The MRC Consortium for Medical Microbial Bioinformatics
Lead Research Organisation:
University of Warwick
Department Name: Warwick Medical School
Abstract
The UNIVERSITY OF WARWICK and SWANSEA UNIVERSITY, in partnership with the UNIVERSITY OF BIRMINGHAM and CARDIFF UNIVERSITY, propose a programme of capital expenditure, recruitment and training to create the MRC CONSORTIUM FOR MEDICAL MICROBIAL BIOINFORMATICS, a state-of-the-art interdisciplinary facility, led by Professor Mark Pallen (an MD PhD at Warwick) and Dr Sam Sheppard in Swansea, for use by the academic, industrial and healthcare communities that will enhance regional and national capability and infrastructure in microbial bioinformatics and improve our understanding of bacteria of medical importance.
RATIONALE: Microbial pathogens still present a MAJOR EXISTENTIAL THREAT to humanity. In addition, the HUMAN MICROBIOME - the rich and dynamic community of host-associated microorganisms and their genes - is now known to play a decisive role in the balance between health and disease, even in medical conditions not usually considered as microbial in origin (e.g. obesity). Harnessing medical bioinformatics to the study of microbial genes, genomes and metagenomes thus represents a DISTINCTIVE UNMET CHALLENGE and a UNIQUE FOCUS AMONG RESPONSES TO THIS MRC CALL. Rather than taking aim at the fixed, relatively tractable target of the human genome, we focus instead on genomic information derived from HUNDREDS OF BACTERIAL PATHOGENS and THOUSANDS OF COMMENSAL SPECIES: a distributed and dynamic system of MANY MILLIONS OF GENES, at least two orders of magnitude larger than the human gene set.
Our four research-active universities are located in neighbouring regions of the UK, thus providing an initial GEOGRAPHICAL COHESION to the Consortium that will facilitate community building and the exchange of ideas, and underpin the formalities of governance. At its inception, the Consortium will benefit from a NATIONAL AND GLOBAL REACH through a dense network of collaborations, collegiality and, through an application process for new partners, will soon grow in a scalable fashion to embrace a national remit.
The Consortium will build on TRACK RECORDS OF INDIVIDUAL RESEARCH EXCELLENCE and impressive INSTITUTIONAL INVESTMENT in medical microbiology and bioinformatics with all partners making a distinctive contribution. Through this initiative we will recruit THREE HIGHLY TALENTED INDIVIDUALS into microbial bioinformatics fellowships from careers outside the discipline or the country. We have LEVERAGED SUPPORT from the host organisations to place these research fellows on a TENURE TRACK. All three fellows will contribute to the goals of the Consortium through research, training and management roles as well as pushing forward their own cutting-edge research programmes.
Building on interests in parallelisation and cloud computing, we will develop a DISTRIBUTED COMPUTING INFRASTRUCTURE in Wales and the West Midlands that will provide an agile, scalable system for the UK microbiology research community.
We will develop an ambitious and exciting TRAINING PROGRAMME that will include bootcamps, hackathons, workshops, modules and courses, suitable for a wide range of users from professional bioinformaticians to undergraduate students.
We will strengthen regional, national and international microbial bioinformatics research through COMMUNITY-BUILDING ACTIVITIES, encouraging knowledge transfer and dissemination of best practice. Meetings of different sorts and scale will be held monthly and quarterly and annually. The Annual Meeting, with an academic and management component, will benefit from participation by our external Steering Group.
We will exploit pump-priming funds together with externally funded research activities to "stress our systems", confirming that the facilities that we have created work as planned and/or priming iterative refinements to our infra-structure. We are confident that the consortium will become self-sustaining through institutional commitments and the recruitment of additional research funding.
RATIONALE: Microbial pathogens still present a MAJOR EXISTENTIAL THREAT to humanity. In addition, the HUMAN MICROBIOME - the rich and dynamic community of host-associated microorganisms and their genes - is now known to play a decisive role in the balance between health and disease, even in medical conditions not usually considered as microbial in origin (e.g. obesity). Harnessing medical bioinformatics to the study of microbial genes, genomes and metagenomes thus represents a DISTINCTIVE UNMET CHALLENGE and a UNIQUE FOCUS AMONG RESPONSES TO THIS MRC CALL. Rather than taking aim at the fixed, relatively tractable target of the human genome, we focus instead on genomic information derived from HUNDREDS OF BACTERIAL PATHOGENS and THOUSANDS OF COMMENSAL SPECIES: a distributed and dynamic system of MANY MILLIONS OF GENES, at least two orders of magnitude larger than the human gene set.
Our four research-active universities are located in neighbouring regions of the UK, thus providing an initial GEOGRAPHICAL COHESION to the Consortium that will facilitate community building and the exchange of ideas, and underpin the formalities of governance. At its inception, the Consortium will benefit from a NATIONAL AND GLOBAL REACH through a dense network of collaborations, collegiality and, through an application process for new partners, will soon grow in a scalable fashion to embrace a national remit.
The Consortium will build on TRACK RECORDS OF INDIVIDUAL RESEARCH EXCELLENCE and impressive INSTITUTIONAL INVESTMENT in medical microbiology and bioinformatics with all partners making a distinctive contribution. Through this initiative we will recruit THREE HIGHLY TALENTED INDIVIDUALS into microbial bioinformatics fellowships from careers outside the discipline or the country. We have LEVERAGED SUPPORT from the host organisations to place these research fellows on a TENURE TRACK. All three fellows will contribute to the goals of the Consortium through research, training and management roles as well as pushing forward their own cutting-edge research programmes.
Building on interests in parallelisation and cloud computing, we will develop a DISTRIBUTED COMPUTING INFRASTRUCTURE in Wales and the West Midlands that will provide an agile, scalable system for the UK microbiology research community.
We will develop an ambitious and exciting TRAINING PROGRAMME that will include bootcamps, hackathons, workshops, modules and courses, suitable for a wide range of users from professional bioinformaticians to undergraduate students.
We will strengthen regional, national and international microbial bioinformatics research through COMMUNITY-BUILDING ACTIVITIES, encouraging knowledge transfer and dissemination of best practice. Meetings of different sorts and scale will be held monthly and quarterly and annually. The Annual Meeting, with an academic and management component, will benefit from participation by our external Steering Group.
We will exploit pump-priming funds together with externally funded research activities to "stress our systems", confirming that the facilities that we have created work as planned and/or priming iterative refinements to our infra-structure. We are confident that the consortium will become self-sustaining through institutional commitments and the recruitment of additional research funding.
Technical Summary
The MRC CONSORTIUM FOR MEDICAL MICROBIAL BIOINFORMATICS (CMMB) will enhance UK capability and infrastructure in microbial bioinformatics. Led by Mark Pallen and Sam Sheppard, the CMMB will recruit THREE HIGHLY TALENTED INDIVIDUALS into UK medical microbial bioinformatics from careers outside the discipline or the country.
We will develop a DISTRIBUTED COMPUTING INFRASTRUCTURE that will operate together to provide:
1. AN AGILE, SCALABLE SYSTEM available to consortium members that can be dynamically provisioned to handle different workloads/projects as needed; this will include:
-FOUR CLUSTERS (one on each site) providing a heterogeneous mix of high-memory/low CPU and low-memory/high CPU servers suitable for both memory-intensive tasks (e.g. metagenomic assembly) and CPU-intensive activities.
-SUBSTANTIAL STORAGE (>2 petabytes).
-sufficient NETWORK CAPACITY for each site to operate at 10 gigabit/second connectivity.
2. a web-based instance of the GALAXY PLATFORM customised for medical microbial research.
3. a freely accessible DATABASE of relevant workflows, pipelines, scripts, programs, virtual machine images built on Galaxy/Github and mirrored across our sites.
4. a DATA ARCHIVE of relevant microbial (meta)genomes
5. a computational infrastructure for linking PATIENT METADATA with microbial (meta)genomic data.
We will develop an ambitious and exciting TRAINING PROGRAMME that will include bootcamps, hackathons, workshops, modules and courses, suitable for a wide range of users from professional bioinformaticians to undergraduate students. We will strengthen national microbial bioinformatics research through COMMUNITY-BUILDING ACTIVITIES, encouraging knowledge transfer and dissemination of best practice. We will exploit pump-priming funds together with externally funded research activities to "stress our systems", confirming that the facilities that we have created work as planned and/or priming ITERATIVE REFINEMENTS TO OUR INFRA-STRUCTURE
We will develop a DISTRIBUTED COMPUTING INFRASTRUCTURE that will operate together to provide:
1. AN AGILE, SCALABLE SYSTEM available to consortium members that can be dynamically provisioned to handle different workloads/projects as needed; this will include:
-FOUR CLUSTERS (one on each site) providing a heterogeneous mix of high-memory/low CPU and low-memory/high CPU servers suitable for both memory-intensive tasks (e.g. metagenomic assembly) and CPU-intensive activities.
-SUBSTANTIAL STORAGE (>2 petabytes).
-sufficient NETWORK CAPACITY for each site to operate at 10 gigabit/second connectivity.
2. a web-based instance of the GALAXY PLATFORM customised for medical microbial research.
3. a freely accessible DATABASE of relevant workflows, pipelines, scripts, programs, virtual machine images built on Galaxy/Github and mirrored across our sites.
4. a DATA ARCHIVE of relevant microbial (meta)genomes
5. a computational infrastructure for linking PATIENT METADATA with microbial (meta)genomic data.
We will develop an ambitious and exciting TRAINING PROGRAMME that will include bootcamps, hackathons, workshops, modules and courses, suitable for a wide range of users from professional bioinformaticians to undergraduate students. We will strengthen national microbial bioinformatics research through COMMUNITY-BUILDING ACTIVITIES, encouraging knowledge transfer and dissemination of best practice. We will exploit pump-priming funds together with externally funded research activities to "stress our systems", confirming that the facilities that we have created work as planned and/or priming ITERATIVE REFINEMENTS TO OUR INFRA-STRUCTURE
Planned Impact
This research will be of benefit to a range of beneficiaries outside the academic discipline of medical microbiology:
CLINICAL AND PUBLIC HEALTH MICROBIOLOGISTS, clinicians and INFECTION CONTROL TEAMS working within the HEALTH SERVICES, including regionally and locally with NHS TRUSTS in Wales and the West Midlands and further afield and nationally with Public Health England and Public Health Wales. These users will be able to use our computational infrastructure to integrate clinical informatics systems, patient metadata, epidemiological disease patterns and microbial (meta)genomic data to elucidate modes and routes of transmission, detect outbreaks, explore the relationships between potential pathogens and disease, with IMPACTS ON HEALTH and WELL-BEING, DISEASE PREVENTION, MANAGEMENT OF INFECTION AND QUALITY OF LIFE. This initiative will also bring new opportunities for productive engagement between the healthcare sector and the academic sector, so that research findings and approaches can be more easily TRANSLATED INTO OUTCOMES that impact on patient management.
INDUSTRIAL AND PUBLIC HEALTH USERS interested in developing NEW THERAPEUTICS, VACCINES OR DIAGNOSTIC TESTS for microbial pathogens by, for example, allowing them to explore genotypic diversity when evaluating novel targets. A greater understanding of the microbiota may also deliver new approaches for dealing with conditions not normally thought of ainfectiions, e.g inflammatory bowel disease, or obesity.
COMMERCIAL BENEFICIARIES include SEQUENCING COMPANIES, COMPUTER COMPANIES and PRIVATE LABORATORIES, who stand to benefit from increased demand for their products and opportunities for innovation and spread of best practice(NB: both Solexa and Oxford nanopore sequencing were developed within the UK, with benefits to our economy).
POLICY MAKERS, who will benefit from grounding their PUBLIC POLICY and LEGISLATION, e.g. on food safety, on a MORE SOLID UNDERSTANDING of bacterial evolution, epidemiology, population genetics and taxonomy. NB: Applicants, particularly Mark Achtman, have been at the forefront of efforts to identify and classify foodborne bacteria using a RATIONAL AND DISCRIMINATORY SYSTEM OF CLASSIFICATION.
The WIDER PUBLIC will benefit from the positive impacts on the NATION'S HEALTH,, including the CONTROL and PREVENTION OF INFECTION and the DEVELOPMENT of new interventions.
This work will also make a decisive contribution through employment and training to enhancing the PROFESSIONAL AND RESEARCH SKILLS BASE of the United Kingdom
CLINICAL AND PUBLIC HEALTH MICROBIOLOGISTS, clinicians and INFECTION CONTROL TEAMS working within the HEALTH SERVICES, including regionally and locally with NHS TRUSTS in Wales and the West Midlands and further afield and nationally with Public Health England and Public Health Wales. These users will be able to use our computational infrastructure to integrate clinical informatics systems, patient metadata, epidemiological disease patterns and microbial (meta)genomic data to elucidate modes and routes of transmission, detect outbreaks, explore the relationships between potential pathogens and disease, with IMPACTS ON HEALTH and WELL-BEING, DISEASE PREVENTION, MANAGEMENT OF INFECTION AND QUALITY OF LIFE. This initiative will also bring new opportunities for productive engagement between the healthcare sector and the academic sector, so that research findings and approaches can be more easily TRANSLATED INTO OUTCOMES that impact on patient management.
INDUSTRIAL AND PUBLIC HEALTH USERS interested in developing NEW THERAPEUTICS, VACCINES OR DIAGNOSTIC TESTS for microbial pathogens by, for example, allowing them to explore genotypic diversity when evaluating novel targets. A greater understanding of the microbiota may also deliver new approaches for dealing with conditions not normally thought of ainfectiions, e.g inflammatory bowel disease, or obesity.
COMMERCIAL BENEFICIARIES include SEQUENCING COMPANIES, COMPUTER COMPANIES and PRIVATE LABORATORIES, who stand to benefit from increased demand for their products and opportunities for innovation and spread of best practice(NB: both Solexa and Oxford nanopore sequencing were developed within the UK, with benefits to our economy).
POLICY MAKERS, who will benefit from grounding their PUBLIC POLICY and LEGISLATION, e.g. on food safety, on a MORE SOLID UNDERSTANDING of bacterial evolution, epidemiology, population genetics and taxonomy. NB: Applicants, particularly Mark Achtman, have been at the forefront of efforts to identify and classify foodborne bacteria using a RATIONAL AND DISCRIMINATORY SYSTEM OF CLASSIFICATION.
The WIDER PUBLIC will benefit from the positive impacts on the NATION'S HEALTH,, including the CONTROL and PREVENTION OF INFECTION and the DEVELOPMENT of new interventions.
This work will also make a decisive contribution through employment and training to enhancing the PROFESSIONAL AND RESEARCH SKILLS BASE of the United Kingdom
Organisations
- University of Warwick (Lead Research Organisation)
- Cardiff University (Collaboration)
- PUBLIC HEALTH ENGLAND (Collaboration)
- Public Health Wales NHS Trust (Collaboration)
- UNIVERSITY OF THE WESTERN CAPE (Collaboration)
- Bill & Melinda Gates Foundation (Collaboration)
- Centers for Disease Control and Prevention (CDC) (Collaboration)
Publications
Kobras CM
(2023)
Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in Streptococcus pneumoniae.
in Proceedings of the National Academy of Sciences of the United States of America
O'Connell L
(2023)
Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing
in Journal of Hospital Infection
Gilroy R
(2023)
A genomic blueprint of the healthy human oesophageal microbiome
Killough N
(2023)
How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom.
in Microbial genomics
Harrison J
(2023)
Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria
in Taxonomy
Armitage E
(2023)
Streptococcus pyogenes carriage acquisition, persistence and transmission dynamics within households in The Gambia (SpyCATS): protocol for a longitudinal household cohort study
in Wellcome Open Research
| 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 | 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 | 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 | DNA and RNA viruses in the rhizosphere |
| Description | This repository contains data used in Muscatt et al. 2022 Futher details on analysis can be found here https://github.com/GeorgeMuscatt/RhizosphereVirome Data is stored in the file RhizosphereVirome.tar The following files are stored. See the README for full details: c1.ntw.gz = vConTACT2 network output file core_protein_concatenation_tree = ssRNA phage phylogenetic tree based on aligned core protein concatenations CP.faa.gz = fasta amino acid file containing coat protein sequences for 11,222 near-complete ssRNA phage vOTUs CP_ref_Leviviricetes.faa.gz = fasta amino acid file containing coat protein sequences for 1,868 reference Leviviricetes genomes dsDNA_gene_annotations.csv.gz = annotations for 20,746 dsDNA vOTU genes dsDNA_vOTUs.faa.gz = fasta amino acid file containing 20,267 dsDNA vOTU genes dsDNA_vOTUs.fna.gz = fasta nucleotide file containing 1,059 dsDNA vOTUs edges.csv.gz = edges for drawing vConTACT2 network gene_2_genome.csv.gz = input file for vConTACT2 containing gene-to-genome index for 1,059 dsDNA vOTUs and 16,540 ssRNA phage vOTUs MP.faa.gz = fasta amino acid file containing maturation protein sequences for 11,222 near-complete ssRNA phage vOTUs MP_ref_Leviviricetes.faa.gz = fasta amino acid file containing maturation protein sequences for 1,868 reference Leviviricetes genomes nodes.csv.gz = nodes for drawing vConTACT2 network RdRp.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 11,222 near-complete ssRNA phage vOTUs RdRp_ref_Leviviricetes.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 1,868 reference Leviviricetes genomes ssRNA_vOTUs.faa.gz = fasta amino acid file containing 52,700 ssRNA phage vOTU genes ssRNA_vOTUs.fna.gz = fasta nucleotide file containing 16,541 ssRNA phage vOTUs viral_cluster_overview.csv = output file from vConTACT2 containing viral cluster information |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://leicester.figshare.com/articles/dataset/DNA_and_RNA_viruses_in_the_rhizosphere/19635336 |
| Title | DNA and RNA viruses in the rhizosphere |
| Description | This repository contains data used in Muscatt et al. 2022 Futher details on analysis can be found here https://github.com/GeorgeMuscatt/RhizosphereVirome Data is stored in the file RhizosphereVirome.tar The following files are stored. See the README for full details: c1.ntw.gz = vConTACT2 network output file core_protein_concatenation_tree = ssRNA phage phylogenetic tree based on aligned core protein concatenations CP.faa.gz = fasta amino acid file containing coat protein sequences for 11,222 near-complete ssRNA phage vOTUs CP_ref_Leviviricetes.faa.gz = fasta amino acid file containing coat protein sequences for 1,868 reference Leviviricetes genomes dsDNA_gene_annotations.csv.gz = annotations for 20,746 dsDNA vOTU genes dsDNA_vOTUs.faa.gz = fasta amino acid file containing 20,267 dsDNA vOTU genes dsDNA_vOTUs.fna.gz = fasta nucleotide file containing 1,059 dsDNA vOTUs edges.csv.gz = edges for drawing vConTACT2 network gene_2_genome.csv.gz = input file for vConTACT2 containing gene-to-genome index for 1,059 dsDNA vOTUs and 16,540 ssRNA phage vOTUs MP.faa.gz = fasta amino acid file containing maturation protein sequences for 11,222 near-complete ssRNA phage vOTUs MP_ref_Leviviricetes.faa.gz = fasta amino acid file containing maturation protein sequences for 1,868 reference Leviviricetes genomes nodes.csv.gz = nodes for drawing vConTACT2 network RdRp.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 11,222 near-complete ssRNA phage vOTUs RdRp_ref_Leviviricetes.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 1,868 reference Leviviricetes genomes ssRNA_vOTUs.faa.gz = fasta amino acid file containing 52,700 ssRNA phage vOTU genes ssRNA_vOTUs.fna.gz = fasta nucleotide file containing 16,541 ssRNA phage vOTUs viral_cluster_overview.csv = output file from vConTACT2 containing viral cluster information |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://leicester.figshare.com/articles/dataset/DNA_and_RNA_viruses_in_the_rhizosphere/19635336/1 |
| Title | GeneCatalog.faa |
| Description | proteins for chicken gene catalog |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/GeneCatalog_faa/19582717 |
| Title | GeneCatalog.faa |
| Description | proteins for chicken gene catalog |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/GeneCatalog_faa/19582717/1 |
| Title | INPHARED_DATABASE |
| Description | inphared.pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible.Useful information, including viral taxonomy and bacterial host data, is extracted from the Genbank files and provided in a summary table. Genes are called on the genomes using Prokka and this output is used to gather metrics which are summarised in the output files, as well as useful input files for vConTACT2. The data provided is all genomes up to Jan 2021. This can be downloaded so users do not have to repeat the process of consistent gene calling on existing genomes. The folder GenomesDB contains subfolders each containing a subfolder that is named on the accession number of each phage. Within each folder are re-called genes in the following format *.ffn*.faa The complete genome *fna and genbank file without any annotation *gbf See https://github.com/RyanCook94/ |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://leicester.figshare.com/articles/dataset/INPHARED_DATABASE/14242085/1 |
| Title | INPHARED_DATABASE |
| Description | inphared.pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible.Useful information, including viral taxonomy and bacterial host data, is extracted from the Genbank files and provided in a summary table. Genes are called on the genomes using Prokka and this output is used to gather metrics which are summarised in the output files, as well as useful input files for vConTACT2. The data provided is all genomes up to Jan 2021. This can be downloaded so users do not have to repeat the process of consistent gene calling on existing genomes. The folder GenomesDB contains subfolders each containing a subfolder that is named on the accession number of each phage. Within each folder are re-called genes in the following format *.ffn*.faa The complete genome *fna and genbank file without any annotation *gbf See https://github.com/RyanCook94/ |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://leicester.figshare.com/articles/dataset/INPHARED_DATABASE/14242085 |
| Title | Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance |
| Description | Supplementary Material for 'Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance', as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/Local_accessory_gene_sharing_among_Egyptian_Campy... |
| Title | Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance |
| Description | Supplementary Material for 'Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance', as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/Local_accessory_gene_sharing_among_Egyptian_Campy... |
| Title | Supporting data for "PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria" |
| Description | Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Description | Collaboration with Public Health England |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The CLIMB infrastructure was used by PHE for a few days to support their public health microbial genomics efforts when their own infrastructure went offline |
| Collaborator Contribution | PHE provided input into the MRC Partnership award application which will prvide follow on funding for this project |
| Impact | Support for public health genomics |
| Start Year | 2020 |
| Description | Collaboration with Public Health Wales |
| Organisation | Public Health Wales NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Provision of cloud computing capacity and software |
| Collaborator Contribution | 500k covering staff and hardware to provide microbial bioinformatics capacity to NHS Wales for 5 year |
| Impact | PHW gains compute capacity for performing microbial genomics analyses. |
| 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 | 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 |
| Description | Bacteriophage Genome Annotation Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A workshop was held at Warwick for a mixed audience of postgraduate students, post docs and PIs using the CLIMB infrastructure and know how to teach the fundamentals of genome annotation. More people signed up to have a CLIMB account after the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Balti and Bioinformatics 2016 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Each year one of the CLIMB fellows runs a bioinformatics course at Birmingham University with the aim of building a community forum for bioinformaticians to talk openly about problems they are encountering, and get the benefit of a diverse group of people in discussions. This has led to connections made that have extended beyond the meetings. |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | Basic Microbial Bioinformatics Workshop in Vietnam |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Elizabeth Batty and Phil Ashton ran a one-week workshop in Ho Chi Minh City, Vietnam, on March 25-29, with participants from the Oxford University units across south-east Asia. They aimed to teach the basics of microbial bioinformatics to complete beginners to bioinformatics, and everything ran on CLIMB. They had 32 participants from six countries. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Bath University HPC Symposium keynote |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk about the CLIMB project: how the cloud was built and the service that the CLIMB project provides for the academic community. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Bioinformatics workshop in Norwich |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | A bioinformatics workshop was run in Norwich using the MRC-CLIMB infrastructure. Attendants' excitement about the platform resulted in more users and more accesses to CLIMB from Norwich Research Institutions. |
| Year(s) Of Engagement Activity | 2017 |
| Description | CLIMB AT THE SMBE SATELLITE MEETING IN ASSAM, INDIA |
| 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 | MRC CLIMB project was presented at the SMBE Satellite meeting "Evolution of microbes in natural and experimental populations" . The meeting took took place in Assam (India) on 14th-16th December 2017, and was hosted by Dr. Siddartha Satapathy and Prof. Suvendra Ray (Tezpur University, Assam, India).During the MRC CLIMB session, Sam Sheppard and Sion Bayliss (both from University of Bath) introduced the MRC CLIMB project, described the infrastructure and detailed the Virtual Machine provisioning model. Sion Bayliss gave an introduction to methodologies used in the analysis of whole genome sequence data for microbial genomics. Dr. Harry Thorpe (University of Bath) provided a video walk-through of a data analysis project, from raw data to phylogenetic tree, by way of a user testimonial for CLIMB. MRC-CLIMB project was well welcomed, as researchers could recognize the power of cloud computing in bioinformatics analysis, the reduced cost it can represent for institutions, and the easy-to-use solutions that CLIMB implemented to facilitate the job for microbiologists. Manifestation of interest in how to build a CLIMB-like infrastructure is one of the best result of this activity. |
| Year(s) Of Engagement Activity | 2017 |
| Description | CLIMB WORKSHOP AT THE OXFORD UNIVERSITY CLINICAL RESEARCH UNIT, HO CHI MINH |
| 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 | A successful MRC CLIMB workshop in Vietnam introduced attendees to CLIMB and to work with their own virtual machine. Participants enthusiastically used CLIMB and its tools to assemble bacterial genomes, and the discussions after the meeting highlighted the importance of a CLIMB-like infrastructure to empower scientific research. New contacts and collaborations were created. |
| Year(s) Of Engagement Activity | 2017 |
| Description | CLIMB at the RCUK-WG in London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | On January 8, 2018, CLIMB was introduced at the third RCUK Cloud Working Group at the Francis Crick Institute in London. CLIMB adopted cloud solutions for microbial research, and the public well received the approach adopted by the Project. CLIMB approach saves time, money, and effort of researchers making scientific research faster and by providing researchers with tools they wouldn't have access to by their own. CLIMB supports almost 300 research groups in the UK. Despite the power of cloud, many biologists find that using cloud resources is quite complex to their analyses (e.g. installing software stacks). MRC-CLIMB ideated and created an appropriate infrastructure that allows researchers to rapidly and easily access preconfigured instances (designed on their needs), on demand. |
| Year(s) Of Engagement Activity | 2018 |
| Description | CLIMB launch event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | In July 2016 the CLIMB team held a launch event to introduce CLIMB (the project) and the bioinformatics service offered to UK academics. The audience was a mix from principal investigators to post graduate students. There was also participation from industrial partners and Public Health organisations. This two day event included a demonstration on how to sign up to and use CLIMB and also talks from researchers who have used CLIMB., talking about how CLIMB has helped their research. After the event the number of groups signed up to use CLIMB increased significantly with over 200 groups from institutes across the UK signed up. Individuals regularly communicate on the CLIMB forum with advice and support on how to use CLIMB. The service that CLIMB offers has enabled researchers in the UK to perform bioinformatics work that they were previously unable to do due to lack of compute resource and know how. It has also been a useful aid to the teaching of undergraduate students. Below is a quote from one of the CLIMB users: 'Yesterday's practical went wonderfully. We started the day with a big blob of raw data and ended up with 12 fully assembled Staphylococcus genomes and nearly 90 happy (we hope) undergrad students. We didn't have a single issue with any of the VMs. Massive thank you to you for setting this up! It is amazing you guys can offer this service to the community for free.' |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.climb.ac.uk/climb-launch/ |
| Description | CLIMB presented in Norway |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Mixed academic audience attended the National Consortium for Microbial Genomics Meeting (Norwegian Institute of Public Health, Lovisenberggata 8, Oslo, Norway) on December 7, 2017. The MRC-CLIMB infrastructure and the applications of the cloud in population genomics of bacterial pathogens in the Cloud received a warm welcome by the audience. The attendants reported a great interest in the infrastructure and recognized the value of the cloud system for microbial bioinformatics. |
| Year(s) Of Engagement Activity | 2017 |
| Description | DEVELOPING PIPELINES FOR BACTERIAL EVOLUTIONARY GENOMICS |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A workshop about the latest techniques for analysis of populations of bacterial genomes and how the CLIMB project can be used for this. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Dell-Intel understanding the challenges of HPC |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A talk to a mixed audience about the CLIMB team's experience in building a cloud system. |
| Year(s) Of Engagement Activity | 2016 |
| Description | EBAME seminar on "Emerging Bioinformatics Applications for Microbial Ecogenomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A talk to a mixed audience on how bioinformatics and the CLIMB infrastructure can be used for studying Microbial Ecogenomics. |
| Year(s) Of Engagement Activity | 2016 |
| Description | EVELIEN ADRIAENSSENS USED CLIMB FOR A WORKSHOP IN THE USA |
| 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 | CLIMB supports training activities organized by its users. In August 2019, CLIMB provided computational capacity for a bioinformatics workshop in Olympia, WA, USA, organized by Evelien Adriaenssens, from the Quadram Institute Bioscience (Norwich, UK) and Alejandro Reyes Muñoz from the Universidad de los Andes (Bogotá, Colombia). Here is Evelien's description of the workshop: "We used CLIMB for a bioinformatics workshop which was part of the Evergreen International Phage Biology Meeting at the Evergreen State College in Olympia, WA, USA (http://blogs.evergreen.edu/phage/about/meetings/2019-2/). The workshop was 4 hours long, repeated on the 3rd and 4th of August 2019. The topic of the workshop was "Viromics" or viral metagenomics, co-organised by Alejandro Reyes Muñoz from the Universidad de los Andes, Bogotá, Colombia, and supported as teaching assistants by three of his graduate students. We covered quality control, assembly, read mapping and exploration of the viral content of the metagenome using a mock published dataset, using state-of-the-art free software tools. Because of support by CLIMB, we were able to give all participants a hands-on experience and they were able to go through the whole workflow themselves. Feedback has been very positive and we are looking to organise this workshop again in two years at the next Evergreen Phage Meeting. Our guide document can be found here: https://tinyurl.com/evergreen-viromics". |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.climb.ac.uk/evelien-adriaenssens-used-climb-for-a-workshop-in-the-usa/ |
| 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 | Genome Science talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk about the CLIMB project: how the cloud was built and the service that the CLIMB project provides for the academic community. |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | Hackathon: CLIMB, Big Data and Public Health Microbiology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A hackathon was held at Warwick University with representatives from academia and Public Health England. The objective was to investigate how analysis of Big Data can help inform public health microbiology. The CLIMB infrastructure was used for the hackathon and the CLIMB fellows were involved in teaching. Since the hackathon there has been further collaboration with CLIMB and PHE. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.climb.ac.uk/hackathon-climb-big-data-and-public-health-microbiology/ |
| Description | Hackathon: Common Bacterial Genome Analyses |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A workshop to develop the bioinformatics community and to look at Common Bacterial Genome Analyses using the CLIMB infrastructure. Led to ongoing connections and more people singing up to use the CLIMB service. |
| Year(s) Of Engagement Activity | 2016 |
| 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 | Introduction to CLIMB for microbial bioinformatics - Leicester |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | The seminar was run by Andy Millard on February 16, 2018, at the University of Leicester. The primary goal was to introduce the system and to get the microbiologists at Leicester using the MRC-CLIMB infrastructure. The easy-to-use CLIMB, together with the softwares that it hosts, was well received and the access from Leicester to CLIMB increased since then. We stride at providing a tool that researchers can use for free, that gives them all the assistance they need in running the analyses and that satisfies the needs of microbiologists. Bioinformatics is a bottle-neck for microbial research, because microbiologists don't have the tools and the expertise to analyze and interpret their data. The MRC-CLIMB project aims at providing them with this expertise, and more microbiologists are using CLIMB after the seminar. Moreover, having more people using CLIMB helps us improving the system, as we want to meet the needs of researchers day by day. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Introduction to Microbial Bioinformatics Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | The Heriot-Watt University and MRC-CLIMB Project organized the workshop "Introduction to Microbial Bioinformatics", which featured talks from Peter C. Morris, Leena Kerr, Mark J. Pallen and Sion Bayliss. Hosts: Leena Kerr and Jennifer Pratscher - Heriot-Watt University, Edinburgh Event date and time: May 13, 2019 - from 1pm to 5pm Venue: Hertiot-Watt University Topics: -Metagenomics for diagnosis and discovery -Use of CLIMB -Microbial bioinformatics on CLIMB |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.climb.ac.uk/introduction-to-microbial-bioinformatics-workshop/ |
| Description | Introductory Workshop on Microbial Community Bioinformatics |
| 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 | A workshop was held at Warwick by some of the CLIMB team to teach Microbial bioinformatics to postgraduate students. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Invited Talk at University of Notre Dame about CLIMB |
| 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 about the CLIMB project: how the cloud was built and the service that the CLIMB project provides for the academic community. |
| Year(s) Of Engagement Activity | 2016 |
| Description | MRC CLIMB workshop at the MRC Unit, Gambia |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Some of the CLIMB team ran a introductory bioinformatics course using CLIMB at the MRC Gambia Unit. This builds on a long standing collaboration between researchers at Warwick and the MRC unit in the Gambia. The audience were a mix of students, postdocs and PIs, who had a greater understanding of bioinformatics and its importance after the course. |
| Year(s) Of Engagement Activity | 2017 |
| Description | MRC-CLIMB workshop in The Gambia, 2018 |
| 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 | A CLIMB delegation ran a bioinformatics workshop in The Gambia, in collaboration with the MRC Unit in Fajara (The Gambia), that hosted the course. One day (Jan.22) was dedicated to set up the course (computer performance test, virtual machine, workshop simulation), then 21 students attended the three-day workshop (January 23-25) and were introduced to bioinformatics, cloud computing, Illumina and Nanopore sequencing, microbial genomics and metagenomics, phylogenesis and phylogenetic trees. Aims of the course were defined with Gambian tutors, and the activities were planned accordingly. The success of the workshop is well documented in a survey filled by participants at the end of the course: quality of presentations, assistance during the workshop, relevance for their research were reported to be very good or excellent. The MRC-CLIMB Unit in The Gambia is interested in making it an annual appointment. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Microbial Data Analysis Hands-on Workshop |
| 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 | This Bioinformatics Hands-on Workshop on the MRC Cloud Infrastructure for Micorbial Bioinformatics was hosted by Leena Kerr and Jennifer Pratscher from the Heriot-Watt University (Edinburgh). Target: all those who wanted to gain insight into Linux command line, basics of genome assembly, and variant calling and tree building. The course consisted of theory and hands-on sessions. When and where: May 14th, 2019 at William Arrol Biolding (Heriot-Watt University, Edinburgh) |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.climb.ac.uk/microbial-data-analysis-workshop/ |
| Description | PHW Antimicrobial Stewardship meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Participation in a workshop about antimicrobials. Discussed how genome analysis using the CLIMB system could contribute to their development. Led to ongoing connections made and an increased interest in the CLIMB service. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Presentation at OpenStack Summit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | One of the CLIMB investigators presented at a compute infrastructure meeting in Texas. The audience were keen to hear and learn about the experience the CLIMB team had putting together a cloud using OpenStack (cloud computing software). Ongoing connections were made at the meeting. |
| Year(s) Of Engagement Activity | 2016 |
| 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 | Press release about our project infrastructure |
| 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 | Other audiences |
| Results and Impact | A press release in a publication read by both academia and industry about the CLIMB team's experience on building the CLIMB infrastructure and the service that it will provide to UK academia. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://edtechnology.co.uk/Article/he-collaborates-for-cloud-hpc-system |
| Description | Press release about our project infrastructure in an IT journal |
| 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 | Other audiences |
| Results and Impact | A press release in a publication read by both academia and industry about the CLIMB team's experience on building the CLIMB infrastructure and the service that it will provide to UK academia. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://primeurmagazine.com/weekly/AE-PR-11-15-25.html |
| Description | Pubic Health Wales Genomic Epidemiology workshop |
| 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 | A workshop including people from across Public Health Wales including epi and lab-based researchers, to discuss the implications and limitations of genomics for health protection. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Public Health Wales Genomics awareness sessions |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Public Health Wales Genomics awareness sessions including coverage of the software/computational challenges and a brief introduction to CLIMB. Led to further collaborations and more people signing up to use CLIMB. |
| Year(s) Of Engagement Activity | 2016 |
| Description | RedHat White Paper on CLIMB |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A talk to a mixed audience about the CLIMB team's experience in building a cloud system. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Strategies and Techniques for Analyzing Microbial Population Structure |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A talk for a mixed academic audience looking at how bioinformatics and the CLIMB infrastructure can be used for Strategies and Techniques for Analyzing Microbial Population Structure |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at BMFZ meeting in Düsseldorf: Genomics and metagenomics in medical microbiology: opportunities and challenges |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk to a mixed academic audience about the CLIMB infrastructure can be used for analysing genomics and metagenomics in medical microbiology. This led to requests for a CLIMB account. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.youtube.com/watch?v=aHY-LKvI0xs |
| Description | Talk at BioData World Congress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk to a mixed audience (academia and industry on the CLIMB team's experience on building the cloud infrastructure. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk at Doherty Institute, Melbourne, Australia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A talk about the CLIMB project: how the cloud was built and the service that the CLIMB project provides for the academic community. |
| Year(s) Of Engagement Activity | 2016 |
| 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 STFC Computing Insight UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk to a mixed audience (academia and industry on the CLIMB team's experience on building the cloud infrastructure. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.stfc.ac.uk/news-events-and-publications/events/computing-insight-uk-2015/ |
| Description | Talk at the Universities and Colleges Information Systems Association (UCISA) Infrastructure Group meeting in Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk and discussion about the CLIMB infrastructure. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk for Dell: Accelarating Understanding in HPC |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A talk to a mixed audience about the CLIMB team's experience in building a cloud system. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk: Applied Bioinformatics and Public Health |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A talk and discussion about how CLIMB can be used for bioinformatics, and how public health can use big data analysis to inform new policies. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk: RedHat Storage Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A talk to a mixed audience about the CLIMB team's experience in building a cloud system. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Teaching Bacterial Genomics as part of MRes Data Handling and Statistics module |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | CLIMB was used to teach undergraduate students in Cardiff about bacteria genomics |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | Teaching Introduction to Bioinformatics as part of integrated MBiol 3rd year project module |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | CLIMB was used to teach undergraduate students in Cardiff about bioinformatics |
| Year(s) Of Engagement Activity | 2016 |
| Description | Work with Public Health Wales to develop a genomics service based upon virtualisation approaches |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Work with Public Health Wales to develop a genomics service based upon virtualisation approaches using the CLIMB infrastructure |
| Year(s) Of Engagement Activity | 2016,2017 |
| Description | Workshop "ESTABLISHING MICROBIAL SEQUENCING AND BIOINFORMATICS CAPACITY IN CHALLENGING ENVIRONMENTS" |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | WHEN AND WHERE MRC Unit in The Gambia at LSHTM - Fajara January 14-17, 2020 Hosts and Organisers This workshop was coordinated by Mark Pallen (Quadram Institute Bioscience and MRC-CLIMB) and Martin Antonio (MRC Unit in The Gambia and LSHTM - The London School of Hygiene & Tropical Medicine). It was supported by the MRC Unit in The Gambia, the Quadram Institute Bioscience, the Univeristy of Surrey and the MRC-CLIMB Project. Rationale High-throughput sequencing is transforming microbiology across the world in academic and clinical settings. However, the capacity to perform microbial sequencing and bioinformatics is distributed unevenly, with many groups working in challenging environments finding it hard to get started or facing tough questions as to what to do locally and what to outsource. This workshop brought together microbiologists and bioinformaticians from across Europe, Asia and Africa to address these problems, while also exchanging practical know-how and building collaborative networks. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.climb.ac.uk/report-on-establishing-microbial-sequencing-and-bioinformatics-capacity-in-c... |
| Description | Workshop at the Society for Applied Microbiology |
| 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 | A bioinformatics workshop was run at the Society for Applied Microbiology during the 6th ECS research symposium. University of Westminster, 19 april 2017. After a CLIMB demo, attendants used the infrastructure to perform fast analysis. CLIMB gained new users during the symposium, and more new accounts were created after the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| 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 | training school on (un)targeted metagenome analysis |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A workshop for a mixed academic audience looking at how bioinformatics and the CLIMB infrastructure can be used for studying metagenomics |
| Year(s) Of Engagement Activity | 2016 |