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ELIXIR UK Node presentation to the ELIXIR Board
1. European Life Sciences Infrastructure for Biological
Information
www.elixir-europe.org
ELIXIR-UK
Carole Goble and Neil Hall
Heads of Node
2. ELIXIR-UK Node: a Network of 18 Organisations
Legal signatory
Node Coordination Office
Head of Node
Head of Node
Cardiff University, Earlham Institute, Edinburgh Genomics, Heriot
Watt University, Imperial College London, Newcastle University,
Rothamsted Research, The University of Birmingham, The University
of Liverpool, The University of Manchester, The University of
Nottingham, University of Bradford, University College London,
University of Cambridge, University of Dundee, University of
Edinburgh, University of Leicester, University of Oxford
Nœud ELIXIR-UK: un réseau de 18 organisations
3. ELIXIR UK Node
Established in 2013 with starter grant (2014-
2017) focused on networking and training
• Training Coordinators
• TeSS Training Portal
• The Carpentries
Expansion in 2016 to full range of Node
activities
• Reflecting the services, activities,
platforms and communities engaged in
Coordination office funded (2017-2020)
• Node Coordinator
• Communications and Networking funds
Neil Hall
Head of Node
Earlham Institute
Carole Goble
Head of Node
Manchester
Nicola Soranzo
TechCoordinator
Earlham Institute
Gabriella Rustici
TrainingCoordinator
Cambridge
Catherine Hunter
Node Coordinator,
Earlham Institute
4. ELIXIR UK Node
Neil Hall
Head of Node
Earlham Institute
Carole Goble
Head of Node
Manchester
Nicola Soranzo
TechCoordinator
Earlham Institute
Gabriella Rustici
TrainingCoordinator
Cambridge
Catherine Hunter
Node Coordinator,
Earlham Institute
Node
Funding
ELIXIR funds
Impl studies,
platform funding,
staff exchange
EU ELIXIR Awards
Competitively won
Investigator won
services and
activities
Node-Node
collaborations
In kind
The UK doesn’t
currently run
dedicated ESFRI
e-Infrastructure
call
5. UK funding landscape
• Coordination office funding
£750k (2 posts)
• Communications
• Workshops
• Meetings and Travel
• Administration of Elixir funds
• 15 node –services receiving ~
£6,000,000 from UKRI, EU
Wellcome Trust and NIH.
• No funding direct from node
£
£
Node Services
Meetings
Comms
Workshops
6. UK funding landscape
• Coordination office funding
£750k (2 posts)
• Communications
• Workshops
• Meetings and Travel
• Administration of Elixir funds
• 15 node –services receiving ~
£6,000,000 from UKRI, EU
Wellcome Trust and NIH.
• No funding direct from node
7. ELIXIR RELATED EU Projects
PROJECT INSTITUTIONS
EOSC-Pilot University of Manchester
University of Oxford
Heriot Watt University
EOSC-Life University of Manchester
University of Oxford
University of Cambridge
University of Dundee
ELIXIR-Excelerate University of Manchester
University of Oxford
University of Cambridge
University of Edinburgh
Heriot Watt University
Earlham institute
ELIXIR-Converge University of Manchester
University of Cambridge
CORBEL University of Manchester
IMI FAIRplus University of Manchester
University of Oxford
Heriot Watt University
EJP-RD University of Manchester
University of Cambridge
EOSC-Enhance University of Manchester
8. ELIXIR and the UK Landscape
The vatican
£8.7 Bn
Funding
£1 Bn
£0.6 Bn
24
research
intensive
universities
9. Policy Wrangling
Revisions to the OECD
Recommendation of the Council
concerning Access to Research
Data from Public Funding
10. UK e-Infrastructure for Life Science Landscape
Biological sciences, health and food themes
“Significant expansion of the UK node
of ELIXIR to support BioFAIR, a data
sustainability institute supporting the
coordination and development of UK
life science data”
11. ELIXIR-UK Serves
Membership ELIXIR UK
BioFAIR
a data sustainability
institute supporting
the coordination and
development of UK
life science data
BioFAIR Digital Object
Commons for UK Life
Science.
Mobilising and
coordinating UK life
science data
infrastructure
community
Accessing funding
and engagement
opportunities by UK
members
Developing ELIXIR
Communities
Executing the
Strategic Plan
Services SDPs
Platforms
Communities
Portals
Activities
EU Projects
Node-Node
cooperations
12. A Network
• Helping our members run and
participate in meetings
• Sponsoring meetings
• 2020 UK Bioinformatics
Conference to coincide with
UK All Hands
ELIXIRAll Hands 2018, Berlin
Biohackathon, November 2018, near Paris
ELIXIR UK All Hands, 2018, Birmingham
Dagstuhl Seminar FAIR e-
Infrastructures Nov 2018
14. Focus A lot of Node
co-operations
EBI are of course
strong partners
• Communities
• Services
• Interoperability
• FAIRification
• Markup
• Workflows
17. Highlight: 3DBioinfo
To develop the infrastructure for FAIR
structural and functional annotations
To create open resources for sharing,
integrating and benchmarking software
tools for modelling the proteome in 3D
To develop tools to Describe, Analyse,
Annotate, and Predict Nucleic Acid
Structures
To help develop models for protein-ligand
interactions
3DBioInfo Launch, Basel, 2018Christine Orengo, UCL
Increasing Interoperability between
ELIXIR Protein Structure and Sequence
Resources and Expanding these
Resources with 3D-Models of CATH
Domains, built by SWISS-MODEL
CATH protein structure
classification Core Data
Resource,
Jalview multiple sequence
alignment editing,
visualisation and analysis
tool
PHYRE2 protein structure
prediction
Co-led Commissioned Service:
18. The ELIXIR Node Services
UK developed Service Best Practice. 9 new services in review.
https://f1000research.com/articles/5-2894/v2
Dundee Resource for
SequenceAnalysis and
Structure Prediction
CDR
RIR
Portal
20. Highlight: The TeSS Training Portal https://tess.elixir-europe.org
ELIXIR training portal to aggregate events and training materials
77%
increase in
users
2018-2019
75
content
providers
284
Upcoming
events
10657
past
1328
materials
1K
users /
month
50:50
manual/auto
Born native of ELIXIR
21. The TeSS Training Portal in a Nutshell
automatically aggregate
training resources
link to registries
content embedded with widgets
in 3rd party sites
curation tools
22. Organising and Navigating Content
Concept Maps and Learning Paths
Experiments Funded
by Commissioned
services
Concept maps
Learning outcome templates
Generate learning paths
Relate to Service Bundles
23. Community Contributions for Content and Code,
and Wider uptake -> from start-up to maturity
Open Development
Framework
Metadata
processors
Scraper
development
Curation
Contributions
Embedded
widgets
Scale Contribution
Modularise, Packaging, Governance
Other communities. Around topics, communities,
organisations, geographical. CZI, EJP-RD, HDR-UK, ARDC, EOSC.
TeSS needs to be packaged, marketed, and supported properly
Content
User UX
Added value
24. TeSS, the UK Node and the ELIXIR Platform
a native ELIXIR infrastructure service
Changes in UK leadership
• Manchester -> Cambridge
Resources challenge
• 1.5 FTE dedicated development in
one organisation (4 people needed)
• Over dependence on Niall
• Lack resources to build UK base
National funding challenges
• Seen as an ELIXIR not UK service
• Incorporation into BioFAIR proposal
Resources for content curation
• Affects quality of service
UK Node
ELIXIR
Platform
Excelerate
Impl Studies
2014 2016 2019 2021
A native ELIXIR Infrastructure
Service to be collective
managed by all ELIXIR Nodes
25. Highlight: Interoperability …. Data, Tools
platform, impl studies and EU grants
FAIRification of data infrastructure
FAIRmetrics, capability models, processes
FAIR Cookbook
Bioschemas
With NL, DE, EBI, LU …
Data FAIRification
Workflows & Software
Workflow Registry
Containerisation, Galaxy
CommonWorkflow Language, GA4GH
Research Objects
FAIR Software Practices
Registries, portability, interoperability
With ES, BE, DE, FR, EBI, NL …
FAIRmetrics
26. Highlight: Interoperability …. Data, Tools
platform, impl studies and EU grants
FAIRification of data infrastructure
FAIRmetrics, capability models, processes
FAIR Cookbook
Bioschemas
With NL, DE, EBI, LU …
Data FAIRification
Workflows & Software
Workflow Registry
Containerisation, Galaxy
CommonWorkflow Language, GA4GH
Research Objects
FAIR Software Practices
Registries, portability, interoperability
With ES, BE, DE, FR, EBI, NL …
28. Highlight: Bioschemas
Exploiting schema.org for FAIRer Life Sciences resources
ELIXIR-UK direct the initiative & promote ResearchSchemas
Community initiative
Schema.org specs
Support software
Foster adoption and use
Find, register, index, search
resources
Resource mark up for tools
Metadata movement
between resources
Registry auto curation
Leveraging a de
facto widely
adopted standard
Alasdair Gray, HWU
32. Community Plant Sciences Genotype-Phenotype
Data Management and Validation Toolkit
FAIR data Analysis
Search engine
Metadata
Access
33. Serving the UK: BioFAIR
bringing together all our expertise for the UK
differentiated from EMBL-EBI
Federated
Digital Object Commons partnered
with national infrastructure
Integrated data services
and toolkits and training
Data sustainability institute
supporting the coordination
and development of UK life
science data
Data Management services and capability ->
ELIXIR CONVERGE
34. Serving the UK: BioFAIR
bringing together all our expertise for the UK
differentiated from EMBL-EBI
Recognition now that this is
needed
BBSRC Review of Data
Driven Bioscience
BBSRC Bioscience Big Ideas
Pipeline
UKRI “infrastructure
roadmap”
Brexit - every crisis is an
opportunity …
35. ELIXIR-UK
Navigating a fragmented national
landscape
Outstanding people and track record
Doing a lot on borrowed resources
Significant contributions to ELIXIR
And EOSC
Node-Node co-operations
BioFAIR
a data sustainability
institute supporting
the coordination and
development of UK
life science data
BioFAIR Digital Object
Commons for UK Life
Science.