Award details

Delivering ELIXIR-UK

ReferenceBB/L005050/1
Principal Investigator / Supervisor Professor Carole Goble
Co-Investigators /
Co-Supervisors
Professor Teresa Attwood
Institution The University of Manchester
DepartmentComputer Science
Funding typeResearch
Value (£) 192,113
StatusCurrent
TypeResearch Grant
Start date 31/03/2014
End date 30/03/2017
Duration36 months

Abstract

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.

Summary

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.

Impact Summary

For Academic Impact please see 'Academic Beneficiaries'. 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). Societal impact: Manchester specifically focuses on: the development of the Training e-Support Service; the adaptation and rollout of Software Carpentry (www.software-carpentry.org, "Helping scientists build better software since 1998") across UK and European Life Science; and in the oversight of the technical infrastructure aspects of ELIXIR-UK. As ELIXIR is an *infrastructure* programme the impact of the work proposed - to ensure better e-infrastructure - is significant: - on the quality, robustness, reliability, sustainability and fidelity of software and software services contributing to the infrastructure; - on the ability of the bioinformatics and developer community to adopt and adapt ELIXIR infrastructure and software from elsewhere; The importance of better and more reproducible and reusable software has been recognised in the Life Sciences in recent years (e.g. Nature 467, 775-777 (2010), Computational science: ...Error ...why scientific programming does not compute). ELIXIR-UK is an opportunity to affect change and affect new and better practice.
Committee Not funded via Committee
Research TopicsX – not assigned to a current Research Topic
Research PriorityX – Research Priority information not available
Research Initiative European Life Science Infrastructure for Biological Information (ELIXIR) [2013]
Funding SchemeX – not Funded via a specific Funding Scheme
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