Delivering ELIXIR-UK

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Outreach and Training

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

ELIXIR-UK will provide a sustained focus on training that will enable users of ELIXIR's services to exploit them to the full. It will address the low capability and capacity prevalent in the UK and among ELIXIR member states in analysing and interpreting large data-sets. The Node will consider the training needs for diverse domains, for example from many types of organisms and different industries. Training will be delivered through a mixture of training modalities from face-to-face training to online courses and resources. The long-term vision for ELIXIR-UK is set out in the ELIXIR Node Application Form - (UK) submitted to the ELIXIR SAB in 2012 and recently accepted. The Node's focus is on training, and thus on developing relevant skills, as opposed to teaching. Its mission is to facilitate training of research scientists and infrastructure technologists (e.g. career bioinformaticians and researcher-developers) in bioinformatics, computing, statistics and biology, in partnership with UK centres, industry and other ELIXIR Nodes. We have a strong focus on building a community of subject-matter experts who also excel at training, on making reusable training materials available to this community, and on training trainers to make use of these. This focus creates a multiplier effect that will enable us to have much stronger impact than if we simply focused on delivering training to end-users.

Exploiting structural data to interpret the impact of genetic variations will inform clinical diagnostics, development of personalised medicines, plant and livestock breeding and pesticide resistance. This ELIXIR-UK activity will capitalise on the wealth of UK expertise in structural bioinformatics to make existing training materials and opportunities openly available to the research community, and to support ELIXIR's training community to use them effectively. It will combine this with existing expertise in elearning to provide a coherent, stand-alone set of re-usable training materials that will provide test materials for the ELIXIR-UK Training e-support service (TeSS). It will build bridges between the structural bioinformatics and the genomics communities, and will enable ELIXIR-UK to plug training gaps both in industry and in the healthcare service.

Publications

10 25 50
 
Description Through undertaking a gap analysis of structural bioinformatics training in the UK and in mainland Europe, we revealed that there is a dearth of structural bioinformatics training beyond the undergraduate level. We identified a need for further development of training aimed at researchers in academia, the healthcare sector and industry. We developed a method, based on research workflows, to make existing training more discoverable and effective. This method has now been implemented in ELIXIR's Training e-support system, TeSS - https://tess.elixir-europe.org/workflows, where the original workflows defined by this project have been developed into annotated, clickable workflows providing links to additional training and helpdesk information; see https://tess.elixir-europe.org/workflows/fork-structural-bioinformatics-1-getting-a-structure-for-a-protein-of-interest for an example.
Exploitation Route Our workflow has been used on ELIXIR-UK's training e-support portal (TeSS) for organising training material into themes associated with real research questions. The approach is sufficiently generic for it to be used to organise training material on any research topic.

Our gap analysis has shown where the greatest need is for development of new training materials; a large number of bioinformatics resources in this field have little or no training material to enable novice users to make the most of them. We have raised this issue with the BBSRC and it is our hope that, in the future, additional calls will provide adequate resources for the development and continual update of high-quality training materials. We believe that, for this to be successful, the effort that goes into developing such materials needs to be recognised and adequately resourced; many training grants only provide funds for the delivery of short courses so there is no sustainable creation of high quality, user-friendly training materials.
Sectors Agriculture, Food and Drink,Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL https://tess.elixir-europe.org/workflows
 
Description The workflow-based approach developed through this project fed into another BBSRC-funded grant, Bioinformatics for Discovery. This is a modular training partnership involving four industrial partners, who have had extensive input into the curriculum. Several individuals from these companies registered for the first iteration of the course. For the second iteration, which started on 15 March 2017, we opened the application process up to academic and industrial audiences. In addition to registrants from our partner companies, representatives from additional companies, including small-to-medium enterprises, registered. Bioinformatics for Discovery has become a regular addition to our annual training programme. The infrastructure developed forms the basis for the eLearning portal of our GCRF-GROW project, CABANA. It's also being used for an EU-funded project, BioExcel-2
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Education,Pharmaceuticals and Medical Biotechnology
 
Description Influence on bioinformatics training discoverability and practice
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://tess.elixir-europe.org/packages
 
Description Bioinformatics for Discovery (BBSRC modular training partnership
Amount £59,945 (GBP)
Funding ID BB/L013614/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 07/2017
 
Description ELIXIR-Excelerate (H2020-EU.1.4.1.1. - Developing new world-class research infrastructures)
Amount € 19,000,000 (EUR)
Funding ID 676559 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2019
 
Description Integrating Domain Structure Annotations from Genome3D with Protein Information in InterPro and PDB (BBSRC-BBR)
Amount £302,741 (GBP)
Funding ID BB/N019172/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description Christine Orengo - Delivering ELIXIR UK 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution We co-organised and hosted a workshop to reach agreement on the training needs of our target audiences for structural bioinformatics, identify existing sources of training material and organise it into themes; identify gaps in training materials and plan how to fill them. This included designing and circulating a pre-workshop survey. Three follow-up meetings have enabled us to work with our collaborators to identify major research questions that our target audiences are likely to have, and structure these into workflows.
Collaborator Contribution Christine Orengo and her collaborators within and beyond the Genome3D consortium provided the subject-matter expertise in structural bioinformatics, and many of the contacts to whom we sent the survey. The idea for organising training material into workflows also came from this group.
Impact A concept for organising existing training material into workflows. This also provides information on training gaps, helping to shape future investments in structural bioinformatics training A case for support for further funding in training for researchers, with a follow-on structural bioinformatics project as a specific use case.
Start Year 2013
 
Description Structural Bioinformatics 2015 
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 This course explored bioinformatics data resources and tools that are available for the interpretation and exploitation of biomacromolecular structures, focusing on how best to use structural information to gain the most from it in specific research contexts. This included investigating the impact of genetic variation on structure, predicting protein structure and function and exploring interactions with other macromolecules as well as with low-MW compounds.
Year(s) Of Engagement Activity 2015
URL https://www.ebi.ac.uk/training/events/2015/structural-bioinformatics
 
Description Structural Bioinformatics 2017 
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 This course explored bioinformatics data resources and tools for the interpretation and exploitation of biomacromolecular structures, focusing on how best to use structural information to gain the most from it in specific research contexts. This included investigating the impact of genetic variation on structure, predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds.
Year(s) Of Engagement Activity 2016
URL https://www.ebi.ac.uk/training/events/2016/structural-bioinformatics-2016
 
Description Workshop to agree on target audiences for ELIXIR-UK's structural biology training 
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 1 1/2-day workshop was designed to reach an agreement on the training needs of our diverse target audiences for structural bioinformatics; identify existing sources of training material and organise it into themes, and identify gaps in training materials and plan how to fill them. The outcomes were that the workshop established a single structural bioinformatics network with sub-themes and assigned a champion for each; we divided the target audiences into two groups: specialists and non-specialists, based on their previous experience with structural biology and bioinformatics; we identified The most important questions asked by our target audiences that should be addressed by training.
Year(s) Of Engagement Activity 2014