MICA: UK MEDical BIOinformatics partnership - aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO).

Lead Research Organisation: Imperial College London
Department Name: School of Public Health

Abstract

This proposal brings together a group of leading multidisciplinary teams in medical, chemical, metabolic, statistical and computational sciences from across Imperial College London (ICL, lead institution) and its partners. These include the Institute of Cancer Research, the European Molecular Biology Laboratory-European Bioinformatics Institute, the Universities of Oxford, Swansea and Nottingham, and the MRC Clinical Sciences Centre and MRC Human Nutrition Research Centre, supported by strong partnerships and collaborative links with industry, the NHS and the National Institute for Health Research funded Biomedical Research Centres and Units. The proposal seeks support to build a DEDICATED INFRASTRUCTURE in data storage, aggregation, analysis and visualisation of diverse types of biomedical data. These come from standard clinical sources through to different types of information including from genetic analysis, and metabolic information, that help us to define patients or people studied in the general population using a holistic "systems medicine" framework. The GLOBAL AIM is to make major advances in understanding the causes and reasons for disease progression of common human diseases such as cancer, cardiovascular disease, respiratory disease and metabolic disorders such as type 2 diabetes and obesity. In this way we aim to create new disease diagnostics and prognostics aimed at the individual patient ("stratified medicine") through innovations in medical bioinformatics with powerful computing capability. The programme will create unprecedented capacity to i) DEVELOP powerful new approaches for computation and analysis of large-scale, complex, multi-source medical data; ii) INTEGRATE information linking multiple different types of biological information from analysis of blood and urine samples (e.g., metabolic, genomic, analysis of the microbial genome) to different diseases, disease progression and outcomes; hence to iii) help UNDERSTAND the causes and mechanisms of disease and improve individual disease classification for better patient treatments and safety; also to iv) TRANSFORM the training of the biomedical researchers of the future through creation of a seamless interdisciplinary environment spanning biomedicine, physical sciences, computing and engineering. In particular we will capitalise on computational expertise that has led to the development of a partnership in medical information infrastructure and service between universities and the pharmaceutical industry called eTRIKS, and related software platforms such as tranSMART, an "open source" solution for managing data and research knowledge in clinical studies. We also have world-leading expertise in metabolic "fingerprinting" and systems medicine approaches manifested in the MRC-NIHR National Phenome Centre located at ICL, and underpinned by excellence in genomics, computational sciences and advanced data modelling and visualisation. This project has a very broad collaboration with industrial sectors including major pharmaceutical companies, instrument vendors, IT and informatics companies. Our project covers the complete healthcare envelope of data generating activity and analysis from the level of basic measurement sciences through to the understanding of gene-environment interactions and disease mechanisms to the creation of knowledge systems for better clinical decision making based on detailed knowledge of individual patient biology. This application is strengthened by the decision of ICL to establish a major interdisciplinary centre for 'big data' at the new Imperial West campus, ensuring sustainability over the longer term. The project aims to deliver top class science, a robust informatics platform and in-depth scientific data and knowledge to contribute to the state of the art of UK and international medical research.

Technical Summary

UK MED-BIO brings together a multidisciplinary team in medical and computing science, statistical analysis, metabolic phenotyping and medical bioinformatics across Imperial College London (ICL, lead institution), Institute of Cancer Research, European Molecular Biology Laboratory-European Bioinformatics Institute, Universities of Oxford, Swansea and Nottingham, MRC Clinical Sciences Centre and MRC Human Nutrition Research - supported by strong industrial partnerships and collaborations. The aim is to bring together the necessary patient data, new omics technologies, computing and other resources, with dedicated infrastructure in data management, storage, integration, visualisation and analysis, to enable major advances in understanding the aetiopathogenesis of chronic human diseases. We have powerful world-leading expertise in metabolic phenotyping through the MRC-NIHR National Phenome Centre at ICL, and in innovative software infrastructure solutions through our leadership position in developing tranSMART and eTRIKS. We will provide unprecedented capacity to i) combine lifestyle/socio-demographic information, clinical data, and disease phenotypes from well characterised patient and population cohorts, with multi-omic information from analysis of linked biological samples; ii) develop powerful new approaches to integration/analysis of such large-scale, complex, multi-source medical data; hence iii) create new knowledge on disease aetiology, underlying biochemical pathways and mechanisms, leading to improved patient stratification, prevention and treatments; iv) transform the training/development of medical bioinformatics future leaders by providing a seamless interdisciplinary environment, bringing together researchers from biomedicine, physical sciences, computing and engineering. This application is strengthened by ICL's decision to establish a major interdisciplinary 'big data' centre at the Imperial West campus, ensuring sustainability over the long term.

Planned Impact

The UK MED-BIO project will provide important benefits in both the personalised and public healthcare arenas, associated medical research environments and the pharma/healthcare industry. Specific benefits include deeper understanding of gene-exposome interactions that underpin disease risks and mechanisms. This information can be used to inform future healthcare policy and help identify new potential therapeutic targets for a range of common diseases. Positive impacts include development of new monitoring and stratification models to augment clinical decision-making during the patient journey. Impacts can be summarised as:

1) Scientific and Clinical: The project has a clear focus on elucidating the aetiopathogenesis of chronic human disease, including cancer, cardio- metabolic and respiratory disease. By developing new systems medicine approaches linking multi-omics datasets (e.g., genomic/epigenomic, metagenomic, transcriptomic and metabolic) to disease phenotypes, progression and outcomes in patient and population cohorts, the project aims to make major scientific and clinical contributions to patient stratification and the development of new precision medicine approaches in real healthcare environments.

2) Methodological and Infrastructure: The computational methods developed for integrated analysis of multimodal data streams with large-scale data processing capacity will provide new tools in medical bioinformatics research and complex systems data and model visualisation. The further development and enhancement of platform technologies underlying the UK MED-BIO infrastructure, such as tranSMART and eTRIKS, in which ICL researchers have played a key developmental role, will enhance the capabilities of the medical bioinformatics community in general.

3) Knowledge: UK MED-BIO supports a new open science paradigm by dedicating specific resources to build a dissemination hub. We will work closely with EMBL-EBI to curate new large-scale research data for public access (e.g. from the MRC-NIHR National Phenome Centre) and to explore EMBL-EBI's public cloud dissemination mechanisms. Through our collaboration with content vendors, e.g. Thomson Reuters, the accuracy of knowledge in published medical databases will be validated.

4) Training: A key objective is to enhance the training of next generation medical informatics scientists by creation of a seamless interdisciplinary environment spanning biomedicine, physical sciences, computing and engineering. The training will be aligned with the ELIXIR-UK Node training activities. The new Imperial International Phenome Training Centre also offers a comprehensive multilevel training programme in omics modeling expressed through a series of courses in computational and systems medicine. We will explore the effective use of the dissemination hub to create a national informatics resource for biomedical research, coupled with focused training, for maximising dissemination and impacts.

5) Organisational: The continued major investments in biomedical research in multiple world class medical research facilities in London requires an advanced informatics infrastructure and networking mechanism across the distributed resources to form a virtual/scalable research environment. this can then be linked further to other national and international networks of medical bioinformatic activity.

Publications

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Andersson KME (2018) Inflammation in the hippocampus affects IGF1 receptor signaling and contributes to neurological sequelae in rheumatoid arthritis. in Proceedings of the National Academy of Sciences of the United States of America

 
Description Answering questions for parliamentary briefing document on the microbiome and human health
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
URL https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0574
 
Description E-infrastructure leadership council
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Impact Professor Robert Glen provided input from his experience of high performance computers and e-infrastructure in a report on entreprenerial academic policies as part of the e-infrastructure leadership council chaired by the Minister of Science and Technology. Professor Glen's contribution has had a big influence on high performance computers, networking and relevant skills training for UK leaderships and entrepreneurial advancements in these areas.
URL https://www.gov.uk/government/groups/e-infrastructure-leadership-council
 
Description MRC Discussion Workshop on Creating a National Health & Medical Bioinformatics - participation/contribution
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description MRC Framework for the Development, Design and Analysis of Stratified Medicine Research
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Invited to provide comments on draft - 'MRC Framework for the Development, Design and Analysis of Stratified Medicine Research' Dec 2015.
 
Description MRC Strategic Meeting on "Challenges in Health and Biomedical Informatics in the UK"- participation/contribution
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description Member of Office of Strategic Coordination for Health Research (OSCHR) sub Board on Health Informatics
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Panel member for BBSRC Tools and Resources Development Fund
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description Policy documents on Stratified Medicine Infrastructure and the second Farr Institute
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Role as Imperial College London AHSC Director of Information Governance
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a advisory committee
Impact In progress: positive impact on functions of HSCIC Data Governance Framework procedures to improve access for academic researchers to clinical data; improved streamlining of data processing via active feedback to senior HSCIC management.
 
Description deNBI - the German National Network for Bioinformatics Infrastructures - evaluation panel member for round two
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description participation in working group - BBSRC Careers and development for non-faculty staff; also production of recommendations to BBSRC Council
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Alzheimer's Research UK Pilot Project
Amount £46,518 (GBP)
Funding ID ARUK-PPG2016B-6 
Organisation Alzheimer's Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2016 
End 08/2018
 
Description BRC/ITMAT Core Research Informatics Infrastructure
Amount £97,395 (GBP)
Organisation National Institute for Health Research 
Department NIHR Imperial Biomedical Research Centre
Sector Academic/University
Country United Kingdom
Start 10/2015 
End 09/2017
 
Description EMBRACE: Engineering, Physical, Natural Sciences and Medicine: Bridging Research in Antimicrobial resistance: Collaboration and Exchange
Amount £10,000 (GBP)
Organisation Embrace UK 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2016 
End 07/2017
 
Description Health Data Research UK (HDR-UK) substantive site award to Imperial College London as part of pan-London consortium
Amount £6,900,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 02/2023
 
Description MRC-PHE Centre for Environment and Health, PPE/PPI Small Grants Scheme
Amount £230 (GBP)
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 11/2017 
End 02/2018
 
Description NIHR Imperial Biomedical Research Centre (BRC) Institute for Translational Medicine and Therapeutics (ITMAT) Developing Capacity
Amount £24,823 (GBP)
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 10/2017 
End 09/2018
 
Description PhenoMeNal H2020
Amount € 8,810,922 (EUR)
Funding ID H2020 -EINFRA-1-2014 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2018
 
Description UKRI Innovation/Rutherford Fund Fellowships (2 awarded)
Amount £652,556 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 02/2021
 
Title System for sharing Consistent versioned public reference databases across UK Med-Bio and other Imperial HPC compute resources 
Description Many types of analysis require access to reference databases and curated datasets which frequently are large, requiring considerable download times and disk utilisation, and typically require indexing using a method appropriate for the desired analysis method. The indexing process itself will also frequently take over 12 hours for a mammalian genome. Frequently, the whole process can take 2-3 days, and is generally carried out by every researcher needing to carry out such analysis requiring reference datasets. To help reduce the overhead associated with obtaining and preparing reference datasets, we have established a centralised collection of reference datasets which are available to all bio-medical researchers across the college. These are accessible on UK Med-Bio, HPC and BDSG systems, and remotely via NFS and HTTP. Databases are automatically updated weekly where appropriate. The following datasets are currently available: Illumina iGenomes (reference database indexed for BWA, bowtie and bowtie2 searches; fasta format chromosome files; annotations as e.g. GTF files). A full list of the datasets available through iGenomes is available at http://support.illumina.com/sequencing/sequencing_software/igenome.html. Of these, we currently hold: Human GRCh37 (Ensembl annotation) Human GRCh38 (NCBI annotation) Mouse GRCm38 (Ensembl annotation) C. elegans WS220 (Ensembl annotation) E. coli K12 DH10B (Ensembl annotation) Human genome resources: Additional reference datasets for related to the Human genome 1000 genomes variant calls GATK resource bundle (including dbSNP, 1000 genomes, hapmap, gold standard indels preformatted for use with the Genome Analysis ToolKit (GATK) Kegg pathway databases - available to registered users only Blast databases: NCBI NR NCBI NT RefSeq Genomic Refseq RNA Refseq protein Uniprot Swissprot Uniprot Trembl 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact reduced replication of mainteinance effort 
 
Title Batch effect exerts a bigger influence on experimental animal urinary metabolome and gut microbiota than uremia 
Description Looking at effects of medically induced chronic kidney disease in rats on microbiome and metabolome. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact Publication has just been submitted for review. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525754/
 
Title Determination of effects of propionate on gene expression in human cerebromicrovascular endothelial cell line hCMEC/D3 
Description The experiment was designed to look at the effect (on gene expression) of exposing human cerebromicrovascular endothelial cell line hCMEC/D3 to propionate (3 micromolar) for 24 h, to determine if circulating metabolites have the potential to affect integrity of the blood-brain barrier. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact First study to show propionate at physiologically relevant concentration has a protective effect on blood-brain barrier in vitro. 
URL https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5686/
 
Title Effect of Down Syndrome genotype on mouse microbiome 
Description Effect of Down Syndrome genotype on mouse microbiome. Metagenomes generated from mouse faecal samples. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publications in preparation. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA473429
 
Title Effect of Fmr1 knockout on mouse microbiome 
Description Faecal metagenomes generated from Fmr1 knockout and wild-type mice. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publications in preparation. 
URL http://www.ncbi.nlm.nih.gov/bioproject/473224
 
Title Effect of GOS on the faecal microbiota in vitro 
Description 16S rRNA gene sequence data generated for in vitro fermentation vessels in presence and absence of prebiotic. 25 samples including negative control. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Useful information on influence of conditions in in vitro fermentation systems in presence and absence of prebiotic. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA472974
 
Title Effect of GOS on the in vitro faecal microbiota (6 metagenomes) 
Description Metagenomes derived from in vitro fermentation vessels after treatment with prebiotic. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Valuable information on species of bacteria likely to be involved in use of prebiotics in the human gut. 
URL http://www.ncbi.nlm.nih.gov/bioproject/472963
 
Title Effect of bariatric surgery on the faecal metagenome 
Description Clinical study looking at the effect of bariatric surgery on the faecal metagenome. Study carried out by Dr Nicholas Penney as part of clinical PhD. I processed and analysed the samples. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publications (including clinical PhD thesis) in preparation. BioProject ID PRJNA473348. 
URL http://www.ncbi.nlm.nih.gov/bioproject/473348
 
Title Effect of enhanced environment on mouse microbiome 
Description Faecal metagenomes generated from control mice and mice kept in enriched environment. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publications in preparation. 
URL http://www.ncbi.nlm.nih.gov/bioproject/473208
 
Title Effect of subinhibitory concentration of ampicillin on human gut microbiota in vitro 
Description In vitro fermentation systems used to examine effect of sub-inhibitory concentration of ampicillin on human faecal microbiota. Metagenomes generated from samples taken before and during antibiotic treatment. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publication in preparation. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA473225
 
Title Effects of gut-derived trimethylamines on an in vitro model of the blood-brain barrier - accession number E-MTAB-6662 
Description The experiment was designed to look at the effect (on gene expression) of exposing human cerebromicrovascular endothelial cell line hCMEC/D3 to trimethylamine (0.4 micromolar) or trimethylamine N-oxide (40 micromolar) for 24 h, to determine if circulating metabolites have the potential to affect integrity of the blood-brain barrier. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Manuscript in preparation to describe effects of TMA and TMAO on blood-brain barrier. 
 
Title FLORINASH WGS human gut microbiome metagenomics dataset - fastq 
Description Data sets arising from the EU FLORINASH project. WGS human gut microbiome datasets. Raw metagenomic sequence data (with human-associated reads removed) have been deposited under study accession number PRJEB14215 (secondary accession number ERP015847). 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Part of the dataset for a paper in press - Hoyles et al (2108) Molecular Phenomics and Metagenomics of Hepatic Steatosis in Non Diabetic Obese Women. Nature Medicine 
URL https://www.ebi.ac.uk/ena
 
Title FLORINASH mouse hepatic steatosis study gut microbiome16s rRNA reads 
Description In this FLORINASH study faecal microbiota from control and steatotic patients (n = 3 per group) was transferred to C57BL6 mice (n=8 per donor) and followed for 15 days before evaluating hepatic steatosis. Data are deposited in European Nucleotide Archive SRA under study accession number PRJEB24891. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This dataset is associated with a manuscript in press - Hoyles et al (2018) Molecular Phenomics and Metagenomics of Hepatic Steatosis in Non Diabetic Obese Women. Nature Medicine. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB24891
 
Title Florinash hepatic transcriptomes 
Description Florinash examined the role on the gut microbiota in NAFLD. Metagenomic, proteomic, metabolomic and transcriptomic data were integrated to give provide a systems biology approach to disease-associated studies. Liver biopsies were obtained from patients undergoing bariatric surgery; one was used to diagnose NAFLD, the other was used to examine the host transcriptome in NAFLD. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Improved understanding of the transcriptome associated with NAFLD. 
URL https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4856/
 
Title Microbiome of ME-CFS - UK cohort 
Description Faecal microbiome of ME-CFS patients and controls. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Detailed analysis of microbiome of ME-CFS patients and controls. Generated in collaboration with the Quadram Institute. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA478719
 
Title Microbiota of adult and aged mice 
Description Characterizing the difference in faecal microbiota of adult and aged mice, then looking at effects of FMT on microbiota and cognitive function. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Publication in preparation. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA524024/
 
Title Recovery of lactose-positive Enterobacteriaceae from preterm neonates 
Description Whole-genome sequences generated from bacteria isolated from faecal microbiota of preterm infants. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Preprint to be uploaded to bioRxiv once complete. 
 
Description A systems biology approach to understanding cerebrovascular damage in diabetic kidney disease 
Organisation Queen Mary University of London
Department William Harvey Research Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise on gut microbiota and its metabolites. Expertise in relation to neuroinflammation. Bioinformatics support.
Collaborator Contribution Animal facilities. Expertise in relation to diabetic kidney disease.
Impact Multi-disciplinary: computational biology, clinical studies, in vitro studies, neuroscience, immunology, microbiome, cognitive function, metabolomics Preparation of funding applications and manuscripts in progress
Start Year 2017
 
Description Airwave collaboration with CIPHER 
Organisation Swansea University
Department Centre for Improvement in Population Health through E-records Research (CIPHER)
Country United Kingdom 
Sector Public 
PI Contribution Airwave study participant data and database and expertise in secure database management
Collaborator Contribution Secure data linkage and expertise in e-records for health data
Impact ongoing collaboration
Start Year 2018
 
Description Airwave collaboration with DPUK - Dementia Platforms UK 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Collection and provision of Airwave study data. Airwave data collected by the study team is being uploaded into the DPUK data portal so that it is available to other researchers. Collaboration with Prof Gallacher, PI of DPUK on pilot use of data including CSR pilot, collaborative grant applications and publications.
Collaborator Contribution DPUK portal coordination and data access procedures
Impact ongoing collaboration
Start Year 2018
 
Description Airwave collaboration with DPUK and SAIL 
Organisation Swansea University
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of Airwave study data and expertise in database management and health data linkage
Collaborator Contribution SAIL Databank is being used as a means of secure data processing and storage for study data
Impact ongoing collaboration
Start Year 2018
 
Description Bacteriophages as alternatives to antibiotics 
Organisation Charing Cross Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts
Collaborator Contribution Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science
Impact Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters)
Start Year 2015
 
Description Bacteriophages as alternatives to antibiotics 
Organisation King's College London
Country United Kingdom 
Sector Academic/University 
PI Contribution supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts
Collaborator Contribution Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science
Impact Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters)
Start Year 2015
 
Description Bacteriophages as alternatives to antibiotics 
Organisation University of Reading
Department Department of Food and Nutritional Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts
Collaborator Contribution Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science
Impact Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters)
Start Year 2015
 
Description Bacteriophages as alternatives to antibiotics 
Organisation University of Westminster
Department Biomedical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts
Collaborator Contribution Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science
Impact Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters)
Start Year 2015
 
Description CFS/ME and the microbiome 
Organisation Quadram Institute Bioscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics (16S rRNA gene sequence analysis, metagenomics, development of virome pipeline); expertise in gut microbiome and virome, particularly in relation to isolation and characterization of phages; co-supervision of two PhD students
Collaborator Contribution UEA: expertise in virology, immunology and pathology, two PhD students QUADRAM: expertise in gut microbiome, immunology, animal facilities, two PhD students co-supervised with UEA
Impact Multi-disciplinary: computational biology, basic laboratory science, immunology, microbiology, biochemistry Invited review submitted to Alimentary Pharmacology and Therapeutics (see publications) Virome pipeline being built by associated student for addition to existing microbiome pipeline (SCAMP).
Start Year 2016
 
Description CFS/ME and the microbiome 
Organisation University of East Anglia
Department Norwich Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics (16S rRNA gene sequence analysis, metagenomics, development of virome pipeline); expertise in gut microbiome and virome, particularly in relation to isolation and characterization of phages; co-supervision of two PhD students
Collaborator Contribution UEA: expertise in virology, immunology and pathology, two PhD students QUADRAM: expertise in gut microbiome, immunology, animal facilities, two PhD students co-supervised with UEA
Impact Multi-disciplinary: computational biology, basic laboratory science, immunology, microbiology, biochemistry Invited review submitted to Alimentary Pharmacology and Therapeutics (see publications) Virome pipeline being built by associated student for addition to existing microbiome pipeline (SCAMP).
Start Year 2016
 
Description Collaboration with Farr and Crick Institute 
Organisation Farr Institute of Health Informatics Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration with Farr and Crick Institute
Collaborator Contribution -
Impact -
Start Year 2016
 
Description Collaboration with Farr and Crick Institute 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Collaboration with Farr and Crick Institute
Collaborator Contribution -
Impact -
Start Year 2016
 
Description Collaboration with University of Cambridge - High Performance Computing 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Professor Robert Glen is collaborating with University of Cambridge on a few calculation projects.
Collaborator Contribution Use of their High Performance Computers
Impact No outputs or outcomes to date
Start Year 2015
 
Description Coriobacteriia of the human gut microbiota 
Organisation University of Reading
Department School of Chemistry, Food and Pharmacy
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics, specific expertise in coriobacteria
Collaborator Contribution DNA for sequencing, anaerobic microbiology, phenotyping
Impact Manuscripts in preparation.
Start Year 2016
 
Description DDN storage user group 
Organisation Farr Institute of Health Informatics Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Collaborator Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Impact disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored.
Start Year 2016
 
Description DDN storage user group 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Collaborator Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Impact disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored.
Start Year 2016
 
Description DDN storage user group 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Collaborator Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Impact disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored.
Start Year 2016
 
Description DDN storage user group 
Organisation University College London
Department UCL Cancer Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Collaborator Contribution Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata.
Impact disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored.
Start Year 2016
 
Description Development and Application of Novel Analytical Methods for Metabolite Structure Elucidation 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave cohort.
Collaborator Contribution Optimisation of spectral data processing methods; metabolite identification; integration of complementary spectral data
Impact No output yet. Multi-disciplinary: Analytical chemistry; Chemometrics / multivariate statistical analysis.
Start Year 2016
 
Description EMBRACE pump-priming 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application
Collaborator Contribution Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment
Impact Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding)
Start Year 2016
 
Description EMBRACE pump-priming 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application
Collaborator Contribution Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment
Impact Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding)
Start Year 2016
 
Description EMBRACE pump-priming 
Organisation University of Reading
Department Department of Meteorology
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application
Collaborator Contribution Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment
Impact Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding)
Start Year 2016
 
Description Establishing a link between the gut-brain axis and Alzheimer's disease 
Organisation Quadram Institute Bioscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Computational biology Expertise in relation to gut microbiome and gut-derived microbial metabolites Expertise in computational chemistry and brain chemistry Preparation of manuscripts and funding applications
Collaborator Contribution (QUODRAM) expertise in immunology and gut microbiome, animal facilities; preparation of manuscripts and funding applications (QMUL) expertise in neuroscience, inflammation, in vitro work; preparation of manuscripts and funding applications
Impact Multi-disciplinary: in vitro cell biology, transcriptomics, bioinformatics, animal experiments Successful funding application to Alzheimer's Research UK Abstract accepted for Alzheimer's Research UK conference 2017 Two abstracts accepted for Alzheimer's Research UK conference 2018 Poster presentation at Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading Oral presentation by McArthur at 13th World Congress on Inflammation (2017) One draft publication in preparation One preprint submitted to bioRxiv (currently under review after revision for Microbiome) McArthur, Hoyles and Glen have applied to Alzheimer's Research UK for a major grant award McArthur and Hoyles preparing funding applications to QMUL, and BBSRC McArthur and Hoyles invited to contribute to strategic plan for Quadram Institute
Start Year 2016
 
Description Establishing a link between the gut-brain axis and Alzheimer's disease 
Organisation Queen Mary University of London
Department Centre for Translational Medicine and Therapeutics
Country United Kingdom 
Sector Academic/University 
PI Contribution Computational biology Expertise in relation to gut microbiome and gut-derived microbial metabolites Expertise in computational chemistry and brain chemistry Preparation of manuscripts and funding applications
Collaborator Contribution (QUODRAM) expertise in immunology and gut microbiome, animal facilities; preparation of manuscripts and funding applications (QMUL) expertise in neuroscience, inflammation, in vitro work; preparation of manuscripts and funding applications
Impact Multi-disciplinary: in vitro cell biology, transcriptomics, bioinformatics, animal experiments Successful funding application to Alzheimer's Research UK Abstract accepted for Alzheimer's Research UK conference 2017 Two abstracts accepted for Alzheimer's Research UK conference 2018 Poster presentation at Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading Oral presentation by McArthur at 13th World Congress on Inflammation (2017) One draft publication in preparation One preprint submitted to bioRxiv (currently under review after revision for Microbiome) McArthur, Hoyles and Glen have applied to Alzheimer's Research UK for a major grant award McArthur and Hoyles preparing funding applications to QMUL, and BBSRC McArthur and Hoyles invited to contribute to strategic plan for Quadram Institute
Start Year 2016
 
Description Farr@CIPHER/MED-BIO Partnership 
Organisation Swansea University
Department Centre for Improvement in Population Health through E-records Research (CIPHER)
Country United Kingdom 
Sector Public 
PI Contribution The Airwave cohort - currently making use of UK Med-Bio computing technology - will seek to link their study data to the health records held in the SAIL Databank, a project which will both be attributed to CIPHER and Airwave, and also has been made possible by collaborating with Dementias Platform UK (DPUK), also led by Swansea University with regard to data sharing and linkage. UK Med-Bio have also suggested the install of their bespoke software in Swansea for the future manipulation of the multi-omics Airwave data.
Collaborator Contribution farr@CIPHER are facilitating access for the Airwave Health Monitoring Study to linked health data currently held by the SAIL (Secure Anonymised Information Linkage) Databank at Swansea University. The Centre will have one one-year FTE post for analysis based on this with the Airwave cohort. CIPHER (via links to other organisations such as the SAIL Databank, Dementias Platform UK (DPUK) and Cloud Infrastructure for Microbial Bioinformatics (CLIMB)) will also be avaialble to host UK Med-Bio software and infrastructure for both the proposed linkage project and future collaborative work.
Impact No major outcomes yet - work is ongoing yet but future impact could be associated with cultural (breaking barriers in data linkage) and policy and public services (linking health records to gain deeper understanding of participants' health))
Start Year 2016
 
Description Genome, metabolome and environmental-wide associations affecting blood pressure 
Organisation Imperial College London
Department School of Public Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave, COMBI-BIO and UK Biobank cohorts.
Collaborator Contribution Imperial: Genetic epidemiological analyses; biostatistics, epidemiological analyses; bioinformatics; metabolomics QMUL: Genetic epidemiological analyses; bioinformatics
Impact Paper by Warren et al.; methods paper by Karaman et al. Multi-disciplinary: Clinical Genetics; Bioinformatics; Epidemiology; Biostatistics; Analytical Chemistry.
Start Year 2016
 
Description Genome, metabolome and environmental-wide associations affecting blood pressure 
Organisation Queen Mary University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave, COMBI-BIO and UK Biobank cohorts.
Collaborator Contribution Imperial: Genetic epidemiological analyses; biostatistics, epidemiological analyses; bioinformatics; metabolomics QMUL: Genetic epidemiological analyses; bioinformatics
Impact Paper by Warren et al.; methods paper by Karaman et al. Multi-disciplinary: Clinical Genetics; Bioinformatics; Epidemiology; Biostatistics; Analytical Chemistry.
Start Year 2016
 
Description Gut-brain axis in cognitive impairment and ageing 
Organisation University of East Anglia
Department Biomedical Research Centre
Country Unknown 
Sector Academic/University 
PI Contribution Expertise on gut-derived microbial metabolites. Expertise with respect to neuroinflammation. Ongoing bioinformatics support.
Collaborator Contribution Access to extensive collection of patient samples. Networking opportunities with relevant researchers. Access to germ-free animals and imaging facilities.
Impact Multi-disciplinary: microbiology, biochemistry, immunology, systems biology, neuroscience, cognition. Introduction to a range of researchers working in the ageing/dementia field. Invitation to contribute to Quadram Institute research programme for the next five years. Two unsuccessful funding applications.
Start Year 2016
 
Description Influence of microbial metabolites cognitive impairment associated with chronic kidney disease 
Organisation Queen Mary University of London
Department William Harvey Research Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in gut microbiota and its metabolites. Metabolomics - analyses of samples and interpretation of data. Ongoing bioinformatics support for 16S rRNA gene sequencing work related to gut microbiota.
Collaborator Contribution Animal facilities and brain samples. Clinical expertise relating to chronic disease.
Impact Multi-disciplinary: microbiology, biochemistry, immunology, systems biology, neuroscience, renal biology. Networking opportunities and increased access to animal facilities. Several manuscripts in preparation. First manuscript to be submitted February 2019.
Start Year 2016
 
Description Influence of the gut microbiome on cognitive function in ageing 
Organisation University of East Anglia
Department Norwich Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics support for analyses of data generated from faecal microbial transplant experiments.
Collaborator Contribution Animal models of cognitive function, metabolomics
Impact Manuscript in preparation. Also investigating potential of incorporating blood-brain barrier work into the collaboration.
Start Year 2018
 
Description MED-BIO : Astra Zeneca 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution We are discussing linking in AZ collaboration to other projects related to MED-BIO
Collaborator Contribution AZ contacts are bringing expertise in large-scale data and sample handling with a focus on technological solutions.
Impact ongoing collaboration
Start Year 2015
 
Description MED-BIO : Thomson Reuters 
Organisation Thomson Reuters
Country United States 
Sector Private 
PI Contribution We are discussing linking other potential projects into the MED-BIO consortium
Collaborator Contribution TR is bringing industrial network contacts and leverage to the project and some new ideas on for example large scale dataset integration, multi-omic data analysis, and functional pathway scoring.
Impact ongoing collaboration
Start Year 2015
 
Description Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. 
Organisation Queen Mary University of London
Department Wolfson Institute of Preventive Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications
Collaborator Contribution St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts
Impact Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017
Start Year 2015
 
Description Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. 
Organisation St Mark's Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications
Collaborator Contribution St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts
Impact Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017
Start Year 2015
 
Description Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. 
Organisation University of Reading
Department Department of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications
Collaborator Contribution St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts
Impact Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017
Start Year 2015
 
Description Metabolic profiling of cardio-vascular disease GWAS hits 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts.
Collaborator Contribution Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology
Impact Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology
Start Year 2016
 
Description Metabolic profiling of cardio-vascular disease GWAS hits 
Organisation Virginia Tech
Country United States 
Sector Academic/University 
PI Contribution Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts.
Collaborator Contribution Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology
Impact Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology
Start Year 2016
 
Description Metabolic profiling of cardio-vascular disease GWAS hits 
Organisation Wake Forest University
Country United States 
Sector Academic/University 
PI Contribution Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts.
Collaborator Contribution Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology
Impact Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology
Start Year 2016
 
Description Metagenomics to study the bariatric surgery-associated microbiome 
Organisation Imperial College London
Department Department of Surgery and Cancer
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics associated with the microbiome; expertise in gut microbiome.
Collaborator Contribution Bariatric surgery, clinical data, gut microbiome
Impact Multi-disciplinary: computational biology, clinical studies, metabonome, immunology, microbiome; cohort studies; surgical interventions. Manuscript(s) in preparation.
Start Year 2017
 
Description Metagenomics to study the colorectal cancer mucosal microbiome 
Organisation Imperial College London
Department Department of Surgery and Cancer
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics associated with the microbiome; expertise in gut microbiome.
Collaborator Contribution Clinical samples and data, expertise in colorectal cancer, expertise in cancer-associated gut microbiome
Impact Multi-disciplinary: computational biology, clinical studies, metabonome, immunology, microbiome; surgical studies. Abstract submitted to Digestive Disease Week (DDW) 2018.
Start Year 2017
 
Description Microbial metabolites cause expression of brain-homing markers on dendritic cells 
Organisation St Mark's Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution Provided expertise on gut microbiota and microbial metabolites to colleagues working in the Antigen Presentation Research Group, Imperial College London. Ongoing bioinformatic support for in vitro and in vivo transcriptome studies. Expertise with respect to neuroinflammation.
Collaborator Contribution Provided expertise in immunology and working with dendritic cells.
Impact Multi-disciplinary: microbiology, biochemistry, systems biology, immunology, in vitro cell culture. Output: abstract submitted on dendritic cell homing to British Society of Immunology Congress 2017.
Start Year 2017
 
Description Microbiome-associated metabolites and brain imaging 
Organisation University College London
Department Centre for Advanced Bioimaging
Country United Kingdom 
Sector Academic/University 
PI Contribution Immunohistochemistry, cell line work, range of metabolites to test.
Collaborator Contribution MSc student, access to imaging facilities and animal models. Collaboration resulted from a discussion at the ARUK conference in London 2018.
Impact MSc student project ongoing, expected publications.
Start Year 2018
 
Description Molecular epidemiology of cardio-metabolic phenotypes 
Organisation Imperial College London
Department School of Public Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Facilitation of analysis and storage of the LOLIPOP cohort: provision of access to high-performance computing resources; data storage, with expertise and support.
Collaborator Contribution Bioinformatics: GWAS, EWAS, MWAS, TWAS on data from the LOLIPOP study.
Impact Multiple papers in high impact journals, grant applications and presentations at meetings. Multi-disciplinary: computational biology, clinical studies, metabolomics, genomics, cardiology, cohort studies.
Start Year 2016
 
Description PhenoMeNal 
Organisation European Commission
Department Horizon 2020
Country European Union (EU) 
Sector Public 
PI Contribution PhenoMeNal - Electronic Infrastructure for Metabolomics, with Partners in 7 EU countries. H2020 funded (EUR 8M). MedBIO contribution: testing scalability of infrastructure and tools; computing with sensitive clinical data test case; local installation test case.
Collaborator Contribution produced shareable workflows for metabolomics analyses
Impact Interdisciplinary: computer science - chemistry - medicine. FULL Phenomenal Outputs detailed at http://phenomenal-h2020.eu/home/ .Main outputs from our collaboration are 'computing with sensitive clinical data' test case; 'workflow local installation' test case, including production of multiple trainining videos and deployment on YouTube.
Start Year 2015
 
Description Quadram - infant microbiota 
Organisation Quadram Institute Bioscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Bioinformatics, expertise is gut microbiome, cultivation
Collaborator Contribution PhD student to conduct data analyses, immunology, infant samples
Impact Manuscripts in preparation. Will be submitted as pre-prints and to journals in due course. MinION manuscript available as a preprint already.
Start Year 2016
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation Erasmus University Rotterdam
Department Department of Epidemiology
Country Netherlands 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation Farr Institute of Health Informatics Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation Harvard University
Department Department of Epidemiology
Country United States 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation Northwestern University
Department Feinberg School of Medicine
Country United States 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation University of Ioannina
Department Department of Hygiene and Epidemiology
Country Greece 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease 
Organisation University of Texas
Department Health Science Center at Houston
Country United States 
Sector Academic/University 
PI Contribution Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods
Collaborator Contribution Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis.
Impact continuing collaboration
Start Year 2018
 
Description The association of socio-economic status and the metabolome 
Organisation Imperial College London
Department Department of Physics
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave cohort.
Collaborator Contribution Analysis of influence of social and behavioral predictors on the metabolome.
Impact Multi-disciplinary: social science; epidemiology; analytical chemistry; statistics and bioinfomatics; molecular biology.
Start Year 2017
 
Description Use of C. elegans as a model to study gut-brain axis 
Organisation Queen Mary University of London
Department School of Biological and Chemical Science QMUL
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in gut microbiota, gut-derived microbial metabolites and neuroinflammation.
Collaborator Contribution C. elegans model, and facilities to run experiments related to ageing and the brain-gut axis.
Impact Multi-disciplinary: microbiology, immunohistochemistry, immunology, neurobiology. Pilot work initiated to pursue research interests.
Start Year 2017
 
Title BugBuilder 
Description BugBuilder is a pipeline for hands-free assembly and analysis of microbial genome sequences. It produces outputs suitable either for direct submission to sequence databases or for use in downstream finishing processes. It is configurable to work with most command-line assembly and scaffolding tools which are selectable at run-time, and supports all common sequence types used in microbial genome assembly.The BugBuilder workflow incorporates sequence pre-processing (quality assessment, read trimming, downsampling), contig assembly, scaffold assembly, annotation and generation of visualisations. Following assembly, validation processes can attempt to identify sequence misassemblies to facilitate genome finishing efforts.BugBuilder is intended to allow high-throughput automated analysis of microbial genome sequences, in addition to allow scientists without specialist knowledge to carry out assembly and annotation tasks. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact Originally designed to support a specific project, as part of MED-Bio infrastructure it has undergone extensive revision and enhancement to improve functionality and support additional analyses. BugBuilder has already been used on a variety of microbial genome projects to date for multiple collaborators and is available for download as a virtual machine. Its use has enabled researchers with little previous bioinformatics knowledge to undertake complex (previously very time-consuming) analyses effectively, reproducibly and rapidly. Data arising from its use has led to a number of publications including Florea M, Reeve B, Abbott J, Freemont PS, Ellis Tet al., 2016, Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582., Scientific Reports, Vol: 6, ISSN: 2045-2322. Software source and virual machine image are freely available via the URL below. 
URL http://www.imperial.ac.uk/bioinformatics-data-science-group/resources/software/bugbuilder/
 
Title Development of Galaxy workflow pipeline for analyzing metabonomics data 
Description Galaxy workflow pipeline for analyzing metabonomics data 3 different pipelines - 1 LC-MS (nearly done), 1 NMR, 1 GC-MS being developed 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact This workflow is linked to Metabolights which is a database for Metabolomics experiments and derived information developed by EMBL-EBI. 
 
Title Metagenomics softwares 
Description Suite of metagenomics softwares in development 
Type Of Technology Software 
Year Produced 2016 
Impact No notable impacts to report yet 
 
Title SCAMP - Scaleable Metagenomics Pipeline 
Description SCAMP is a pipeline for assembly and analysis of metagenomes, allowing scaleble automated and reproducible analyses of whole microbiomes and other microbiomes. The system incorporates a number of third-party pre-published programs in a modular framework. It combines a number of well-known tools to provide a comprehensive analysis incorporating partitioning samples into reads derived from different phyla, relative species abundance determination, metagenome assembly, gene prediction, clustering of predicted genes, cluster abundance determination and gene characterisation. The software orchestrates the data management of the analysis process forming a loosely-coupled pipeline allowing different stages to be moved to appropriate computational resources. For example, some stages are embarrasingly parallel and can be optimally run on a compute cluster, whereas other components (i.e. metagenome assembly, gene clustering) require access to large amounts of memory which are typically found on standalone servers. The pipeline has been validated by reanalysing the data of Qin et al (2014, Nature 513, 59-64), and has been demonstrated to be capable of reproducing the results published in this study, while improving the contig assembly such that a number of additional genes were identified. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The pipeline has already been used to analyse a large human gut microbiome dataset arising from an EU project - FLORINASH (The role of intestinal microflora in non-alcoholic fatty liver disease (NAFLD). These results form part of a paper currently in revision for Nature (Hoyles, Abbott et al). The pipeline can be used to analyse other microbiomes and allows fast processing of laarge datasets with reproducible documented procedures, parameters etc. This will also allow direct comparison of datasets arising from multiple sources. The pipeline is currently being run on Med-Bio hardware, but is being msde ready for distribution and a paper on the methodology is in preparation (Abbott, Hoyles, Butcher et al). 
URL http://www.imperial.ac.uk/bioinformatics-data-science-group/resources/software/scamp/
 
Title mzML2ISA & nmrML2ISA 
Description mzML2ISA & nmrML2ISA are Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Documetation is available from http://2isa.readthedocs.io/en/latest/ 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. Theses tools would be used and integrated within EMBL-EBI MetaboLights repository. 
URL https://github.com/ISA-tools
 
Description Chair of Bio-HPC special interest area workshop at HPC summer school Imperial College september 2016 and 2017 (sarah Butcher) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Organised speakers for a half day workshop with discussion sessions on using high performance computing for bio-medical applications. Ensouraged discussion on shared experiences, and areas of joint interest iparticularly in the areas of scheduling and access to software. Started a mailing list to encourage sharing of information and expertise in bio-HPC use.
Year(s) Of Engagement Activity 2016,2017
 
Description Invited talk - Workshop on 'Data Science Challenges and Opportunities in Translational Medicine' (Sarah Butcher) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Sarah Butcher gave an invited talk on the MED-Bio project as part of a one day workshop on Data Science Challenges and Opportunities in Translational Medicine'. The workshop included discussion sessions on the challenges of working with large multi-disciplinary datasets with input from international speakers. The talk led to requests for new collaborations with 2 separate research groups.
Year(s) Of Engagement Activity 2017
URL https://saphir746.github.io/ITMAT-DSG-2017/
 
Description invited talk (Reza Salek) at The CHARME of standardisation in life sciences workshop 21-22 June, Warsaw 
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 gave invited tal on "Data sharing, standards and workflows in metabolomics; towards reproducibility in Metabolomics" at ELIXIR workshop in Warsaw, Poland. CHARME brings together various projects and collaborations in standardisation of life science data and facilitates information exchange, together with Elixir facilitators. CHARME will develop a framework to harmonise standards and formats in systems biology data. It will also act as a mediator between scientific standardisation efforts and relevant standardisation bodies and committees. The presented talk represented current staet of the art in data standards and sharing for metbolomics data.
Year(s) Of Engagement Activity 2016
URL https://www.elixir-europe.org/news/charme-standardisation-life-sciences-21-22-june-warsaw
 
Description workshop facilitator for Turing House CoderDojo, coding club held once a term for children aged 7-11 (Lesley Hoyles) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact CoderDojo (https://coderdojo.com) Children got an introduction into coding in Scratch, python, arduino and html, and went away with worksheets to continue their learning at home in their own time. Children were enthusiastic about coding and wanted to learn more.
Year(s) Of Engagement Activity 2016,2017,2018
URL https://turinghousecoderdojo.wordpress.com/
 
Description -Lesley Hoyles - Invited talk - "Dietary methylamines, the gut microbiota and host health" Technical University of Munich, Freising, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave invited talk. Talk sparked many questions from and discussions with postgraduate students and academics present. Future collaborative work was discussed.
Year(s) Of Engagement Activity 2016
 
Description 12th Invest in ME Research International ME Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Patients, carers and/or patient groups
Results and Impact Invited to attend meeting to discuss integrated systems biology approaches for ME/CFS research.
Year(s) Of Engagement Activity 2017
URL http://www.investinme.eu/iimec12.shtml
 
Description A New Facet to the Gut-Brain Axis: Microbe-derived Metabolites and the Blood-Brain Barrier - King's College London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Invited talk to facilitate dissemination of research findings and networking.
Year(s) Of Engagement Activity 2018
 
Description A New Facet to the Gut-Brain Axis: Microbe-derived Metabolites and the Blood-Brain Barrier - University of Roehampton 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Invited talk to facilitate dissemination of research and networking.
Year(s) Of Engagement Activity 2018
 
Description Academia/Industry Careers & Networking event - ARUK Oxford network 
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 Opportunity to present our work to researchers associated with the ARUK Oxford network. Prompted interesting discussions with other researchers, and led to providing bioinformatics support for one of the University of Reading students attending.
Year(s) Of Engagement Activity 2017
 
Description Antonio Berlanga - congress session chair, immunogenomics session, National Congress of Immunology, Mexican Society of Immunology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This event led to another invitation in November 2016 to give a talk and continue the collaboration. As a result, working together on several research projects and planning a 2nd Genomics of Inflammation Workshop and Course (the first one was in 2015, Newton Fund). Applying for further funds for research and capacity building.
Year(s) Of Engagement Activity 2016
 
Description Antonio Berlanga - invited talk "Clinical applications of cellular and molecular inflammation", XXV National Forum on Health Research, Mexican Institute of Social Security 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited to establish an international collaboration in Genomics of Immunology.
Year(s) Of Engagement Activity 2016
 
Description Antonio Berlanga - workshop "Introduction to computational methods in biology: unix, command line and R", XXII National Immunology Conference, Mexico 
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 We had an anonymous pre- and post- workshop survey which showed that:
- 90% (of 11) participants thought the course met their expectations;
- 82% replied that the quality of the instructors was excellent and the rest replied that it was very good;
- All participants said they were motivated to continue learning.
- A workshop participant (PhD student) is hoping to visit Imperial this summer to collaborate on a research project and continue developing data analysis skills.
Year(s) Of Engagement Activity 2016
 
Description Are bacteria good for your brain? Linking gut microbes, blood and the brain's defences - LGBT+ STEMinar 2019, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presenting work to a lay audience.
Year(s) Of Engagement Activity 2019
URL http://lgbtsteminar2019.iopconfs.org/programme
 
Description BBSRC 'careers for non-faculty research staff' 
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 Invited discussion group member - BBSRC 'careers for non-faculty research staff' led by Michael Ball - outcome led to creation and distribution of UK-wide questionnaire for non-faculty research staff and ongoing discussion on policy
Year(s) Of Engagement Activity 2015
 
Description BBSRC China Partnering award (BB/M027635/1), CUDDEL - meeting UK 23-25 November 2016 workshop (Reza Salek) 
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 Assisted with Workshops on hands on standards and data curation for metabolomics for participants in China partnering award. 16 participants.
Year(s) Of Engagement Activity 2016
 
Description BBSRC Workshop to discuss Non-Faculty Researchers Careers and Recognition - (Sarah Butcher) 
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 Sarah Butcher was an invited attendee to BBSRC Workshop to discuss Non-Faculty Researchers Careers and Recognition in Manchester March 2017. The workshop was convened to discuss the outcomes of an earlier survey run by the BBSRC (which Dr Butcher helped to design), to collect information on careers of non-faculty staff. The workshop brought together representatives from BBSRC, other RCUK funders, and non-faculty staff from a variety of backgrounds to discuss ways of improving career progression, metrics and methods of recognition. Following the meeting Dr Butcher was invited by BBSRC to join a small working group following up on actions arising from the meeting.
Year(s) Of Engagement Activity 2017
URL http://www.bbsrc.ac.uk/news/events/2017/1703-workshop-non-faculty-researcher-careers/
 
Description Big Data: Innovation in analysis, usability and curation' workshop Southampton 
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 Invited speaker for 'Big Data: Innovation in analysis, usability and curation' workshop Southampton 2015.
Year(s) Of Engagement Activity 2015
 
Description Bugs In Your Guts - personal blog on gut microbiology and the gut microbiota 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Introducing the science associated with the gut microbiota and gut microbiology.
Year(s) Of Engagement Activity 2016,2017,2018
URL http://bugs-in-your-guts.com
 
Description Combined CHARME, EMBnet and NETTAB Workshop, Reproducibility, standards and SOP in bioinformatics, November 24-26 2016 Rome (Reza Salek) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation on metabolomics data standards to workshop partcipants.
Year(s) Of Engagement Activity 2016
 
Description EMBL-EBI, EMBO Practical Course on Metabolomics bioinformatics for life scientists, 13- 17 February 2016 (Reza Salek) 
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 teaching and training - hands on metabolomics data analysis course for researhers and postgraduate students. Participants learned how to produce and analyse metabolomics data; also learnt about public metbolomics resources such as Metabolights database.
Year(s) Of Engagement Activity 2016
 
Description EMN Webinar Dr. Reza Salek (March 24, 2016) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact British Metabolomics society - public webinar. "How close are we to metabolomics reproducibility? Data sharing, data standards and workflows for metabolomics " still available on the British Metabolomics Society web-site.
Year(s) Of Engagement Activity 2016
URL http://metabolomicssociety.org/resources/videos/88-videos/218-2016-emn-webinars-public#
 
Description EU Project Informatics Alignment Workshop (April 2015) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact The aims and objectives of the workshop were to:
1) Understand your project research objectives.
2) Understand the informatics needs to realise your research objectives.
3) Collect project informatics use cases.
4) Uncover synergies and propose collaborations between partners.
5) Report on the impact of project needs on the future eTRIKS / tranSMART roadmap.
Year(s) Of Engagement Activity 2015
URL https://www.eventbrite.co.uk/e/eu-project-informatics-alignment-workshop-etriksimi-registration-1627...
 
Description Ealing Primary Science Fair - The Ellen Wilkinson School for Girls, year 5 and 6 students, STEMNET Ambassador (Lesley Hoyles) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Assessed students' science projects, and awarded prizes for best biology, chemistry, physics and overall projects. Children were excited to show what they had done and were enthusiastic about future work.
Year(s) Of Engagement Activity 2016
 
Description Effects of gut-derived methylamines on the blood-brain barrier - ARUK Conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presented at ARUK Conference, Aberdeen March 2017 on our preliminary work. Invited to contribute review based on our work/ideas to Geriatrics (submission due November 2017).
Year(s) Of Engagement Activity 2017
 
Description Effects of gut-derived trimethylamines on the blood-brain barrier, ARUK meeting London 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented work on effects of dietary methylamines on blood-brain barrier integrity.
Year(s) Of Engagement Activity 2018
 
Description Five-week after-school gut health science club, Primrose Hill Primary School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact The presentations and activities we gave to the children over the first three weeks of the club improved their understanding of how the digestive system works, and encouraged lots of interesting questions and discussions. The children were able to present all they had learnt to their parents. All the parents reported the children had really benefitted from attending the club. We were particularly pleased to hear that some of the girls were know considering becoming scientists when they are older.
Year(s) Of Engagement Activity 2018
URL https://wwwf.imperial.ac.uk/blog/gut-health-science-club/
 
Description Gave a talk on recent metagenomic work at "Integrating knowledge and approaches across microbiomes..." 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The aim of this one-day meeting, jointly hosted by the British Ecological Society, the Microbiology Society and the Society for Applied Microbiology, was to discuss approaches and findings from across a broad suite of environments and hosts.
Year(s) Of Engagement Activity 2018
URL https://www.eventbrite.co.uk/e/integrating-knowledge-and-approaches-across-microbiomes-from-plants-t...
 
Description Gut microbial dysfunction and its influence on the brain: Microbe-derived metabolites and the blood-brain barrier - University of Westminster 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited talk to disseminate research findings and facilitate networking.
Year(s) Of Engagement Activity 2018
 
Description High Level Biology/Chemistry speaker Burlington Danes Academy, STEMNET Ambassador (Lesley Hoyles) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact keynote speaker for STEMNET schools meeting- promoting science. Talk was on the importance of the gut microbiome to human health and disease. Talk sparked lots of questions and discussion afterwards, as students didn't appreciate how important the gut microbiota is to host health. Considerable interest from students led to the visit being written-up by one of the students for the school newsletter.
Year(s) Of Engagement Activity 2017
 
Description Hosting International Phenome Centre meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact The MEDBIO working group hosts the international phenome centre meeting twice a year in 2015 and 2016 with policy makers, industry and academics participating in this meeting. The meetings have resulted in Singapore, Canada and China setting up phenome centres.
Year(s) Of Engagement Activity 2015,2016
 
Description INVEST IN ME RESEARCH BIOMEDICAL RESEARCH COLLOQUIUM - 2017 
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 Invited to contribute to discussions on ME/CFS research because of my areas of research expertise.
Year(s) Of Engagement Activity 2017
URL http://www.investinme.eu/brmec%20colloquiums.shtml
 
Description ISBE (Infrastructure Systems Biology Europe) and UK MED BIO - workshop on High Performance Computing in Health Research 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Attendee on behalf of ISBE (Infrastructure Systems Biology Europe) and UK Med-BIO - workshop on High Performance Computing in Health Research (Brussels, October 2014) organised by the European Commission's Directorates-General for Research and Innovation and for Communications Networks, Content and Technology. The overall objective of this was to identify current and future health research needs for HPC and to explore mechanisms of addressing them through co-operation of relevant stakeholders.
Year(s) Of Engagement Activity 2014
 
Description Imperial College NIHR BRC Digital Health workshop - chair of session on Maximising capabilities in digital health technologies 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invitation to chair session to debate capacity building in digital health technologies to build on existing strengths and increase collaboration between academic researchers and clinicians and focus activities towards implementation of leading edge technologies with health applications.
Year(s) Of Engagement Activity 2019
 
Description Integrated systems biology to study non-alcoholic fatty liver disease in obese women - Gut Microbiota for Health World Summit 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited talk allowed me to present my work to a wide audience, and to network.
Year(s) Of Engagement Activity 2017
 
Description Integrated systems biology to study non-alcoholic fatty liver disease in obese women - International Scientific Association for Probiotics and Prebiotics Students and Fellows Association Annual Meeting 
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 Florinash work given at the ISAPP meeting to introduce concept of integrated microbiome research to industry figures. Led to me being invited to contribute to workshop, and to contributing to (in preparation) workshop write-up.
Year(s) Of Engagement Activity 2017
URL http://isappscience.org/2017-annual-meeting/
 
Description Integrated systems biology to study non-alcoholic fatty liver disease in obese women - The 11th London Surgical Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Introducing integrated systems biology to surgeons, to demonstrate how clinical, host and microbiome data can allow us to identify disease biomarkers. Won prize for best poster.
Year(s) Of Engagement Activity 2017
 
Description Integrated systems biology to study non-alcoholic fatty liver disease in obese women - Translational Bioinformatics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Intended purpose was to present our integrated systems biology approach to characterizing host-microbiome interactions. No impacts have arisen from activity, as title of conference was misleading.
Year(s) Of Engagement Activity 2017
 
Description Invited talk - Data Science Meeting, Imperial College London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Talk was intended to share information on the kind of work I'm doing with other members of the College.
Year(s) Of Engagement Activity 2017
 
Description Invited talk - Institute of Biomedical Science Congress, Birmingham 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Intended purpose - To stimulate thinking. Talk encouraged lots of interesting questions and discussions from health professionals who knew little to nothing about gut microbiome research.
Year(s) Of Engagement Activity 2017
URL http://www.meetbirmingham.com/organise-an-event/meet-birmingham-conference-guide-2017-18/
 
Description Invited talk - University of Warwick 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Purpose of talk was to share information. The talk encouraged lots of interesting questions and discussions from researchers who knew little to nothing about gut microbiome research in the context of liver disease.
Year(s) Of Engagement Activity 2017
 
Description Invited to give talk at IMER BRMEC8 RESEARCH MEETING LONDON, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave an invited talk to colloquium attendees - Integrated systems biology to understand the role of the gut microbiome in health and disease. Intended to introduce new concepts to ME-CFS research, and to highlight the work I've been doing during my Fellowship. Had many fruitful conversations, and identified potential funding streams.
Year(s) Of Engagement Activity 2018
URL http://www.investinme.eu/BRMEC%20Colloquiums.shtml#brmec8
 
Description LGBT STEM 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Improving LGBT visibility in Science, Technology, Engineering and Mathematics
Year(s) Of Engagement Activity 2017
URL https://lgbtstem.wordpress.com/2017/08/17/an-interview-with-lesley-hoyles/
 
Description Lesley Hoyles - Invited speaker - "Integrated systems biology to study non-alcoholic fatty liver disease in obese women", Middlesex University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact invited speaker for departmental seminar. Sparked interesting questions and discussions among students and academics present in the audience. Also raised interest in potential collaborative work with colleagues in microbiology department.
Year(s) Of Engagement Activity 2017
 
Description Lesley Hoyles - invited talk "Use of next-generation sequencing in microbiome studies", University of Westminster 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact invited talk to MSc students. Students were surprised how important the microbiome was to host health, and had many questions about how to characterize the microbiome. Some of the students w.ere interested in pursuing PhD studies in microbiome research.
Year(s) Of Engagement Activity 2016
 
Description London Farr Institute "Developing a Trusted Research Environment for London - a Meeting for Frontiers" 
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 Workshop discussion to explore the idea of creating a national safe haven for clinical data accessible to academic researchers.
Year(s) Of Engagement Activity 2015
 
Description MRC-HSCIC joint discussion meeting on HSCIC Data Services Platform 
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 Invited attendee on behalf of UK MED-BIO: MRC-HSCIC joint discussion meeting on HSCIC Data Services Platform (Des 2015), 1st and 2nd Farr - Medical Bioinformatics - ADRN - Jisc Annual Technical Leads Meeting (Jan 2015, 2016)- outputs were feeding requirements on e-infrastructure to support medical informatics to RCUK national eInfrastructure group.
Year(s) Of Engagement Activity 2015,2016
 
Description MetaboInterview - Reza salek interview for 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Published in partnership between TMIC and the Metabolomics Society Issue 60 - August 2016 his issue featured an interview with Reza Salek.
This section features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story.
Year(s) Of Engagement Activity 2016
URL http://www.metabonews.ca/Aug2016/MetaboNews_Aug2016.htm#MetaboInterviews
 
Description Microbe-derived metabolites, the blood-brain barrier - Nottingham Trent University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited talk to facilitate dissemination of research findings and networking, to meet up with collaborators and discuss future research direction.
Year(s) Of Engagement Activity 2019
 
Description Microbiome-host interactions: protective effects of propionate upon the blood-brain barrier - Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Make food industry figures aware of the link between diet, the microbiome and cognitive function.
Year(s) Of Engagement Activity 2018
 
Description New Scientist Live - Royal Society of Biology Ask A Biologist (Lesley Hoyles) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Keynote/Invited Speaker, answering questions posed by the generl public on "How do gut bacteria keep us healthy?". Members of the public were surprised how important gut bacteria were to their health and wellbeing.
Year(s) Of Engagement Activity 2016
URL https://live.newscientist.com/
 
Description Organising Hackathon workshop with workflow4metabolomics consortium 
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 EBI is organising a Hackathon workshop in March 2016, inviting anyone who works on galaxy platform to learn from each other and to discuss what's missing for tools development. The outcome of which would be collaborative work
Year(s) Of Engagement Activity 2016
 
Description Paul Elliott presentation to Imperial College London HPC Summer School on UK MED-BIO: A new platform for the analysis of omic data 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This was a presentation to the annual High Performance Computing Summer School at Imperial run by the HPC Group. It was particularly aimed at raising the profile of the project to highlight the resource that we are developing and excite interest in its use across the College and with collaborators. So we were aiming to reach out to HPC users in particular.
Year(s) Of Engagement Activity 2015
 
Description Press release and quote for Warren et al. Nature Genetics paper publication 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release accompanied publication of paper by Helen Warren et al. in Nature Genetics on "Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk: The UK Biobank Cardio-metabolic Traits Consortium Blood Pressure Working Group."
P Elliott quoted ""Ultimately, blood pressure in the general UK population is too high, and we encourage everyone to maintain healthy lifestyles by eating properly and exercising enough, as this will reduce the risk of all sorts of diseases. However, our new findings may help doctors to identify earlier those who are most at risk of high blood pressure in mid-life and intervene to prevent that occurring."
Year(s) Of Engagement Activity 2017
 
Description Propionate has protective and anti-inflammatory effects on the blood-brain barrier - ARUK conference 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Allowed us to present our work on the interaction of the microbiome with host systems, and implications for neurodegenerative diseases.
Year(s) Of Engagement Activity 2018
 
Description Propionate has protective and anti-inflammatory effects on the blood-brain barrier - Dementia Symposium Imperial College London 
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 Dementia symposium held at Imperial College London to launch the Dementia Research Institute. Novel work presented to researchers who had not considered the gut microbiota and its metabolites could influence the blood-brain barrier and potentially contribute to health/disease.
Year(s) Of Engagement Activity 2017
 
Description Propionate has protective and anti-inflammatory effects on the blood-brain barrier - Exploring Human Host-Microbiome Interactions in Health and Disease 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented our work on propionate, which is available as a preprint and has been submitted for publication. Novel work not seen by members of the research community before. Led to many questions, and much interest in our work.
Year(s) Of Engagement Activity 2017
URL https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=637
 
Description ROIS International Workshop on Data Centric Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited speaker - ROIS (Research Organisation of Information and Systems) International Workshop on Data Centric Science, Feb 2015, Tokyo Japan, representing the Data Science Institute Imperial College. Also 1 day closed meeting with ROIS Institutes (together with Prof Yi-Ke Guo and Dr Martin Siegert, Grantham Institute) to discuss future collaborations and strengthening links with ROIS and Imperial through the Data Science Institute, in the areas of data-intensive sciences.
Year(s) Of Engagement Activity 2016
 
Description Regulatory effects of gut-derived methylamines on blood-brain barrier integrity - Exploring Human Host-Microbiome Interactions in Health & Disease 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Offered paper chosen for oral presentation to share our findings on dietary methylamines and the blood-brain barrier.
Year(s) Of Engagement Activity 2018
URL https://coursesandconferences.wellcomegenomecampus.org/our-events/exploring-human-host-microbiome-in...
 
Description Reza Salek - Talk Glasgow Poly-omics 10-11 August 2016, Metabolomics data analysis reproducibility: data sharing, data standards and workflows for metabolomics. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact gave talk -Metabolomics data analysis reproducibility: data sharing, data standards and workflows for metabolomics. to ~30 attendees.
Year(s) Of Engagement Activity 2016
 
Description Reza Salek - US NIHMetabolomics Common Funds, UCSD, San Diego, USA, 24-26 February 2016 - talk "Metabolomics Data sharing, MetaboLights and data standards." 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact gave presentation on Metabolomics Data sharing, MetaboLights and data standards to audiene of approx 60.
Year(s) Of Engagement Activity 2016
 
Description Sarah Butcher - key note speaker and co-presenter at European Bioinformatics Institute training workshop - Bioinformatics for Core Facilities - June 2017 
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 This training workshop - supported by the Core Faculities for the Life Sciences (CTLS) organisation, is aimed at aspiring, new and experienced managers of bioinformatics core facilities, or other facilities that support their users to analyse and interpret large biomolecular data sets. The course aims to introduce new ways of working, foster collaborations, as well as offer training support from experienced facility managers. As well as providing a keynote talk, I led several discussion areas, and also provided a seminar and discussion session for the back-to-back course Bioinformatics for PIs. Both courses were welll received, and are being run again in June 2018. In addition, an EMBO training grant has been submitted to enable the core facility course to be run in Turkey in 2019.
Year(s) Of Engagement Activity 2017,2018
URL https://www.ebi.ac.uk/training/events/2017/bioinformatics-core-facility-managers
 
Description Science and Engineering South Consortium - Research data management workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact Invited speaker for Science and Engineering South Consortium - Research data management workshop (March 2015, Imperial)
Year(s) Of Engagement Activity 2015
 
Description Silvia Ottovani - poster at Cambridge Pancreatic Cancer Symposium 2017, Cambridge, United Kingdom 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact presented poster - TGF-ß regulating microRNAs as modulators of epithelial-to-mesenchymal transition, metastasis and stemness in pancreatic ductal adenocarcinoma.
Year(s) Of Engagement Activity 2017
 
Description Silvia Ottovani - poster at Non-coding RNAs in cancer and development. London, United Kingdom. May 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact presented a poster for discussion at the meeting Non-coding RNAs in cancer and development. London, United Kingdom. Poster title - TGF-ß regulating microRNAs as modulators of epithelial-to-mesenchymal transition, metastasis and stemness in pancreatic ductal adenocarcinoma.
Year(s) Of Engagement Activity 2017
 
Description Silvia Ottovani - poster presentation at meeting - Noncoding RNAs: Form, Function, Physiology. Keystone, Colorado, USA, Feb 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave poster presentation at international meeting - Noncoding RNAs: Form, Function, Physiology. Keystone, Colorado, USA. Poster title - TGF-ß induces miR-100 and miR-125b but blocks let-7a through co-regulation of lncRNA MIR100HG and LIN28B to mediate tumourigenesis in pancreatic ductal adenocarcinoma. The work has been written up for publication and is in review at present.
Year(s) Of Engagement Activity 2018
 
Description UK Microbiome workshop - London 10 July 2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Innovate UK and the Microbiology Society organized a one-day workshop to facilitate academic-industrial engagement. "Identifying Cross Sectoral Challenges and Needs for Effective UK Microbiome Related Technology Exploitation"
Year(s) Of Engagement Activity 2018
 
Description UK's Largest Careers Speed Networking Event for Young People, Lord's Cricket Ground (Lesley Hoyles) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact TeamLondon workshop facilitator for careers workshops aimed at school children. Schoolchildren came away with an overview of what jobs in a number of different sectors involve, and were made aware of opportunities they did not know were available to them for future careers -particularly in the sciences sector.
Students left with increased awareness of careers available to them in science and other industries.
Year(s) Of Engagement Activity 2017
 
Description Workshop facilitator - Regent High School Early Summer Fair 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Helped run school-organized activity for primary school children, arranged via STEMNET. Getting the students more interested in science using a fun activity.
Year(s) Of Engagement Activity 2017
 
Description Workshop on the e-Infrastructure part of the National Data Infrastructure 
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 Attendee on behalf of UK-MED BIO - 'Workshop on the e-Infrastructure part of the National Data Infrastructure' organised by the DiRAC National E-Infrastructure Project Directors Group Dec. 2014 (representing requirements for bio-medical compute and data storage) - output was feeding information on requirements to National E-Infrastructure Project Directors Group
Year(s) Of Engagement Activity 2014
 
Description Workshop to advise researchers associated with the Indian microbiome project 
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 Part of invited panel of international researchers invited to attend workshop in Pune, India to advise the Indian microbiome project.
Year(s) Of Engagement Activity 2018
 
Description eTRIKS-UBIOPRED-Clinical-Data-Analysis-Training - Professor Yi-KE Guo 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Professor Yi-Ke Guo conducted a series of web and face-to-face training to UbioPred scientists on clinical data analysis, AZ data anlysts and tranSMART users at NOVARTIS (UK), scientists (bioinformaticians, biologists, clinicians) at University of Southampton, GSK scientists etc.
Year(s) Of Engagement Activity 2015,2016
 
Description webinar Dr Reza Salek - Metabolomics: molecules of life, an introduction. 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The webinar gives an introductory tour of metabolomics. This webinar helps users to understand what metabolomics is and how it can be used to inform biological research. It also introduces the basics of the analytical technologies and data analysis methods commonly used in metabolomics Thwe webinar is available from the EBI training site.
Year(s) Of Engagement Activity 2016
URL http://www.ebi.ac.uk/training/online/course/metabolomics-molecules-life-introduction?platform=hootsu...