Research Infrastructure
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
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
World class data intensive bioscience requires world class infrastructure and software. This theme focuses on the bioinformatics research and development to build the core software and informatics offerings that will underpin the research undertaken within the Quadram Institute more generally, and within the Microbes in the Food Chain ISP specifically.
The project will design and provision a local cloud computing environment with launcher and software stack to enable researchers within the Quadram Institute to utilise standardised bioinformatics pipelines (developed within this theme and by core bioinformatics activity at the Quadram), or to develop their own software. The cloud system will be defined using DevOps tools (ansible and salt), which will be shared externally, so others can develop their own system externally. Our local cloud system will be based on open source software, and the launcher will be built to make use of cloud APIs to enable future system expansion and to enable it to access other NBI cloud resources.
As part of this development we will aim to accredit our system to ISO 27001 and will deploy next generation firewalls locally to provide additional security to collectively enable the holding of sensitive data.
There are a wide range of technologies in use across the Quadram Institute for the generation of ‘omics-type data. All of these generate some form of digital data, which is often linked (e.g. all coming from the same sample, or the same experiment, or the same project). Building on our cloud resource, we will develop a system to collate, integrate and catalogue this data, providing a core set of analysis tools to enable mining of that data. This system will enable data to be presented for more advanced methods such as AI/Machine learning.
Because we will be collecting and collating experimental data within the Quadram Institute, there is an opportunity for the presentation of this data to external users, to enhance the value of the data generated and to enable external users to simultaneously access a range of data types linked to individual samples. This will complement the upload of data to resources such as the European Nucleotide, providing a ‘next generation culture collection’ that includes data beyond what is currently stored in an NCBI bioproject, for example. The next generation culture collection will include the ability to order strains from the Quadram Institute, and will feature a set of tools for data export and data analysis using computational resources hosted within the NRP institutes.
Lastly, to support research activities within the Quadram Institute we will develop a simplified sequencing pipeline combining automated QC, de novo assembly, variant calling and isolate characterisation. The system will be designed to be deployable as a virtual machine, and will be designed to support the attachment of sequencing instruments (including Illumina and Nanpore) to the VM, providing an end-to-end analysis solution for small labs as well as Quadram Institute researchers. We will develop the pipelines using NextFlow, and will seek to add to these tools as new software and technologies become available.
The project will design and provision a local cloud computing environment with launcher and software stack to enable researchers within the Quadram Institute to utilise standardised bioinformatics pipelines (developed within this theme and by core bioinformatics activity at the Quadram), or to develop their own software. The cloud system will be defined using DevOps tools (ansible and salt), which will be shared externally, so others can develop their own system externally. Our local cloud system will be based on open source software, and the launcher will be built to make use of cloud APIs to enable future system expansion and to enable it to access other NBI cloud resources.
As part of this development we will aim to accredit our system to ISO 27001 and will deploy next generation firewalls locally to provide additional security to collectively enable the holding of sensitive data.
There are a wide range of technologies in use across the Quadram Institute for the generation of ‘omics-type data. All of these generate some form of digital data, which is often linked (e.g. all coming from the same sample, or the same experiment, or the same project). Building on our cloud resource, we will develop a system to collate, integrate and catalogue this data, providing a core set of analysis tools to enable mining of that data. This system will enable data to be presented for more advanced methods such as AI/Machine learning.
Because we will be collecting and collating experimental data within the Quadram Institute, there is an opportunity for the presentation of this data to external users, to enhance the value of the data generated and to enable external users to simultaneously access a range of data types linked to individual samples. This will complement the upload of data to resources such as the European Nucleotide, providing a ‘next generation culture collection’ that includes data beyond what is currently stored in an NCBI bioproject, for example. The next generation culture collection will include the ability to order strains from the Quadram Institute, and will feature a set of tools for data export and data analysis using computational resources hosted within the NRP institutes.
Lastly, to support research activities within the Quadram Institute we will develop a simplified sequencing pipeline combining automated QC, de novo assembly, variant calling and isolate characterisation. The system will be designed to be deployable as a virtual machine, and will be designed to support the attachment of sequencing instruments (including Illumina and Nanpore) to the VM, providing an end-to-end analysis solution for small labs as well as Quadram Institute researchers. We will develop the pipelines using NextFlow, and will seek to add to these tools as new software and technologies become available.
Planned Impact
unavailable
Organisations
- QUADRAM INSTITUTE BIOSCIENCE (Lead Research Organisation)
- Animal and Plant Health Agency (Collaboration)
- PUBLIC HEALTH ENGLAND (Collaboration)
- National Microbiology Reference Laboratory (Collaboration)
- University of the Western Cape (Collaboration)
- NHS National Services Scotland (NSS) (Collaboration)
- Centers for Disease Control and Prevention (CDC) (Collaboration)
- Utrecht University (Collaboration)
- Bill and Melinda Gates Foundation (Collaboration)
- Public Health Wales NHS Trust (Collaboration)
- University of Washington (Collaboration)
- Hebrew University of Jerusalem (Collaboration)
- University of Oxford (Collaboration)
- Lebanese American University (Collaboration)
- Cardiff University (Collaboration)
- Child Health Research Foundation (Collaboration)
- George Washington University (Collaboration)
Publications
Abdoulie Kanteh
(2021)
Invasive atypical non-typhoidal Salmonella serovars in The Gambia
Abdoulie Kanteh
(2021)
Invasive atypical non-typhoidal Salmonella serovars in The Gambia
Achtman M
(2020)
Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project.
in Wellcome open research
Achtman M
(2020)
Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project
in Wellcome Open Research
Aggarwal D
(2022)
The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.
in The Lancet. Microbe
Aggarwal D
(2022)
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.
in Nature communications
Aggarwal D
(2022)
Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
in Nature Communications
| Description | - Software development and publication of socru, a tool for typing the order and orientation of complete bacterial genomes: Rearrangements of large genome fragments occur in bacteria between repeat sequences and can impact on growth and gene expression. One form of rearrangement occurs around ribosomal operons, found in multiple copies across many bacteria, but identification of these rearrangements by sequencing requires reads of several thousand bases to span the ribosomal operons. With long-read sequencing aiding the routine generation of complete bacterial assemblies, we developed socru, a typing method for the order and orientation of genome fragments between ribosomal operons. It allows for a single identifier to convey the order and orientation of genome-level structure and we have successfully applied this typing to 433 of the most common bacterial species. In a focused analysis, we observed the presence of multiple structural genotypes in nine bacterial pathogens, underscoring the importance of routinely assessing this form of variation alongside traditional single-nucleotide polymorphism (SNP) typing. Its conda package has been downloaded over 37,000 times since its release in 2019 (https://github.com/quadram-institute-bioscience/socru) - Software development and publication of tatajuba, for describing the distribution of homopolymerics tracts (HTs) within a bacterial isolate and compare its differences across samples: Changes in homopolymeric tract (HT) lengths are known to be involved in phenotypic changes, as protein truncation and shifts in expression levels. We developed a tool, tatajuba, which based on raw reads, stores the statistical distribution of lengths for every HT found. It assumes that a bacterial isolate can be composed of a population of individuals with potentially different HTs due to its fast response and high variability. Therefore, given a set of isolates it can describes their changes in terms of HT lengths, and this can be used as a trait which can be associated to a condition (environment, disease status, time), or it can be used directly as a complement to other phylogenetic markers. Its conda package has been downloaded 8,000 times since 2021 (https://github.com/quadram-institute-bioscience/tatajuba) - Software development and publication of uvaia, for reference-based alignment and sequence database search of SARS-CoV-2 genomes: As the SARS-CoV-2 sequencing efforts at the Quadram increased, so did the globally shared genomes, surpassing 10 million sequences available by 2022. We developed a software that can be run on a laptop to search amongst these huge databases for sequences of interest, by using novel similarity measures that take into account typical uncertainties in SARS-CoV-2 sequencing. We applied it both to enrich phylogenetic analyses by limiting them to similar sequences, and to explore countrywise diversity in epidemiological studies. It has been used in many publications where the Quadram was involved in the sequencing and analysis of local and global SARS-CoV-2 genomes, and it can be deployed in future pandemics. It has been downloaded 3,800 times on conda since its first version in 2021 (https://github.com/quadram-institute-bioscience/uvaia) A preliminary version of this software had been used internally as part of our phylogenetic reporting tool peroba (https://github.com/quadram-institute-bioscience/peroba) during the first year of the pandemics. A web application, Ronaldo (https://github.com/quadram-institute-bioscience/ronaldo), was also developed for easy quality checking of individual SARS-CoV-2 sequencing samples. - SARS-CoV-2 sequencing and analyses: The QIB was a member of the COVID-19 Genomics UK (COG-UK) Consortium, due to our expertise in large-scale sequencing and genomic analysis. Through this consortium we sequenced most SARS-CoV-2 genomes of the region, where we were also involved in nation-wide epidemiologic and phylogenetic analyses. Including the detection and establishment of lineage definitions, and participation in the REal-time Assessment of Community Transmission (REACT) epidemiologic study. Through collaborations, we were also involved in international sequencing efforts, having sequenced most SARS-CoV-2 genomes from Zimbabwe and tranferred them know-how through training and discussions. From this collaboration, we engaged with the Pan-African inniciative "Africa COVID19 Genomes" seminar series and participated in the publication of transnational African SARS-CoV-2 epidemics. We also created partnerships with academics in Lebanon and Palestine to help in their sequencing and bioinformatic analysis. We were also engaged with the Public Health Alliance for Genomic Epidemiology (PHA4GE) coallition in the establishment of bioinformatics standards (availability, harmonisation, etc.) |
| Exploitation Route | As the commoditisation of genomic sequencing and analysis increases, so does the importance of sequencing microbes in the environment, and in clinical and industrial settings. The tools we developed to describe bacterial genomes (socru, tatajuba) can be used to pinpoint potential novelties in the isolates, which may be used as an indicator of pollution, spoilage, or pathogenicity. The markers these tools look into, like the order of genome fragments and homopolymer lengths, have evolutionary information, and we can therefore infer where these isolates most likely came from. The tools and work with SARS-CoV-2 can be quickly deployed in future pandemics, and are specially useful in limited computational settings. So they can be used by academics where it really matters, even without supercomputing resources. The tool can be adapted to other pathogens, where it can become invaluable to search local samples against large databases, even without specialised training. Importantly, the infrastructure we developed through open source tools and publications allows for a reevaluation of the vast online databases. Not only by academics, but by all actors with a data science component, like the food industry, governmental agencies, and the healthcare sector. |
| Sectors | Agriculture Food and Drink Environment Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | The outputs from this project have contributed to the development of clinical genomics services within Public Health Wales NHS Trust. Software and expertise from this project have fed into the development of clinical services focused on the characterisation of C. difficile, as well as providing underpinning research related to the development of genomics infrastructure for processing data. These impacts are combined with other UKRI grant impacts and collectively have enabled the development of sequencing services that have analysed over 10,000 patient samples to date. With the COVID-19 pandemic, the expertise and research infrastructure was channeled into the responding to the pandemic by undertaking SARS-CoV-2 genome sequencing and bioinformatics analysis. To date over 50,000 SARS-CoV-2 samples have been sequenced, with substantial impact on regional and national and international pandemic management. A member of the team is part of the SAGE Social Care Working Group, providing insights into the use of genomics and helping to shape government policy, and they lead a review on the use of genomics in care homes. |
| Sector | Education,Healthcare,Government, Democracy and Justice,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal Policy & public services |
| Description | Clinical training in bioinformatics |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | The training has enabled clinicians and clinical scientists in Wales to begin making use of genomics data in routine clinical practice. This has had effects on three different areas: Infuenza Wales is HIV C. difficile |
| Description | Culture free pathogen detection methods with CDC (US) and PHE (UK), with monthly meetings |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Founding member and chair of the Public Health Alliance for Genomic Epidemiology Validation and QC working group |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Founding member of the Public Health Alliance for Genomic Epidemiology Infrastructures working group |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | GenomeTrakr Meeting with US federal government and state labs using genomics |
| Geographic Reach | North America |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Routine genome sequencing by state and federal government labs has decreased the turn around time for pathogen detection and typing. This is important for finding outbreaks of food borne pathogens. Whilst this meeting was restricted to US regulatory labs, including federal (CDC, FDA, USDA,..) and state labs, Andrew Page was one of 5 international scientists invited to take part & provide input (others were federal/state labs from Canada, Australia, and Germany). |
| Description | Member of the Genomics Partnership Wales IT Working Group |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The IT working group has overseen the development of strategy for the implementation of the IT infrastructure to support genomics in healthcare in Wales. This has underpinned the development of clinical services based on genomics for the whole of Wales. In the pathogen area this has seen over 8,000 patient samples analysed using the infrastructure developed within the IT group. |
| Description | Membership of Pathogen Genomics Operational Committee |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | This work has seen the development of 4 clinical services based on next generation sequencing. This has enabled the analysis of over 8,000 patient samples using NGS approaches, underpinned by software and infrastructure developed through UKRI funded research to Cardiff University. The systems that have been built have resulted in improvements in the speed of diagnoses/characterisation of pathogens, drops in cost of testing and increased generation of clinically actionable information from the tests undertaken. |
| Description | Membership of Welsh Government Technical Advisory Group |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The work saw (and continues to see) the generation of significant amounts of advice, which informed every aspect of the Welsh Government pandemic response. This includes, advice regarding lockdowns and easing of restrictions, winter planning for the NHS and management and surveillance of the pandemic in Wales. |
| URL | https://www.gov.wales/technical-advisory-cell |
| Description | Participated on panel to discuss AI networks |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Public health alliance for genomic epidemiology (PHA4GE) - Founding member of Data Structures working group |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| URL | https://pha4ge.github.io/ |
| Description | Rob Kingsley - Assistance of the Zimbabwe Government for SARS-CoV-2 sequencing and analysis |
| Geographic Reach | Africa |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | We were approached by the Zimbabwe Health Minister to provide support in sequencing SARS-CoV-2 samples for genomic epidemiology analysis. This work is helping track COVID-19 spread, its lineages, and its burden to populations. |
| Description | Rob Kingsley - Discussion with Senior Health Adviser from the Foreign, Commonwealth & Development Office |
| Geographic Reach | Africa |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | Meeting to discuss our findings and give advice on the spread of COVID-19. |
| Description | SAGE Social Care Working Group |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Core member of the Scientific Advisory Group for Emergencies (SAGE) Social Care Working Group. My role is to advise on the use of genomics in the COVID-19 pandemic. Recommendations of the committee to SAGE have included testing strategies for care homes and residential homes, analysis of mortality and demographics, training, genomic lineages circulating and ingress of COVID-19, etc... all with the goal of providing the best scientific advise in a rapidly changing environment, to minimise mortali |
| Description | UK COVID-19 Genomics Strategic Advisory Board |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | We identified a range of next steps and provided recommendations to change procedures that improved the speed at which SARS-CoV-2 data could be generated / used across the UK. We developed a plan/roadmap for a future federated system for bioinformatics between the UK Public Health Agencies. |
| Description | Variants and Mutations of Concern Oversight Group |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The VAMC groups work was to oversee the response to variants of concern. This had a direct impact on the planning and provision of surveillance and response services to SARS-CoV-2 variants from 2021 in Wales. Most of the work was carried out within government ; so there is limited sharable documentary evidence. But the role of genomics/genomic insight in the group was critical to its success. |
| Description | BBSRC Flexible Talent Mobility Award to bring Queens University Belfast researcher to Quadram Institute |
| Amount | £3,850 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 03/2019 |
| Description | BBSRC Funding for Computational infrastructure |
| Amount | £1,471,551 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2019 |
| Description | BBSRC IAA |
| Amount | £8,230 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 09/2019 |
| Description | BBSRC Proof of Concept fund |
| Amount | £9,954 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 05/2019 |
| Description | CLIMB-BIG-DATA: A Cloud Infrastructure for Big-Data Microbial Bioinformatics |
| Amount | £1,994,477 (GBP) |
| Funding ID | MR/T030062/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 03/2025 |
| Description | Covid-19 Sequencing Research |
| Amount | £866,982 (GBP) |
| Organisation | Public Health England |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2020 |
| End | 09/2021 |
| Description | Covid-19 Sequencing Research |
| Amount | £3,549,889 (GBP) |
| Organisation | UK Health Security Agency |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 03/2022 |
| Description | Food safety bioinformatics hackathon |
| Amount | £10,081 (GBP) |
| Funding ID | BB/S020527/1 |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 07/2019 |
| Description | SP3: Scalable Software for Pathogen Reads to Clinical Results using Next Generation Sequencing |
| Amount | £1,000,000 (GBP) |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 02/2022 |
| Title | CoronaHiT - protocol for high-throughput sequencing of SARS-CoV-2 genomes |
| Description | CoronaHiT is a validated protocol developed for SARS-CoV-2 sequencing, which allows for cheap, high-throughput sequencing of the SARS-CoV-2 virus. It has been used to sequenced tens of thousands of samples and has been adopted by multiple other SARS-CoV-2 sequencing labs in the UK. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Currently 3 resilience sequencing labs in the UK are using the protocol we developed for sequencing SARS-CoV-2. The samples they are sequencing are from ONS & REACT community prevalence studies, and Pillar 1 (hospital) samples which covers the most seriously ill patients with COVID-19. It provides for a 10 fold cost reduction in sequencing costs. It simplifies the steps required thus reducing hands on time. It can be used with long read sequencing (Nanopore) or short read sequencing (Illumina), so is flexible. |
| URL | https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5 |
| Title | AMR-Hackathon-2021/benchmarking_datasets: v1.0.0 |
| Description | What's Changed adds script to get card data #1 by @raphenya in https://github.com/AMR-Hackathon-2021/benchmarking_datasets/pull/4 updates by @raphenya in https://github.com/AMR-Hackathon-2021/benchmarking_datasets/pull/5 New Contributors @raphenya made their first contribution in https://github.com/AMR-Hackathon-2021/benchmarking_datasets/pull/4 Full Changelog: https://github.com/AMR-Hackathon-2021/benchmarking_datasets/commits/v1.0.0 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Supporting data for https://www.nature.com/articles/s41597-022-01463-7 |
| URL | https://zenodo.org/record/6509953 |
| Title | Additional file 1 of CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes |
| Description | Additional file 1: Table S1. Barcode sequences. Table S2a. Sample metrics for the Routine dataset. Table S2b. Sample metrics for the Rapid Response dataset. Table S3. The differences between the consensus genomes of each sequencing method, for all samples with differences reported. Table S4. Reagent costs for the three methods when sequencing 96 samples (CoronaHiT-ONT and ARTIC LoCost) or 384 samples (CoronaHiT-Illumina). Table S5. Sample identifiers and accession numbers. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_CoronaHiT_high-throughput_... |
| Title | Host removal database: Homo sapiens, Sars-Cov-2, PhiX174 |
| Description | cleanup-db Kraken2 database, built upon a viral sequence masked human reference from: Handley, Scott A. (2020). Virus+ Sequence Masked Human Reference Genome (hg19) (1.0) [Data set]. Zenodo. [10.5281/zenodo.4116107] but separating chromosomes as artificial taxa to allow for QC, and includes Sars-Cov-2 and PhiX 174 gutcheck-db A very small DB containg some common gut bacteria and Human and Murine mitochondrial genome: Akkermansia muciniphila Bacteroides fragilis Bifidobacterium longum Blautia obeum strain Escherichia coli Enterococcus faecium Prevotella copri See: https://github.com/telatin/cleanup |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | custom database to remove common contaminants from metagenomics samples (Homo, Sars-Cov-2 and PhiX-174); by splitting the human genome in individual chromosomes, this database enable a quality check against reads wrognly classified as human. |
| URL | https://zenodo.org/record/7050266 |
| Title | SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021 |
| Description | Supplementary Material for 'SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021' |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/SARS-CoV-2_variants_of_concern_dominate_in_Lahore... |
| Title | SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021 |
| Description | Supplementary Material for 'SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021' |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/SARS-CoV-2_variants_of_concern_dominate_in_Lahore... |
| Title | Supporting data for "Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package" |
| Description | The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonisable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonisation and submission of sequence data and contextual information to public biorepositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the National Center for Biotechnology (NCBI)'s BioSample database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This specification is now being used by the 2 major public sequencing archives for SARS-CoV-2 datasets. It is now the defacto international standard for sharing SARS-CoV-2 metadata. |
| URL | http://gigadb.org/dataset/100977 |
| Description | Bioinformatic pipelines for Campylobacter population structure |
| Organisation | Utrecht University |
| Department | Institute for Risk Assessment Sciences |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | This partnership is a shared interest in the population structure and strain level difference in Campylobacter. We have contributed >1,000 genomes for shared analysis and testing of novel bioinformatic pipeline approaches. |
| Collaborator Contribution | Our Risk Assessment Institute, Utrecht University |
| Impact | Outcomes thus far have been the appointment of a Master's student (Utrecht University) to the project and monthly progress meetings |
| Start Year | 2022 |
| Description | Capacity building of SARS-CoV-2 sequencing using ONT in Bangladesh |
| Organisation | Child Health Research Foundation |
| Country | Bangladesh |
| Sector | Charity/Non Profit |
| PI Contribution | Knowledge and in-kind contribution was set up as part of an existing collaboration to build laboratory capacity at CHRF in Dhaka, Bangladesh for SARS-CoV-2 sequencing on Oxford Nanopore Technologies using QIB published multiplexing methodology. |
| Collaborator Contribution | Contribution to science and Bangladeshi Ministry of Health by CHRF was made by sequencing and mapping SARS-CoV-2 variants circulating in Bangladesh. |
| Impact | Collaboration is multidisciplinary with the following disciplines involved: -Molecular biologists -Researchers (QIB and CHRF) -Ministry of Health (public health) -Hospital (Bangladesh clinical patient care) -National health surveillance teams (Bangladesh) |
| Start Year | 2020 |
| Description | Collaboration with Amira Roess - Dept of Global Health, George Washington University |
| Organisation | George Washington University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This collaboration stems from a successful Gates foundation grant that Amira Roess (George Mason University) is a PI for and John Wain (QIB) a Co-I titled Transmission of Campylobacter in rural Bangladesh. I, as part of the QIB research team aided in building a sequencing laboratory infrastructure fo Oxford Nanopore Technologies sequencing for genomes and metagenomes in Dhaka, Bangladesh. During 2020-2021 we have leveraged that infrastructure to build further capacity within the Dhaka laboratory to sequence SARS-CoV-2. |
| Collaborator Contribution | The collaboration, led by Amira Roess, GMU has progressed to further capacity building in the Bangladesh laboratories. This collaboration is leading to new grant application opportunities and further work on global health. |
| Impact | This collaboration is interdisciplinary with microbiologist, bioinformatiticians, field epidemiologist and molecular biologist working together on assessing the routes of transmission of Campylobacter in rural Bangladesh. |
| Start Year | 2019 |
| Description | Collaboration with Public Health Wales related to pipeline development and C. difficile tracking/typing |
| Organisation | Public Health Wales NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The research team is contributing: - Expertise in software development and software outputs generated by this research activity to aid the development of pathogen processing pipelines that will be used in clinical service use. - Training for interpretation of software results - Resources for the analysis and interpretation of samples isolated from food sources, linking this to clinical data |
| Collaborator Contribution | Public Health Wales have developed a set of clinical services built on an HPC infrastructure to examine C. difficile, and is building services for examining antimicrobial resistant pathogens. As part of this collaboration, PHW have shared existing software they have developed, and are providing access to the genomic sequence data for over 1,000 samples that they have sequenced, as well as support in clinical interpretation and specialist knowledge around anaerobic bacteria. |
| Impact | The outputs from the collaboration to date are still internal, and are currently under development but are scheduled to include; A large linked dataset of C. difficile from clinical, environmental and food sources Software for performing QC on sequence data A pipeline for performing relatedness analysis for food and clinical samples for a range of species |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | Cardiff University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | NHS National Services Scotland (NSS) |
| Department | Health Protection Scotland |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | Public Health Wales NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | Development of the Scalable Pathogen Pipeline |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Scalable Pathogen Pipeline is a UK-wide initiative to develop an integrated pathogen pipeline for processing bacterial sequence data from reads to reports. We have contributed expertise to guide the design of the system, and are contributing expertise in software development. We have also provided expertise around articulating the needs of researchers as well as contributing expertise relating to the microbiological needs that the pipeline will have to address. We also expect to be able to host the pipeline within QIB to support specific food-related pathogens. |
| Collaborator Contribution | Our partners have provided extensive software development expertise, producing a large portion of the software itself as well as working with us to develop the design for the system. Our partners have also provided considerable expertise around specific public health, service and microbiology needs. |
| Impact | The project is still ongoing, and currently the results are not released. To date we have generated a working prototype of the pipeline, and are now seeking to produce a public-facing version of the system for users to test. This collaboration is multidisciplinary bringing together computer science, bioinformatics, clinical microbiology and population health/epidemiology |
| Start Year | 2018 |
| Description | PHA4GE: Public Health Alliance for Genomic Epidemiology |
| Organisation | University of Washington |
| Department | Department of Epidemiology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Invited members of the PHA4GE consortium on 3 different working groups. |
| Collaborator Contribution | The Bill and Melinda Gates foundation have provided seed funding for a secretariat (4 full time staff) in South Africa to coordinate the running of this consortium. |
| Impact | None yet. |
| Start Year | 2019 |
| Description | SARS-CoV-2 sequencing and bioinformatics with Lebanon |
| Organisation | Lebanese American University |
| Country | Lebanon |
| Sector | Academic/University |
| PI Contribution | We are working with academics, government, public health labs, and WHO in Lebanon to genome sequence SARS-CoV-2 and to use bioinformatics analyse the data. We have sequenced over 1200 samples so far, accounting for the majority of SARS-CoV-2 genomes from the country over the course of the pandemic. |
| Collaborator Contribution | Our partners have undertaken microbial genomics and bioinformatics analysis, sample collection, surveillance strategies, additional funding (WHO), and sample logistics. |
| Impact | A manuscript is currently under review at Microbial Genomics (preprint https://www.medrxiv.org/content/10.1101/2021.08.10.21261847v1 ) |
| Start Year | 2021 |
| Description | SARS-CoV-2 sequencing and bioinformatics with Palestine |
| Organisation | Hebrew University of Jerusalem |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | We have sequenced SARS-CoV-2 samples for Palestine (West Bank) and undertaken collaborative bioinformatics analysis. Our collaborators systematically collected the samples and assisted with interpretation. This had substantial input from the Foreign Office and was funded by a BBSRC IAA. |
| Collaborator Contribution | Our collaborators collected samples according to a sampling strategy they devised to maximise genomic epidemiological value. They provided logistics support for shipping and have assisted with bioinformatics analysis. |
| Impact | None yet. |
| Start Year | 2021 |
| Description | SARS-CoV-2 sequencing and bioinformatics with Zimbabwe |
| Organisation | National Microbiology Reference Laboratory |
| Country | Zimbabwe |
| Sector | Hospitals |
| PI Contribution | We have provided assistance to sequence SARS-CoV-2 genomes to Zimbabwe, which are currently the only genomes from the country. We sequenced 100 at QIB and will be sequencing a further 400. We have also sent all the equipment for them to undertake their own sequencing in country to allow them to be self sufficient. We have also provided assistance with bioinformatics and genomic analysis. |
| Collaborator Contribution | They have provided samples, epidemiological analysis and insights, and microbiology experience. |
| Impact | A paper has been released on the early epidemic in Zimbabwe: https://www.medrxiv.org/content/10.1101/2021.01.04.20232520v1 |
| Start Year | 2020 |
| Description | Workstream leadership in the Public Health Alliance for Genomic Epidemiology |
| Organisation | Bill and Melinda Gates Foundation |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | We are providing leadership around the Research Infrastructure and the Validation and QC workstreams. This involves developing outputs around best practice associated with these workstreams, as well as holding/managing meetings and contributing to the development of the overall programme. Contributions included initial input into the drafting of the founding documents of PHA4GE. |
| Collaborator Contribution | We have helped to shape the project from the start, contributing expertise to build the alliance and we are now heavily engaged with the development of two workstreams where we are playing a leading role |
| Impact | none as yet. |
| Start Year | 2019 |
| Description | Workstream leadership in the Public Health Alliance for Genomic Epidemiology |
| Organisation | Cardiff University |
| Department | School of Biosciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are providing leadership around the Research Infrastructure and the Validation and QC workstreams. This involves developing outputs around best practice associated with these workstreams, as well as holding/managing meetings and contributing to the development of the overall programme. Contributions included initial input into the drafting of the founding documents of PHA4GE. |
| Collaborator Contribution | We have helped to shape the project from the start, contributing expertise to build the alliance and we are now heavily engaged with the development of two workstreams where we are playing a leading role |
| Impact | none as yet. |
| Start Year | 2019 |
| Description | Workstream leadership in the Public Health Alliance for Genomic Epidemiology |
| Organisation | Centers for Disease Control and Prevention (CDC) |
| Country | United States |
| Sector | Public |
| PI Contribution | We are providing leadership around the Research Infrastructure and the Validation and QC workstreams. This involves developing outputs around best practice associated with these workstreams, as well as holding/managing meetings and contributing to the development of the overall programme. Contributions included initial input into the drafting of the founding documents of PHA4GE. |
| Collaborator Contribution | We have helped to shape the project from the start, contributing expertise to build the alliance and we are now heavily engaged with the development of two workstreams where we are playing a leading role |
| Impact | none as yet. |
| Start Year | 2019 |
| Description | Workstream leadership in the Public Health Alliance for Genomic Epidemiology |
| Organisation | University of the Western Cape |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | We are providing leadership around the Research Infrastructure and the Validation and QC workstreams. This involves developing outputs around best practice associated with these workstreams, as well as holding/managing meetings and contributing to the development of the overall programme. Contributions included initial input into the drafting of the founding documents of PHA4GE. |
| Collaborator Contribution | We have helped to shape the project from the start, contributing expertise to build the alliance and we are now heavily engaged with the development of two workstreams where we are playing a leading role |
| Impact | none as yet. |
| Start Year | 2019 |
| Title | Genomic epidemiology of SARS-CoV-2 in a hospital lead to halt of 2 large outbreaks |
| Description | Introduction of rapid genome sequencing of SARS-CoV-2, with regular reporting of the genomic epidemiology results to hospitals. The sequencing was funded by the MRC under the COVID-19 Genomics consortium (COG-UK). |
| Type | Management of Diseases and Conditions |
| Current Stage Of Development | Late clinical evaluation |
| Year Development Stage Completed | 2020 |
| Development Status | Under active development/distribution |
| Impact | We genome sequenced all SARS-CoV-2 positive samples from a 500 bed hospital. Through genomic epidemiology we identified a probable nosocomial outbreak, backed up by continuous surveillance. The infection control team identified a single positive staff member had resulted in a large staff outbreak, which spread to 1 ward, then within 2 weeks to 11 wards, involving over 80 patients. The genomic data identified that the hospital was not dealing with multiple introductions from the community, or 11 different out breaks, rather staff driven spread. This resulted in staff movements between wards being stopped, the building from scratch of a rapid testing facility using the evidence we provided, with all patients tested before moving in the hospital, and ward closures for deep cleaning. A second outbreak was detected which was linked to patient spread, again over a large number of wards. Both of these outbreaks were brought to a halt and the infection control practice was fundamentally changed in the hospital. The NHS reported that this was the first use of such data in the East of England and represented a substantial leap forward in tackling nosocomial spread of SARS-CoV-2. |
| Title | AlbaTraDIS: Comparative TraDIS analysis |
| Description | AlbaTraDIS is a software application for performing rapid large-scale comparative analysis of TraDIS experiments whilst also predicting the impact of inserts on nearby genes. It allows for experiements with multiple conditions to be easily analysed using statistical methods developed in the Bio-TraDIS toolkit. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | It is being used as the platform to analyse data for multiple upcoming papers. It is too new to have any notable impacts yet. |
| URL | https://github.com/quadram-institute-bioscience/albatradis |
| Title | FASTX::Reader perl module for FASTX parsing |
| Description | Pure-perl module to parse FASTA and FASTQ files, gzipped. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Updated during the IAA collaboration to improve support for phage annotation, re-instating Genetic Code 15 that was removed from NCBI Genetic Code tables. This was implemented in Metaprokka, and improved DNA translation for phage annotation. |
| URL | https://metacpan.org/dist/FASTX-Reader |
| Title | Galru: rapid pathogen typing using CRISPR spacer repertoire |
| Description | Galru is a Python 3 program that defines CRISPR spacer repertoire directly from uncorrected metagenomic long reads. Galru first identifies long reads that map to CRISPR-associated genes and searches along the read for the CRISPR spacer array. This array is compared to a database of known arrays to identify the sequence type (MLST). |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | None yet |
| URL | https://github.com/quadram-institute-bioscience/galru |
| Title | Krocus: Predict MLST directly from uncorrected long reads |
| Description | Genome sequencing is rapidly being adopted in reference labs and hospitals for bacterial outbreak investigation and diagnostics where time is critical. Seven gene multi-locus sequence typing is a standard tool for broadly classifying samples into sequence types, allowing, in many cases, to rule a sample in or out of an outbreak, or allowing for general characteristics about a bacterial strain to be inferred. Long read sequencing technologies, such as from PacBio or Oxford Nanopore, can produce read data within minutes of an experiment starting, unlike short read sequencing technologies which require many hours/days. However, the error rates of raw uncorrected long read data are very high. We present Krocus which can predict a sequence type directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes. It is the only tool which can do this from uncorrected long reads. We tested Krocus on over 600 samples sequenced with using long read sequencing technologies from PacBio and Oxford Nanopore. It provides sequence types on average within 90 seconds, with a sensitivity of 94% and specificity of 97%, directly from uncorrected raw sequence reads. The software is written in Python and is available under the open source license GNU GPL version 3. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | This software has been used in public health outbreak investigations to rapidly identify the type of infectious disease outbreaks. As it works from the raw reads of a nanopore, you can get an answer much faster than with traditional microbiology techniques. |
| URL | https://github.com/andrewjpage/krocus |
| Title | Metaprokka |
| Description | A fork of "prokka" focused on improving annotation results when analysing phage genomes (or metagenomes including virome) |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | A publication (https://pmc.ncbi.nlm.nih.gov/articles/PMC11210395/) where the impact of using appropriate genetic codes for gene prediction in phages was analysed. Metaprokka implements the methods and allows others to apply it to their datasets. |
| URL | https://bioconda.github.io/recipes/metaprokka/README.html |
| Title | Peroba - Phylogenetic Epidemiology with ROBust Assignment |
| Description | Peroba is a tool for continuous updating of outbreak information as new sequences are incorporated, generating reports and large data sets with sequences of interest. It was developed as a phylogenetic tracking tool to aggregate samples sequenced at the QIB with global information (sequence and metadata) from COG-UK and GISAID. The reports include phylogenetic clusters, and metadata information (anonymised if needed). |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | It has been used to generate reports of clusters of related sequences (potentially associated to outbreaks) to sequences generated locally or related to the Norfolk region. It is used (with the related software "uvaia") to automatically update the phylogenetic classification table for all local SARS-COV2 genomic samples. It has also been used in the phylogenetic analysis of the SARS-COV2 epidemics in Zimbabwe (https://www.medrxiv.org/content/10.1101/2021.01.04.20232520v1.full) |
| URL | https://github.com/quadram-institute-bioscience/peroba |
| Title | Ronaldo |
| Description | Comparison tool of SARSCOV2 sequence and limit of detection assays. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | Its results are being discussed with other COGUK consortium members. |
| URL | https://github.com/quadram-institute-bioscience/ronaldo |
| Title | Socru: Order and orientation of complete bacterial genomes |
| Description | Socru allows you to easily identify and communicate the order and orientation of complete genomes around ribosomal operons. These large scale structural variants have real impacts on the phenotype of the organism, and with the advent of long read sequencing, we can now start to delve into the mechanisms at work. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | For the first time researchers can investigate large structural rearrangements in bacteria in a systematic, standardised fashion. The software included the top 400 most commonly sequenced bacteria, so covers most infectious diseases caused by bacteria. A preprint gained an alt-metric score of 54, so was quite well received. |
| URL | https://github.com/quadram-institute-bioscience/socru |
| Title | Super_distance - Supertree estimation from gene trees to species trees |
| Description | Supertree estimation from gene trees to species trees, using matrix representation with distances. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | None yet |
| URL | https://github.com/quadram-institute-bioscience/super_distance |
| Title | Tatajuba - Identification and classification of homopolymeric tracts from reads |
| Description | Instead of assuming a fixed length for a given homopolymer tract, tatajubá allows for its whole distribution of sizes to be analysed. The rationale is that 1. our sequence might represent a population of non-identical individuals, with diversity of tract lengths, and 2. sequencing errors might be more frequent near or within homopolymers (so we should not remove uncertainty prematurely). Tatajubá also assumes that what we call a "tract" is a homopolymeric base flanked by a specific sequence (allowing for variability). |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | It will be used in several projects in the Institute, specially those involving Campylobacter or other microbes where homopolymeric tracts (or phase variation) can be of relevance. It is already been used to analyse Campylobacter Jejuni microevolution experiments since it can detect fine-grained, populational changes. It has also been used to validade results reported by Esson et al. "Genomic variations leading to alterations in cell morphology of Campylobacter spp." (2016) (https://doi.org/10.1038/srep38303). |
| URL | https://github.com/quadram-institute-bioscience/tatajuba |
| Title | Uvaia - Reference-based alignment and search against an alignment database |
| Description | Uvaia is a program for pairwise reference-based alignment, and subsequent search against an aligned database. The alignment uses the WFA library implemented by Santiago Marco-Sola, and the database search is based on score distances from my biomcmc-lib library. Uvaia has been developed to help with SARS-CoV-2 analysis, and is been used as a quick replacement for civet. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | Uvaia has been used internally to assign lineages and phylotypes to SARS-COV2 sequences generated locally as soon as they are completed. It has also been used to quickly deploy alignments around sequences of interest (e.g. for a phylogenetic analysis of samples related to an outbreak of interest). |
| URL | https://github.com/quadram-institute-bioscience/uvaia |
| Title | VAPOR |
| Description | We built a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of Influenza of non-human origin. Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR was built to retrieve references for viral genomes to enable read recovery from whole genome sequencing data. Using VAPOR instead of other existing approaches, VAPOR increased the proportion of mapped reads by up to 13.3% in testing compared to other software using standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | This work has underpinned the development of the clinical genomics pipeline for Influenza, in use in Public Health Wales now. |
| URL | https://github.com/connor-lab/vapor |
| Title | covtobed: a simple and fast tool to extract coverage tracks from BAM files |
| Description | covtobed: a simple and fast tool to extract coverage tracks from BAM files |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | It was the result of a joint collaboration with Italian collegues. |
| URL | https://github.com/telatin/covtobed |
| Title | tiptoft: Predict plasmids from uncorrected long read data |
| Description | Given some raw uncorrected long reads, such as those from PacBio or Oxford Nanopore, predict which plasmid should be present. Assemblies of long read data can often miss out on plasmids, particularly if they are very small or have a copy number which is too high/low when compared to the chromosome. This software gives you an indication of which plasmids to expect, flagging potential issues with an assembly. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | This has allowed for researchers to probe their uncorrected long reads to figure out if they are missing important pieces of the puzzle. Often plasmids contain anti-microbial resistance genes or virulence genes which are medically important, so if they are missing from the genomic information, the scientists will only have part of the puzzle. |
| URL | https://github.com/andrewjpage/tiptoft |
| Description | 7th Microbial Bioinformatics Hackathon with a special focus on Antimicrobial Resistance |
| 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 | Over 70 people attended the JPIAMR/CLIMB/PHA4GE virtual hackathon, hosted by Quadram, with a special focus on AMR tools and methods, happening from the 11-13 Oct 2021. This has lead to a paper being submitted and some software enhancements. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.climb.ac.uk/amr-hackathon/ |
| Description | Africa COVID-19 Genomes: Training Webinar Series --- High Throughput Sequencing - Genome Assembly and Quality Control |
| 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 | One-hour online training module titled "SARS-CoV2 phylogenetic curation" presented at the AfricaCDC network on Sars-CoV2 related techiniques training. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Anvi'o Workshop 2024 |
| 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 | 40 researchers at different career stage engaged with the authors of Anvi'o to learn how to curate and explore pangenomes, metagenomes and metabolic pathways datasets. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/anvio |
| Description | Article on SARS-CoV-2 scientist in Walden Local |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on local scientist involved in SARS-CoV-2 work in Walden Local news paper, "Saffron Walden scientist on team tackling public health challenges". |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Look East interview about SARS-CoV-2 Delta 21/7/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | TV interview with BBC Look East, broadcast on BBC 1 regional news in East Anglia, on SARS-CoV-2 |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Look East interview about SARS-CoV-2 Omicron on 27/11/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Zoom call on BBC Look East, broadcast on BBC 1 in East Anglia, providing expert scientific opinions on SARS-CoV-2. |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Look East interview about SARS-CoV-2 on 1/2/2022 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | 3 members of my group gave expert opinions in an interview to BBC Look East on SARS-CoV-2 and the film crew was in our lab seeing how we sequence genomes. It aired on lunchtime news and evening news in all regions of East Anglia. |
| Year(s) Of Engagement Activity | 2022 |
| Description | BBC Look East interview about SARS-CoV-2 on 14/5/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | TV interview on BBC Look East, broadcast on BBC 1 evening regional news in East Anglia. Providing expert opinion on SARS-CoV-2 genomics |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Look East interview about SARS-CoV-2 on 24/5/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | TV interview on BBC Look East, broadcast on BBC 1 regional news in East Anglia, providing expert scientific opinion on SARS-CoV-2 |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Look East interview about SARS-CoV-2 on 3/2/2022 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Gave an expert interview to BBC Look East on the BA.2 SARS-CoV-2 variant and rates in the East Anglia region. It aired on the evening news in 2 different versions in East Anglia. |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC Radio Norfolk SARS-CoV-2 Omicron interview on 29/11/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | BBC Radio Norfolk interview during the Breakfast show at 8am (prime slot), discussing the emergence of the SARS-CoV-2 Omicron variant. |
| Year(s) Of Engagement Activity | 2021 |
| Description | BBC radio Norfolk expert interview on COVID-19 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | BBC radio Norfolk expert interview on COVID-19 |
| Year(s) Of Engagement Activity | 2020 |
| Description | BBC radio Norfolk expert interview on COVID-19 on 21/5/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Local radio interview on SARS-CoV-2. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Bioinformatics based food-borne contamination detection poster with the CDC at a major US conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Collaborated with the CDC in the US on a bioinformatics method for food-borne pathogen detection (Kraken with Kalamari), at a major international conference held in the US (ASM Microbe). Andrew Page was the only non US federal government employee listed as an author. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Bioinformatics workshop at Al Quds University, Palestine |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | Bioinformatics workshop foraround 30 staff and students |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.facebook.com/watch/?v=384072965758371 |
| Description | Bioinformatics workshop in Belfast |
| 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 | 30 participants from across Northern ireland attended this event. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Bioinformatics workshop in Belfast |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The activity was led by team members, and was undertaken following engagement with Queens University Belfast, who hosted the event. To undertake the event, we made use of computational time on the MRC CLIMB resource, and generated a set of teaching materials. The workshop ran for a day. We undertook a training workshop to introduce bioinformatics/sequence analysis to a mixed audience focused on medical microbiology including a significant proportion of professionals from animal health organisations and (human) public health organisations. Hosted in Belfast, attendees came from organisations in both the Republic of Ireland and Northern Ireland. The workshop received excellent feedback, and provided a basis for a number of the attendees to begin building key skills that will be required as genomics becomes more widely used within their organisations. Attendees expressed an interest for a longer course, possibly to take place in 2019 to develop skills further. The workshop also provoked discussion around collaborative activities that would involve translation of academic approaches into clinical/animal health organisations. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Bioinmformatics workshop at Hebrew University in Israel |
| 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 | 20 people attended this workshop |
| Year(s) Of Engagement Activity | 2019 |
| Description | Coronavirus Covid expert urges city not to ditch masks in face of winter wave |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Eastern Daily Press interview on SARS-CoV-2 public health measures, providing expert opinion. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Coronavirus Norfolk scientists leading hunt to track Omicron Covid variant in UK - Eastern Daily Press 27/11/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Newspaper article on SARS-CoV-2 genomics. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Engaged with Industry by gaving a talk to US pharma company |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Engaged with Industry by gaving a talk to US pharma company, details subject to NDA |
| Year(s) Of Engagement Activity | 2019 |
| Description | Engaged with Industry by giving a talk to multinational biotech company |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Engaged with Industry by giving a talk to multinational biotech company, subject to NDA |
| Year(s) Of Engagement Activity | 2018 |
| Description | Engagement with Genomics Partnership Wales meeting with Bahraini delegation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Introducing pathogen genomics to a delegation from Bahrain who are working to plan for setting up a genomics programme |
| Year(s) Of Engagement Activity | 2019 |
| Description | Food Safety activity with 21 Beaver Scouts in Saffron Walden Essex |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | 21 Beaver Scouts (aged 6 and 7) in Saffron Walden learnt about microbes and swabbed kitchen surfaces onto agar, with images of what grows returned. They got to dress up like a microbiologist with lab coats, gloves, swabs and real agar plates. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Galaxy directions summit |
| 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 | Invited to take part in a scientific advisory meeting in Frieberg Germany on the Galaxy project, to provide high level direction and leadership for this international bioinformaics consortium. Expenses paid by the organisers and it was limited to 15 PIs from around the world. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Hackathon at Quadram Institute |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A 3 day hackathon was held at the Quadram Institute Bioscience with participants from Australia, Canada, Netherlands, Portugal, France, Scotland, Qatar, Germany and Scotland. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://quadram.ac.uk/hackathon0619/ |
| Description | Ideation workshop with Queens University Belfast and University College Dublin |
| 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 | Round table discussion to identify topics for joint funding applications with University College Dublin (Rep of Ireland) and Queens University Belfast (Northern Ireland). 2 ideas identified at the end of the workshop |
| Year(s) Of Engagement Activity | 2018 |
| Description | Impact showcase talk at Supercomputing, Denver |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This talk introduced how the application of HPC/Cloud computing is being used to derive insight from genomics to track and treat pathogens. The venue for the talk was the Supercomputing conference, one of the largest conferences for computer science in the world, with many of the audience being from industry and other areas. Further engagement with industry followed the talk. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Interview with Eastern Daily Press on COVID-19 deaths on 11/2/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview on SARS-CoV-2 as Norwich hit 250 deaths from COVID-19. Provided expert opinion. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.eveningnews24.co.uk/news/health/call-for-norwich-covid-memorial-8682926 |
| Description | Interviewed for US news article on research from European Bioinformatics Institute |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Interviewed by The Atlantic, a US based magazine, about a Nature Biotechnology paper published by the European Bioinformatics Institute. This was reported widely internationally. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.theatlantic.com/science/archive/2019/02/bigsi-search-bacteria-dna/581977/ |
| Description | Invitation to speak at Cambridge Infection Seminar series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was asked to present on the translational work we have undertaken in Wales, developing clinical pathogen genomics services as part of a seminar series covering a network of clinical and laboratory staff. The talk outlined what we have built in Wales, and provided an overview of what others could achieve. The talk provided advice and suggestions based on our experiences. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited talk at UEA School of Computing Sciences on Infectious Disease Bioinformatics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave an invited keynote talk at the University of East Anglia, School of Computing Sciences. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.uea.ac.uk/computing/events-and-seminars/-/asset_publisher/Tn5SWp1zkiIz/blog/infectious-d... |
| Description | Micro Binfie Virtual Conference 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | An online seminar series chaired by the Micro Binfie Podcast |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://microbinfie.github.io/conference2020/ |
| Description | Microbial Bioinformatics Virtual Lab Talk series |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I co-host a monthly webcast with the CDC on the theme of microbial bioinformatics. This allows researchers, scientists, public health clinicians, and epidemiologists, drawn from academia, government, and the commercial world, to share and learn about the latest advances in the field. It is recorded live over Zoom.us allowing for questions and answers, and available afterwards on YouTube. The content is highly technical, and this is the only regular way of sharing information in this international community. The audience is drawn from all over the world, usually including the USA & Canada, Australia, UK, EU & Norway and South Africa. |
| Year(s) Of Engagement Activity | 2018,2019 |
| URL | https://www.youtube.com/playlist?list=PLutg7pT5QK4RV9_eo_NHZX1nd48kkw1-Q |
| Description | Microbial Bioinformatics podcast |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Over 100 episodes of the MicroBinfie podcast with over 50000 listens. |
| Year(s) Of Engagement Activity | 2022,2023 |
| Description | Microbinfie podcast: History of Genotyping - The early years |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/02-history-of-genotyping-the-early-years |
| Description | Microbinfie podcast: History of file formats |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/10-history-of-file-formats |
| Description | Microbinfie podcast: Looking back at 2019 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/looking-back-at-the |
| Description | Microbinfie podcast: Phylogenetics with the arborists part 1 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/11-phylogenetics-with-the-arborists-part1 |
| Description | Microbinfie podcast: Phylogenetics with the arborists part 2 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/12-phylogenetics-with-the-arborists-part2 |
| Description | Microbinfie podcast: Questions not to ask |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/13-questions-not-to-ask |
| Description | Microbinfie podcast: What bioinformatics software not to write part 1 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/what-software-not-to-write-1 |
| Description | Microbinfie podcast: What bioinformatics software not to write part 2 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/what-software-not-to-write |
| Description | Microbinfie podcast: FASTQ - all your bases are belong to us |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/fastq-all-your-bases |
| Description | Microbinfie podcast: History of Genotyping - Decentralised Future |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/05-history-of-genotyping-decentralised-future |
| Description | Microbinfie podcast: Nobel prize or contamination |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/09-nobel-prize-or-contamination |
| Description | Microbinfie podcast: Wham, BAM, thank you SAM. |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/07-wham-bam-thank-you-sam |
| Description | Microbinfie podcast: Writing good bioinformatics software with Torsten Seemann |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the CDC (US) on microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/microbinfie/05-writing-good-bioinformatics-software-with-torsten-seemann |
| Description | Microbinfie podcasts |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Microbial bioinformatics podcast with 36 episodes in the past year, resulting in 14k listens. A dozen of these podcasts were on SARS-CoV-2 genomics and sequencing. |
| Year(s) Of Engagement Activity | 2020,2021 |
| URL | https://soundcloud.com/microbinfie |
| Description | Online lecture on Principles of Phylogenetics |
| 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 | Lecture presented at the Microbial Genomics Workshop organised by the MicroGenomeUA Educational initiative. This was a 3-day workshop, and MicroGenomeUA is an initiative created by Ukrainian microbiologists inspired by microbes, their genomics and biotechnology potential. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Organiser for the 4th Microbial Bioinformatics Hackathon at the National Institutes of Health in MD, USA |
| 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 | Andrew Page co-organised the 4th Microbial Bioinformatics Hackathon in the National Institutes of Health in Maryland, USA, along with Torsten Seemann of the MDU in Melbourne Australia and Adam Phillippy of the NIH. This was a 4 day event bringing bioinformaticians together from all over the world (US/Canada/EU/Australia) to work on open problems in the bioinformatics community involving primarily infectious diseases. The participants were drawn from government funded organisations, such as the FDA/CDC/PHE/MDU, industry (including startups), research institutes and academia. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Parliamentary Reception for official launch of the Quadram Institute |
| 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 | Was part of a small team of senior management who attended Parliamentary Reception for official launch of the Quadram Institute in Westminister. Discussed our research with politicians, members of the media, and with people working in industry in the same domain. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Participation at meeting to establish the Public Health Alliance for Genomic Epidemiology |
| 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 participated in work to establish an international organisation to facilitate the development of standards for the application of genomics to epidemiology and public health. This work particularly involved engagement with researchers from Africa and the US CDC. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participation in the SMBE workshop on Pathogen Transmission |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I participated in the SMBE workshop on Pathogen Transmission, which involved engagement with public health professionals, epidemiologists, basic scientists and other bioinformaticians. The engagement activity included presenting a talk, and engaging with colleagues, which have since resulted in at least one international grant applicataion. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Phylogenomic models, for when knowing the history of a gene is not enough |
| 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 | Invited lecture at the Midsummer Phylogenetics Workshop at UEA 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation of the Quadram Institute and QIB science at the 4th European Microbiome Congress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation of the Quadram Institute and QIB science at the 4th European Microbiome Congress. This was primarily an industry conference, so we engaged widely with industry. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://microbiomecongress.com/events/microbiome-congress-2018 |
| Description | Presentation to Welsh Assembly Comittee |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | This talk introduced pathogen genomics, and how it is enabled to a Welsh Assembly Committee, stimulating increased interest in this subject area and informing the committee on the uses of computational resources for the processing of pathogen genomic data. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presenting a talk at the Clostpath 2019 conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented a talk summarising the results of collaborative work between Public Health Wales, Cardiff University and QIB in the area of whole genome sequencing and analysis of C. difficile in a clinical setting. The talk was presented at the main international conference for researchers working in the area, and was very well received. Outputs from the talk have included engagement with Chinese CDC, ECDC and infection control and public health surveillance in the Netherlands. Plans are already in progress to develop new projects building off of this work. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Press briefing on COVID-19 new variant |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Part of an expert panel on SARS-CoV-2 on the new variant for a science media centre press briefing. It lasted 1 hour with over 60 journalists, primarily UK based but there were many from overseas. Lead to substantial 'top billed' media coverage on radio, TV and print. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Primary school visit and microbiology activity |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Ran a microbiology activity for 30 year 6 pupils. They swabed surfaces, put on plates which were then grown in the lab, and went in a week later to show photos of results. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Providing content to be displayed at 'Food Matters Live' Industry Network Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Provided written content to be displayed, alongside images, during the Food Matters Live industry network meeting (please see below for exact content). The content focused on the transmission of pathogens through the food chain and highlighted the work being undertaken as part of this theme. "By walking across different livestock farming sites and testing the mud samples on their boots, scientists from the Quadram Institute are looking at the transmission routes of harmful bacteria into the food chain. Knowing exactly at what point these pathogens enter the food chain, and how they evolve, spread, survive and compete with each other, will help in the development of strategies for more targeted interventions to reduce the burden of foodborne illness." |
| Year(s) Of Engagement Activity | 2018 |
| Description | QIB/CDC Micro binfie podcast; Bayesian Genomics with Conor Meehan |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | One hour interview and discussion related to the use of Bayesian Phylogenetics in Microbial Genomics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/17-bayesian-magic-in-practice |
| Description | QIB/CDC Micro binfie podcast; The Arborists with Conor Meehan |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | One hour interview and discussion with Dr. Conor Meehan (Lecturer in Molecular Microbiology at University of Bradford) regarding the use of phylogenetics in microbial genomics. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://soundcloud.com/microbinfie/11-phylogenetics-with-the-arborists-part1 |
| Description | QIB/CDC Micro binfie podcast; Nextstrain with Emma Hodcroft |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | One hour of interview and discussion with one of the lead scientists behind the updated phylogenetic analysis and classification of SARS-CoV-2 genomes |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://soundcloud.com/microbinfie/nextstrain-sarscov2-and-dealing-with-a-data-deluge |
| Description | Ran a workshop at a Pathogen Transmission Conference. |
| 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 | Ran a workshop during the Pathogen Transmission Conference, with a focus on audience participation. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Remote seminar at the Federal University of Para/Brazil on public resources for SARS-CoV-2 genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Discussion with graduate students (virology, biomedical sciences) about my trajectory and work, followed by description of publicly available resources for analysing SARS-CoV2. It served as a "motivational" talk (since I'm Brazilian) and also as a training activity, of one hour. Students were engaged in discussing the tools and were looking forward trying it themselves. The organiser, prof. Elcio Leal, has been in touch and showed interest in further discussions. Pará is in the Amazon region of Brazil, and these students feel responsible for disseminating information and in keeping up with most recent developments in COVID research. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Research Pages podcast: DORA the explora: rethinking research assessment |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/dora-the-explora-rethinking-research-assessment |
| Description | Research Pages podcast: Mechanics of scientific paper writing |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/mechanics-of-scientific-paper-writing |
| Description | Research Pages podcast: Peer Review from the other side |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/peer-review |
| Description | Research Pages podcast: Reference managers: easing the pain of referencing |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/reference-managers-easing-the-pain-of-referencing |
| Description | Research Pages podcast: Resources for Research |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/ep6-resources-for-research |
| Description | Research Pages podcast: The challenge of reproducibility |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/the-challenge-of-reproducibility |
| Description | Research Pages podcast: Why we all need Information Professionals in our research groups |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Podcast in collaboration with the University of Cambridge on supporting academic research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://soundcloud.com/research-pages/information-professionals |
| Description | Rise of Omicron sub-variant could bring 'another peak' - Eastern Daily Press on 2/2/2022 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview on SARS-CoV-2 variant BA.2 with the Eastern Daily Press providing expert opinion |
| Year(s) Of Engagement Activity | 2021 |
| Description | SARS-CoV-2 Omicron interview on ITV Anglia evening news 29/11/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | ITV Anglia film crew came into our lab and interviewed multiple people about our SARS-CoV-2 genome sequencing work. I gave an expert interview on topic. |
| Year(s) Of Engagement Activity | 2021 |
| Description | SARS-CoV-2 expert panel for ARTIC/CLIMB |
| 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 | Member of expert panel providing advise to international audience of 120 people on SARS-CoV-2 sequencing and genomics analysis to directly support international efforts to get SARS-CoV-2 genomic epidemiology established internationally. This was also put on to youtube and was turned into a podcast. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=5g8LUYM5U4M&list=PLKz9Fzwt-TsrDHKllpL4txQb0BB2qBDbR&index=3 |
| Description | SARS-CoV-2 new variant on BBC Look East |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | SARS-CoV-2 new variant on BBC Look East |
| Year(s) Of Engagement Activity | 2020 |
| Description | School Visit Teaching all pupils in School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Did presentation to each class and did two activities, hand washing and a live DNA extraction. -David Baker |
| Year(s) Of Engagement Activity | 2020 |
| Description | Sequencing and Bioinformatics Workshop Quadram Institute, MRC Gambia, London School of Hygiene and Tropical Medicine |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A workshop was run for 1 week in The Gambia with participants from all over West Africa. It was funded by an internal Flexible Talent Mobility award from the BBSRC. The participants learnt about bioinformatics, cloud computing and genome sequencing. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Sky News article on publication findings on SARS-CoV-2 |
| 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 | Public/other audiences |
| Results and Impact | National news article on SARS-CoV-2 publication findings. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://news.sky.com/story/covid-19-greece-travel-corridor-brought-in-a-large-amount-of-virus-say-ex... |
| Description | Talk at NHS meeting on pathogen genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk introducing bioinformatics for the analysis of pathogen genomic sequences in healthcare |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talk at School of Veterinary Medicine University of Surrey Research Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Team member delivered talk on "Sequencing technologies at the cross-roads: how to get the best out of short and long read sequencing". |
| Year(s) Of Engagement Activity | 2020 |
| Description | Talk in The Gambia at meeting on Establishing sequencing capacity in challenging environments |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk on "PacBio sequencing: a hands-on guide" at Establishing Microbial Sequencing and Bioinformatics Capacity in Challenging Environments Workshop January 15-17, 2020 MRC Unit, the Gambia at LSHTM Fajara, the Gambia. There were participants from multiple African countries, Palestine, Lebanon, and the UK. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Talk in The Gambia at meeting on Establishing sequencing capacity in challenging environments |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | How to get the best out of Illumina Reagents Establishing Microbial Sequencing and Bioinformatics Capacity in Challenging Environments Workshop January 15-17, 2020 MRC Unit, the Gambiaat LSHTM Fajara, the Gambia |
| Year(s) Of Engagement Activity | 2020 |
| Description | Talk to Norwich Research Park Institutes on the informatics challenges of infectious diseases |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | An invited seminar talk to the Norwich Research Park informatics groups at the John Innes Centre. The audience were mostly computer scientists and IT professionals, so this gave some good practical examples of where computing can be used for public good in bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talk to the Doctoral Training Programme at the Norwich Research Park on long read sequencing technologies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Talk to ~20 PhD students as part of the doctoral training programme at the Norwich research park. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Training provided to Environmental Health Officers |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | As a subject matter expert in the area of genomics, we provided a team member to participate in a training day for Environmental Health officers across Wales. The training provided an introduction and overview to Genomics. The training resulted in good feedback, which included an indication that following the session the attendees understood the potential of genomics in their work, and would look to use genomics services in their roles in environmental health. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Visiting The Biomedical Research Centre (CINBIO) at Universidad de Vigo, and the ECIMAT (Toralla Marine Science Station) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Meeting to learn about the research infrastructure of the centres, and to establish collaborations. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop on WGS in healthcare |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I spoke at, and engaged with a workshop organised at RIVM in the Netherlands to introduce the pathogen genomics work that is going on in Wales. The engagement provoked detailed discussions following the event, with both researchers and with clinical staff. |
| Year(s) Of Engagement Activity | 2020 |
| Description | nf-core hackathon 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 | Local site of "nf-core" hackathon to improve the open source pipelines and documentation from the nf-core organization |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/nf-core |