UK's support for DSI helped COP16 reach a ground breaking decision on operationalising a multilateral mechanism for the use of digital sequencing information from genetic resources. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/value-dsi-global-genomics-research-must-be-heard-cop16 |
| Description | Engaging with DEFRA and the Food Standards Agency on implementing the Genetic Technology (Precision Breeding) Act 2023 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Series of meetings with officials working on the implementation of the Genetic Technology (Precision Breeding) Act 2023 to determine key aspects of policy related to the resulting regulation. We took part in policy workshops and online briefing events organised across the Norwich Research Park. Some of these workshops involved representatives from the commercial sector involved in plant science and R&D. |
| Year(s) Of Engagement Activity | 2023 |
| Description | FAIR workshop for Spatial Transcriptomics |
| 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 | Discussed and presented single cell schemas, made plans to join other working groups for further dissemination. |
| Year(s) Of Engagement Activity | 2025 |
| Description | FTMA4, visit at MRC Stem cell institute, Cambridge |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDRA< RA and a group leader visited the lab at MRC Stem Cell Institute to gain practical knowledge and experience in new cell assays. Possibility of joint funding application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Find My Future STEMM 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | FindMyFuture is an engagement event aimed at introducing Year 8 students to various STEMM careers. Members of EI chatted about their research and careers with the many students who visited our stand. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Gordon Research Conference in Single Cell Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented poster, lightning talk and networked. Discovered collaborators with whom I am currently preparing a grant. |
| 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 | Image Processing Carpentries |
| 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 | Devlivered Training |
| Year(s) Of Engagement Activity | 2023 |
| Description | Image Processing with Python (11-12 June 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 | This two-day, in-person workshop gave researchers a thorough grounding in using Python to process and analyse image data. It was aimed at researchers who have a working knowledge of Python and who expect to be producing volumes of image data that would benefit from some automated analysis. Participants learnt the fundamentals of image processing using the skimage library to analyse many different properties of an image, primarily focused on morphometrics, but which are widely applicable to a range of image analysis problems. Starting with how images are represented in digital format, the pros and cons of different image file formats, metadata and how images are stored in arrays, the course moved through various lessons to explore image data, implementing bitwise operations, masks, filtering and thresholding to optimise your analysis. The workshop culminated in a hands-on exercise that provided participants with the opportunity to combine the approaches learned throughout all the previous lessons. 56% of attendees were from Norwich Research Park, with the others with the UK. All attendees who provided feedback rated the Trainers and the Overall Quality as very good/excellent, 100% would also recommend the course to others. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/image-processing-python-2024 |
| Description | Initial meeting with German collaborators to discuss standards |
| 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 | Met with Hannah to discuss standards |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.fz-juelich.de/profile/doerpholz_h |
| Description | Initial meeting with JIC spatial group (Cristobal) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussion of requirements for metadata and data management |
| Year(s) Of Engagement Activity | 2024 |
| Description | Invited Talk - Differential isoform regulation in the human brain - at King's Genomics Launch Event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the launch of a genomics facility at King's College London. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.eventbrite.co.uk/e/kings-genomics-launch-event-shaping-the-future-of-genomics-research-t... |
| Description | Invited Talk - Differential isoform regulation in the human brain - at Oxford Nanopore WYMM Tour: Birmingham |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a Oxford Nanopore Technology Event |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://nanoporetech.com/about/events/nanopore-days/wymm-tour-birmingham |
| Description | Invited seminar - Institut Pasteur - Characterisation of gene and transcript regulation in the brain across scales |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker at the annual single cell symposium at the Institut Pasteur |
| Year(s) Of Engagement Activity | 2024 |
| Description | Invited seminar - Stockholm - What Your Are Missing Matters - Characterisation of novel splicing events across brain tissues and during development |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a Oxford Nanopore Technology Event |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://nanoporetech.com/about/events/nanopore-days/nanopore-day-stockholm-2024#event-overview |
| Description | Invited seminar at Astrazeneca Gothenburg - Characterisation of gene and transcript regulation in the brain across scales |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited seminar at Astrazeneca (Gothenburg, Sweden), to present and discuss the power of long read RNA-Seq to enable the identification of therapeutic targets |
| Year(s) Of Engagement Activity | 2024 |
| Description | Invited speaker at Norwich Single Cell Symposium 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to talk about my research in front of an audience of around 80 experts on the topic, which sparked very interesting questions and conversations during networking sessions and had very positive feedback with potential for collaborations |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/norwich-single-cell-symposium-2024 |
| Description | Made Co-Chair of PCA metadata and infrastructure 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 | This is a steering committee to advise the Plant Cell Atlas consortia of best practice in data management and data infrastructure,. |
| Year(s) Of Engagement Activity | 2023,2024 |
| URL | https://www.plantcellatlas.org/people.html |
| Description | Made memeber of steering committee for AI-BIO |
| 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 | Elected to the steering committee of AI-BIO and involved in grant panel for first round of grants. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Meeting with Prof Gideon Henderson, DEFRA Chief Scientific Adviser |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Prof Gideon Henderson visited the Earlham Institute and discussed a range of DEFRA related research activity and innovation. He invited EI to have follow up engagement with DEFRA officials leading relevant policy and regulatory work. |
| Year(s) Of Engagement Activity | 2024 |
| Description | ON Helix New Horizons in Genetic Screening |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | 300 participants from private sector, NHS and academia attended ON Helix workshops over 4 days to discuss progress and challenges of personalised medicine, genetic screening to open up the discussion how to tackle new challenges the field encounters. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.onhelix.com/ |
| Description | Oral presentation at British Phycological Society Winter Meeting (Hull, UK January 2025) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I delivered an oral presentation on the functional subpopulations of Trebouxia (green algae) in the lichen symbiosis that I identified using single-nuclei transcriptomics to an audience of researchers at different career stages spanning undergraduate to senior faculty. |
| Year(s) Of Engagement Activity | 2025 |
| Description | PCA Core Network Participant Meeting (CPN) |
| 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 | Made connections and panned for future grant submission. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Parliamentary briefings on Genetic Technology (Precision Breeding Bill) for members of the House of Commons |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Parliamentary briefings at each stage of the passage of the Bill through the House of Commons. The briefings explained the provisions in the legislation and why Earlham Institute and the Norwich Research Park supported them. We gave case studies about relevant crop research that would benefit if the legislation was passed. The purpose of the briefings were to inform the parliamentary debate, persuade the Opposition not to oppose the Bill and help legislators to understand the need for public policy based on scientific evidence. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Parliamentary briefings on Genetic Technology (Precision Breeding) Bill for members of the House of Lords |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In person and written briefings for peers interested in the Genetic Technology (Precision Breeding) Bill. Our briefings explained key provisions in the Bill, made the case for why the Bill is needed and how the legislation would work in practice. We included case studies to show current research projects that would benefit from implementation of this new legislation. We worked with the DEFRA Bill Team to target parliamentarians that needed this information to support or at least not block the Bill through the House of Lords. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Parliamentary exhibition on precision breeding |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Earlham Institute exhibited alongside partners from the Norwich Research Park in Parliament to draw parliamentarians' attention to secondary legislation on precision breeding. The event was designed to give parliamentarians an opportunity to discuss the legislation with researchers to prepare for the debate on the legislation. More than 20 parliamentarians attended the exhibition including the DEFRA Minister. Following their interest we have engaged these MPs and peers further with parliamentary briefings and case studies of how the new legislation will help the research sector. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Poster Presentation - Muex: a method to identify novel microexons from long-read RNA sequence data - Kamil Hepak |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the ISMB/ECCB 2023 |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.iscb.org/ismbeccb2023 |
| Description | Poster at Norwich Cancer Research Network (NCRN) symposium 2024 - Single-cell and spatial transcriptomics analysis of megakaryocytes in the healthy bone marrow |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster at Norwich Cancer Research Network (NCRN) symposium 2024, attended by around 100 scientists. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://cancerresearchnorwich.org.uk/ncrn-symposium-2024-please-register/ |
| Description | Poster presentation at the Molecular Haemopoiesis, 2024 |
| 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 | 250 researchers from around the world met to discuss most recent advance in molecular haematopoiesis and shared unpublished data. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Invited Seminar - University College Dublin - Characterization of novel splicing events across tissues and during cellular differentiation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the School of Biology and Environmental Science University College Dublin |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation - Invited seminar - Norwich Cancer Research Network |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the CELLGEN ISP and Single cell genomics platform to the NCRN |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Invited talk -BioIndustry Association - Genomics Advisory Committee - Characterisation of novel potential targets through the characterisation of novel splicing events |
| 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 | Presentation as part of the Q1 genomics advisory committee meeting (BioIndusrty Association) |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - LongTrec meeting - Single cell sequencing with PACBIO |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation of library preparation and data analysis of single cell long read sequencing to graduate students as part of the Maric Curie LongTrec network |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation - Nucleic Acids Therapy Accelerator |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation to the research team of the Nucleic Acids Therapy Accelerator following meeting with Director at BIA meeting, discussion of interactions between NATA and EI, NATA showing interest in the platforms and services from EI. Discussion of potential collaborations with NATA around splicing regulation and setting up pilot projects |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Oral Presentation - Activation Manifold of The Mouse Visual Cortex - Biological Complexity Group (University of Cambridge) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | A presentation on the application of manifold theory to representation learning in the mouse visual cortex at The University of Cambridge, Department of Chemical Engineering and Biotechnology. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation - Oral Presentation - Annotation and characterisation of functional noncoding RNA - DARPA meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation in Boston as part of a DARPA initiative |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation - Oral Presentation - Characterization of novel splicing events across tissues and during cellular differentiation - WCBR |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Winter Conference on Brain Research as part of the session Fostering Successful Partnerships Between Academia and Industry |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Oral Presentation - Megakaryocyte Flow Cytometry Image Analysis - Image Analysis Across Domains Seminar (Alan Turing Institute) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation to the Alan Turing Institute image analysis community showing early data from megakaryocyte flow cytometry experiments and requesting feedback and possible methodological approaches to determine how best to analyse the images produced by the project so far and in the future (e.g. from upcoming widefield spatial transcriptomics images). |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Oral Presentation - Philosophical Implications of Physicalism for the Natural Sciences - Philosophy and History Seminar (Alan Turing Institute) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Start of a new seminar series on the interaction between the sciences, AI and humanities open to Alan Turing Institute employees and partner institutions (e.g. Roche pharmaceuticals and universities), aimed at fostering new understanding through interdisciplinary dialogue on foundational topics in these areas. The seminar was attended by a group of roughly 15 (including online and in person) with plans to deceminate to a wider group via a video recording (link not yet available). Talked fostered discussion and interest in the metaphysical and ethical consequences of philosophical naturalism. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing |
| 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 | Presentation to the LongTrec Consortium |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation at Norwich Cancer research network |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | 20 scientists attended the presentation on new methods and their applications and how to implement them in their own research. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation at the Festival of Genomics and Biodata 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Presentation on RNA barcoding and its application to study the platelet biogenesis in different contexts. It sparked questions and the discussion on potential applications in other research groups and a potential interaction with the industrial partner. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://festivalofgenomics.com/london/en/page/home |
| 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 | Presentation to the Kick-off meeting of LongTrec - Single cell sequencing on PACBIO |
| 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 | Attendance and presentation to the LongTrec kickoff meeting in Valencia |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation, Pint of Science, Norwich |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | I gave the presentation on the effect of diet on the immune system function. It sparked questions about the food choices impacting our immunity, health and longevity. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://pintofscience.co.uk/events/norwich |
| Description | Presented data management talk on single cell RNA course |
| 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 | half hour section as part of the course to train early career researchers about best practice in research data management |
| 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 | Researcher visit from Rijksuniversiteit of Groningen, Groningen, Netherlands |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at EI on the history of clonal studies from bacteria to mammals, outlook into naturally occurring barcodes-possibilites and limitations. Discussion about new algorithms/pipelines to improve the analysis. Individual discussions on current practices and available pipelines. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Roslin meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | discussions around work on single cell standards |
| Year(s) Of Engagement Activity | 2025 |
| Description | SAB Networking Dinners (x2) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | 2 dinners during which I networked with senior advisory board of EI, to elucidate them on COPO |
| Year(s) Of Engagement Activity | 2023 |
| Description | SAB Poster Session |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented COPO at a poster session for the 2023 SAB |
| Year(s) Of Engagement Activity | 2023 |
| Description | Scilifelab presentation 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 | Demonstration of the efficacy of COPO as a brokering solution for Scilifelab. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Shaping the future of data-intensive bioscience |
| 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 | An introductory article to Prof Irene Papatheodorou's work at the Earlham Institute. The article highlight's Irene's career path, the Cellular Genomics research programme, data tools such as COPO, and EI's work in cell atlas programms like the Biodiversity Cell Atlas and Gut Cell Atlas. The aim of the article was to highlight the expertise Irene brings to data science at the Earlham Institute. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/shaping-future-data-intensive-bioscience |
| Description | Single Cell RNAseq Bioinformatics Course (11-14 November 2024) |
| 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 | This in-person course provided a deep dive into single-cell genomics, for researchers who are in the early stages of planning a single-cell project. The course consisted of a mixture of conceptual and methodological lectures and hands-on bioinformatics sessions, including best practice and tips as learned first-hand by Earlham Institute's faculty. Participants gained first-hand experience by learning how to assess data quality with the guidance of the faculty, troubleshoot small problems, and review the results. Hands-on sessions used data generated using both Smartseq2 and 10X protocols, from both short- and long-read platforms. Registration for the course was offered on an open application basis with selection, with 23 applications resulting in 16 attendees. Demographics of attendees, 50% were from the UK, with participants also from France, Hungary, India, Iran, Spain and Turkey. The cohort was made up of 31% PhD students and 31% Post Docs, with the remainder 'Other', post-graduate students, and professors/PIs. 87.5% were based in academia, and 12.5% were from industry. Of the feedback received, 91% rated the trainers as Excellent and would recommend the course, and gave an overall quality rating of Very Good or Excellent. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-bioinformatics-2024 |
| Description | Single-cell show and tell |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | We organized the single-cell show and tell to showcase our equipment in the single-cell laboratories, talk about our workflows and provide some hands on lab experience to our colleagues within EI. We had 38 participants with different scientific and non-scientific backgrounds. The feedback was very positive, and most people would like to see other groups organize similar events. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Single-cell show-and-tell: Activity based tours of the EI single-cell labs |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | 40 staff from EI were given an interactive tour of the single-cell labs. We introduced them to the different platforms and concepts behind single-cell analysis. We hosted staff from operations, communications, business development and faculty, all staff at EI were invited. The event stimulated questions and discussion about both the biology and technology associated with single cell work. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Software Carpentries |
| 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 | Delivered training |
| Year(s) Of Engagement Activity | 2023 |
| Description | Sphere Fluidics -Cambridge |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDRA, RA and Group Leader engaged with the industry-Sphere Fluidics to optimise bespoke microfluidc assays using their equipment. Obtained preliminary data for a grant application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk - Postgrad Data Literacy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Part of an annual PGR education programme |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk at AGBT-AG field day pre-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 | Talked about single cell schemas and COPO to delegates from AGBT-AG conference |
| Year(s) Of Engagement Activity | 2025 |
| Description | Talk at Festival of Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Talk at Festival of Genomics to promote ultra-long read nanopore sequencing project (collaboration with Technical Genomics). |
| Year(s) Of Engagement Activity | 2025 |
| Description | Talk in Big Data training session |
| 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 | Presented best practice in current research data management technology to UEA/NRP PhD students. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk to PHD DTP cohort on data management and COPO |
| 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 | As part of a day of training, I talked for an hour about research data management, FAIR and the importance of these |
| Year(s) Of Engagement Activity | 2025 |
| 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 | UEA Pharmacology Student Visit - 12 Feb 2024 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | 13 students, plus a staff member, from the University of East Anglia, attended Earlham Institute for an afternoon. They participated in lab tours of Genomics Pipelines, Single-cell Labs, and the Biofoundry. They then heard talks from researchers (talk titles below), and had an informal discussion with current PhD students at EI. Overview: What it means to do a PhD DNA replication singled out Characterisation of alternative splicing regulation in the brain Clonal and molecular studies of haematopoiesis Mining Meadows: Exploring the biosynthesis of bioactive compounds in medicinal plants |
| Year(s) Of Engagement Activity | 2024 |
| Description | Visit from Chief Scientific Adviser |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In February 2023, Professor Sir Patrick Vallance visited the Norwich Research Park alongside officials from the Government Office for Science and the Chief Scientific Adviser to the Food Standards Agency, Professor Robin May. Earlham Institute engaged Sir Patrick on two specific issues; reforming VAT rules applied to research, and incentivising FAIR data management. Sir Patrick gave assurances that he would raise both issues in policy discussions in Whitehall. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit from NNUH clinicians to the Earlham Institute on 19 June 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | BDI team and IM of the Earlham Institute organised the visit from NNUH clinicians to the Earlham Institute. We held a workshop for researchers and clinicians to discuss their interests in developing potential collaborative projects that would utilise earlham expertise and capabilities and NNUH access to patients and patient data, and to the Norwich Biorepository. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Webinar 'Ask the PI' organised by International Society of Experimental Hematology (ISEH) |
| 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 | Small-group setting offers the perfect opportunity for trainees to learn about career transitions, gain expert insight, and build valuable connections.The event consisted of three rounds of breakout sessions, where participants got to meet and engage with multiple Junior Faculty for personalized conversations and insights on navigating their path to independence. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.iseh.org/page/2024NICAskthePIs |
| Description | Webinar: Optimizing Challenging Sample Types on the Merscope® Platform |
| 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 | Webinar about our experience using the Vizgen platform for spatial transcriptomics Merscope, with focus on challenging samples. Different research groups contacted EI after the webinar showing interest about the service provision side of our experience with Merscope. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://global-engage.com/product/optimizing-challenging-sample-types-on-the-merscope-platform/ |
| 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 | Workshop for MRes students in Genomics and Evolution |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Workshop on capabilities enabled by single cell genomics, discussion of a selected scientific article. Critical assessment of the strengths and weaknesses of performed experiments. |
| 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 |