Research Infrastructure

Lead Research Organisation: Quadram Institute Bioscience
Department Name: Contracts

Abstract

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.

Publications

10 25 50
 
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.
First Year Of Impact 2019
Sector Healthcare
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 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 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 (FNS-Cloud) - Food Nutrition Security Cloud
Amount € 10,912,775 (EUR)
Funding ID 863059 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 10/2019 
End 09/2023
 
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 06/2018 
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 04/2019 
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 Food safety bioinformatics hackathon
Amount £10,081 (GBP)
Funding ID BB/S020527/1 
Organisation Quadram Institute Bioscience 
Sector Academic/University
Country United Kingdom
Start 06/2019 
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
 
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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