Delivering ELIXIR-UK

Lead Research Organisation: University of Birmingham
Department Name: Sch of Biosciences

Abstract

ELIXIR is a project that is designed to construct and operate a sustainable infrastructure for biological information in Europe. Owing to the dearth of individuals who can take advantage of large biological data sets, we have decided to focus the UK's ELIXIR node on training.

This is the century of biology, and genomics, transcriptomics, proteomics and metabolomics ('omics and bioinformatics) lie at its heart. The computer is an essential tool and now drives many critical aspects of the scientific process hence scientists need to know how to gain most advantage from it. Despite the central role of computing in science today:

- Most research scientists are ill-equipped to take advantage of the data 'bonanza' that is emanating from new technologies. Critical training needs across the community are, broadly, in the analysis and the interpretation of genome-scale data of many types, including next generation sequencing (NGS) data. Genomics is the area of greatest training need as it lies at the intersection of many fast-moving research disciplines.

- Many infrastructure technologists (career bioinformaticians) are ill-equipped to offer scalable, sustainable solutions for managing and interpreting data arising from this flood of technological advances. Critical training needs are in techniques and practices for data management, integration, compute and software, tools, services and standards.

The ELIXIR-UK Core Organisations are: the Universities of Oxford, Manchester, Liverpool, Birmingham, and Edinburgh; the NERC Environmental Omics Synthesis Centre; the Wellcome Trust Sanger Institute; the Genome Analysis Centre; and, University College London. Additional participating organisations are: the Software Sustainability Institute UK; the Hartree Centre; and the University of Dundee. Other organisations (UK and ELIXIR-wide) will be incorporated to provision training.

Technical Summary

The Node's training mission will be delivered in four ways:

(a) The organisation of training through ten cooperating Training Sectors where UK skills are strong, training needs have been identified, and training capabilities already exist. Each sector is led by established researchers in their fields, and many co-operations between the Sector Leads already exist. Each Sector Lead is responsible for: (i) representing the sector at initial Training the Trainers (TTT) events; (ii) organisation of an initial workshop that performs a training gap analysis for the sector, and (iii) fund-raising for resources that aim to plug these training gaps.

(b) These training gaps will also be filled by trainers' skills being developed by workshops that exchange ideas and best practice among sectors. ELIXIR-UK will be particularly supportive of training delivered at the
interface between different sectors. Existing training resources will be collated and new training materials
developed and disseminated at every opportunity.

(c) The development of a pilot Training e-Support Service platform that will seek, among other things, to offer the crucial means of registering and discovering training materials, face-to-face training opportunities
and training-relevant resources, and will progressively deliver forms of training online. A feasibility study will
be undertaken on whether pipelines could be developed to permit ELIXIR trainers to disseminate their own
training content on-line, whilst maintaining a separate copy in their home training institution.

(d) Development, management and monitoring of outcomes of the training activities through three posts who (i) support the Training Sector Leads, (ii) coordinate the redefinition of of training agendas with UK scientists, industry, grant-giving bodies and other ELIXIR Nodes, and (iii) will foster, mentor and support the community of trainings, across all sectors, in the UK and Europe.

Planned Impact

For Academic Impact please see 'Academic Beneficiaries' in the Lead Organisation's application.

Industrial Impact.
Industry has a critical requirement for data sources, data integration, visualization and analysis tools, and for training related to these, across the broad spectrum of data types relevant to life sciences. The ELIXIR WP3 industry report refers to: protein and nucleotide sequencing; genomic information; genetic variation; small molecules; proteomics; transcriptomics; macromolecular structures; scientific literature analysis; ontologies or controlled vocabularies; and pathway and interaction information. In the pharmaceutical, consumer goods, consumer markets and agri-food sectors small molecule data, protein sequence and structure, as well as pathways are of critical importance. Genomic data, genomic variation, and links to phenotypes are important in plant and animal breeding. Food security can only be supported by scientifically driven research and by making the fruits of this research available to academic, governmental and industrial scientists. Scientists in large companies, medium and small size organizations can be overwhelmed by the complexity and volume of data. Repetition of in house custom solutions is not cost effective so a new landscape of pre-competitive collaborations is emerging. Training in understanding ranges of data types, interactions and agile integration are prerequisites for efficient industrial research. Tools such as semantic web data integration techniques, controlled vocabulary / ontology definition and metadata capture are key for modern data driven biological research but adoption of these techniques in industry will require education and training. ELIXIR-UK will engage with industry in a number of ways:
- through industry organisations such as EFPIA, Pistoia (Pharma), and BioNOW (BioTech SMEs), systematically
developing those links to inform its training content and training methods;
- awareness raising in industry of ELIXIR tools and resources, and providing training in them;
- packaging platform distributions such as BioLinux in other informatics sectors, such as cheminformatics;
- using industry for provisioning training and hosting training events;
- brokering access to high-end training needs in ICT literacy (e.g. HPC).

Publications

10 25 50

publication icon
Weber RJ (2015) Training needs in metabolomics. in Metabolomics : Official journal of the Metabolomic Society

 
Description Our first finding arises from the completion of a questionnaire (sent to the international research community) to assess the needs for training in metabolomics. This has been published as an Open Access paper (see Publications). The conclusions within this paper have had considerable impact as they justified the urgent need for developing training programmes in metabolomics in the UK, Europe and globally.

In response to this paper, and seed funded by this Research Council award, we have established the Birmingham Metabolomics Training Centre (BMTC). This centre provides training to empower the next generation of metabolomics researchers, by delivering training in both analytical and computational methods. The BMTC partners with both the Phenome Centre - Birmingham and NERC Biomolecular Analysis Facility - Birmingham to provide vocational training in clinical and environmental metabolomics. A combination of face-to-face and online courses are provided. The face-to-face courses include lectures, laboratory practicals and computer workshops, with significant hands-on training utilising state-of-the-art analytical instruments and software. The online courses are available to a wide audience and offer flexibility in time and study on a social learning platform.

A further finding from this project arises from the recent completion of another questionnaire (sent to the international research community) to assess the use of computational workflows (and Galaxy in particular) in metabolomics. We are now writing up that questionnaire and drawing conclusions about the need to develop Galaxy workflows more extensively in metabolomics.
Exploitation Route Through establishment of a training centre and hence training to the UK science community.
Sectors Agriculture, Food and Drink,Chemicals,Environment,Healthcare

URL http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/index.aspx
 
Description Our first finding arises from the completion of a questionnaire (sent to the international research community) to assess the needs for training in metabolomics. This has been published as an Open Access paper (see Publications). The conclusions within this paper have had considerable impact as they justified the urgent need for developing training programmes in metabolomics in the UK, Europe and globally. In response to this paper, and seed funded by this Research Council award, we have established the Birmingham Metabolomics Training Centre (BMTC). This centre provides training to empower the next generation of metabolomics researchers, by delivering training in both analytical and computational methods. The BMTC partners with both the Phenome Centre - Birmingham and NERC Biomolecular Analysis Facility - Birmingham to provide vocational training in clinical and environmental metabolomics. A combination of face-to-face and online courses are provided. The face-to-face courses include lectures, laboratory practicals and computer workshops, with significant hands-on training utilising state-of-the-art analytical instruments and software. The online courses are available to a wide audience and offer flexibility in time and study on a social learning platform. A further finding from this project arises from the recent completion of another questionnaire (sent to the international research community) to assess the use of computational workflows (and Galaxy in particular) in metabolomics. We are now writing up that questionnaire and drawing conclusions about the need to develop Galaxy workflows more extensively in metabolomics.
First Year Of Impact 2015
Sector Chemicals,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Policy & public services

 
Description Influencing the development of much needed training in OMICS technologies (in particular metabolomics)
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Research collaboration with Thermo Fisher Scientific 
Organisation Thermo Fisher Scientific
Country United States 
Sector Private 
PI Contribution Domain specific expertise in environmental, analytical, computational and biomedical metabolomics
Collaborator Contribution Financial, early access to hardware and software, expert technical advice, the loan of a mass spectrometer for training within Birmingham Metabolomics Training Centre.
Impact See publications
Start Year 2012
 
Description Research collaboration with Waters Corporation 
Organisation Waters Corporation
Department Waters Corporation Centre of Mass Spectrometry Excellence
Country United Kingdom 
Sector Private 
PI Contribution My research team has a partnership with Waters Corporation, specifically in the context of Phenome Centre Birmingham and the Birmingham Metabolomics Training Centre (the latter was pump primed by ELIXIR-UK funding from the Research Councils). We provide domain specific advice to the company in medical metabolomics.
Collaborator Contribution Waters Corporation contribute analytical expertise to the operation of Phenome Centre Birmingham and they have loaned the Birmingham Metabolomics Training Centre a QTOF mass spectrometer for training.
Impact Training of scientists in metabolomics
Start Year 2015
 
Description First ever Massive Open Online Course (MOOC) on metabolomics titled 'Metabolomics: Understanding Metabolism in the 21st Century' 
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 We developed and ran the first ever Massive Open Online Course (MOOC) on metabolomics, title as above. The course ran for 4 weeks with >2000 active learners.
Year(s) Of Engagement Activity 2015
URL https://www.futurelearn.com/courses/metabolomics