ELIXIR-UK
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Introduction to ELIXIR and ELIXIR-UK presented by Carole Goble at the ELIXIR-UK Workshop during Genome Science 2016 in Liverpool on 31st August 2016
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ELIXIR-UK
- 1. ELIXIR, ELIXIR-UK and how you can get involved Carole Goble Head of Node, ELIXIR-UK http://elixir-uk.org GenomeScience 2016, Liverpool, UK, 31 Aug 2016
- 2. 2 agriculture medicine bioindustries environment ELIXIR connects national centres and EMBL- EBI to build a sustainable European infrastructure for biological research data. ELIXIR underpins life science research – across academia and industry.
- 3. Europe have 500 000 life science researchers All produce data. A lot of data. http://omicsmaps.com • Simplifies access to quality- controlled data, services • Enables life science researchers to make the most of the rapidly growing life science data • Ensures long-term sustainability of Europe’s core • Facilitates open access and open science in life science research
- 4. A robust infrastructure for biological information. A bigger task than any individual organisation or nation can take on alone 20 ELIXIR membersmajor bioinformatics service providers (~150) Co-operation Long term support
- 5. A robust infrastructure for biological information. A bigger task than Europe can take on NIH BD2K Programme Human Data Beacons NSF and NIH Infrastructures CyVerse, dataONE EMBL Australia
- 6. Implemented as a network of national nodes a distributed coordinated infrastructure • ELIXIR Nodes are funded nationally • ELIXIR Nodes build on national strengths and priorities • ELIXIR Nodes support national research with data management • ELIXIR Nodes provides a national framework for long-term resource management.
- 7. Nodes … commit services, lead platforms, coordinate activities, participate in funded awards 8 Chris Ponting Rita Hendricusdottir Carole Goble
- 8. 9 ELIXIR Selected Activities and Achievements • Bio.tools Registry • Indicators for Core Data Resources • Harmonisation of identifier resolution services Europe-USA • Software and Data Carpentry Training • Human data Beacons • Human Protein Atlas – Uniprot interoperability • A local EGA …
- 9. ELIXIR Authorisation and Authentication Infrastructure (AAI) ELIXIR AAI allows individual researchers to access different services across ELIXIR, using an ELIXIR identity and a single sign-on process: www.elixir-europe.org/services/compute/aai
- 10. Accessible data: ELIXIR – IMI OncoTrack • Scoping study to understand long-term knowledge management requirements • Data storage, Meta data mappings, Data governance - Consent and Access management
- 12. ELIXIR-UK Node • Oversee UK’s interests in ELIXIR • Participate and lead ELIXIR activities and related global initiatives • Showcase, contribute and deliver UK services and resources to ELIXIR and related international consortia • Showcase and channel ELIXIR services and activities to the UK • Drive and support UK life science data infrastructure community and infrastructure sustainability. • Reflect strategic emphasis of our major funders 13
- 13. Formal Agreements, Service Delivery Plans 14 ELIXIRConsortium Agreement Lead institute Earlham Institute Manchester Edinburgh Roslin Birmingham Cambridge Heriot-Watt Dundee Liverpool Imperial Newcastle Nottingham UK Node united by Collaboration Agreement Oxford Rothamsted UCL
- 14. Head of Node Co-lead ELIXIR Interop Platform Carole Goble Node Coordinator John Hancock Chris Ponting Co-lead ELIXIR Training Platform PI training grant Rita Hendricusdottir Training Coordinator Tim Stitt Compute Coordinator Terri Attwood GOBLET Liaison TeSS portal lead Susanna Sansone RDA Liaison TeSS co-lead
- 15. Key Node roles populated by membership 16 Head of Node Training Coordinator Technical Coordinator Node Coordinator Working Groups Specialist roles Training Sectors Service providers Activities Liaisons
- 16. Staffing and Funding Profile 18 Node Core Coordination Office Node Grants UK training node pump-prime EU EXCELERATE,CORBEL In Kind Members awards for activities and services Members voluntary in kind ELIXIR-Hub Contracts
- 17. Key Staff funded by grant awards Lee Larcombe Training Coordinator for Research Science Edinburgh Rita Hendricusdottir Training Outreach Manager Edinburgh Niall Beard TeSS Portal Training Coordinator for Infrastructure Tech Manchester Milo Thurston TeSS Portal BioSharing Oxford Gabriella Rustici Training Quality Cambridge Anna Leida Mölder Identifiers Manchester Metadata Manchester
- 18. ELIXIR Services: A rigorous selection process and a National commitment 20 ELIXIR Services: Backbone of the ELIXIR life science data infrastructure providing stable access to biological data ELIXIRCore Resources: Flagships, examples of excellence Data,Tools, Interop, Compute,Training Node funded in the Node Service Delivery Plan Implementation Studies LongTerm Infrastructure Services Commissioned (e.g. Beacons) undertaken by Nodes/Hub Node Services not included in the Node Application Services under development through projects undertaken by Nodes/Hub Non-node services e.g. Galaxy
- 19. ELIXIR-UK ELIXIR Services 21 Training Interoperability Data &Tools Phyre2 CATH/Gene3D JalView Protein Structure and Function The Mouse Atlas HuDSeN Chick Atlas …. Human Health and Disease IUPHAR/BPS Guide to PHARMACOLOGY Farmed Animals and Plants PHI-base Ensembl farmed and domestic animals Metadata Standards ISATools and Commons BioSharing Interoperability Frameworks InterMine Training Services Bioinformatics Training Program (Cambridge) Birmingham Metabolomics Training Centre (BMTC) Edinburgh Genomics Advanced Training in Bioinformatics Training Infrastructure TeSS ELIXIR training portal Expression Atlases
- 20. Benefits of offering a service • Influence the development of a major effort in data integration • Exposure to a wide range of potential users and collaborators across Europe and globally • Recognition as a core data resource on a par with EBI and SIB resources • Potential funding (a tunnel post-Brexit) • Provide your service on a stable (sustainable) basis • Work towards integration with ELIXIR interoperability standards • Participate in ELIXIR activities 22
- 21. 23 ELIXIR-UK ELIXIR Activities Training Interoperability Data &Tools Pan-ELIXIR UKInternational co-Lead Training Platform ChairTraining Coordinators Group Training Portal Training quality Software Carpentry Data Carpentry NIH BD2KTraining Coordination Centre GOBLET BioSchemas.org BioSchemas.org Samples specification Biosharing Metadata StandardsCatalogue UKBioBanking co-lead Interoperability Platform Identifier services Data Citation Services - Force11 Dataset description/discovery - NIH BD2K CommonWorkflow Language – CoE BioExcel Software practice metrics Galaxy Recommendations Software / Data Carpentry workshops StaTS project training in statistics. Genome3D, Metabolomics FAIR Data Principles Software Sustainability Institute NHS Clinical Genomics Farr Institute Standards -CHARMECost Action, Research Data Alliance EuroBioimaging
- 22. Coming up….. 24 12-14 September 2016 , Manchester, UK 4th Workshop on Sustainable Software for Science: Practice and Experiences 25-26 October 2016, Rome, Italy Combined CHARME – EMBnet and NETTAB 2016 Workshop, ‘Reproducibility, standards and SOP in bioinformatics‘ 7-8 November 2016, Harpenden, UK ELIXIR-UKAll-Hands meeting 19-20 September 2016, Cambridge Software Carpentry R instructor training Join our mailing lists Take part in our telcons Set up a working group Propose a Service Help us overhaul the website! 5-8 December 2016, Amsterdam, NL 9th SWAT4LSWorkshop 20-21 October 2016, Barcelona, Spain BioExcel: workflow training for computational biomolecular research info@elixir-europe.org. elixir-uk-all-hands@googlegroups.com
Editor's Notes
- ELIXIR is a unique undertaking that consolidates Europe’s core bioinformatics resources, services, and national centres into a single, coherent platform. ELIXIR support international collaboration, decision making and secures long-term sustainability. Scientific services are brought together and connected to support scientific communities across the life-sciences - from marine research through plants and agriculture to health research on rare diseases. Since last update in September ELIXIR pilot actions: Marine, Data management and secure high volume data transfer building on gridFTP/Globus Projects are all under way, report back outcomes next meeting Established Training coordinators group – best practices and sharing of content across nodes Talk through 3 developments today Training Industry advisory committee and long term planning Planning for the large ELIXIR implementation project next year
- Data production and using at a large number of sites Human genomics projects but also plants, microbiota, environmental marker organisms Metabolomics & Proteomics coming of age Be scalable to 1000s of sites Over 500 000 Life scientists in Europe Deal with incomplete, conflicting data and rapidly evolving knowledge
- Creating a robust infrastructure for biological information is a bigger task than any individual organisation or nation can take on alone Five new ELIXIR Members in 2015-2016: France, Spain, Belgium, Italy, Slovenia Luxembourg, Germany and Ireland Latest member – Germany! (joined in August 2016 its all self serving - how many people joined, how many datasets included. nothing about how ELixir made any difference to a bioinformatician or a biologist
- Creating a robust infrastructure for biological information is a bigger task than any individual organisation or nation can take on alone
- Creating a robust infrastructure for biological information is a bigger task than any individual organisation or nation can take on alone These are issues of such complexity that no single institution or country can tackle alone ELIXIR Nodes ensures local bioinformatics capacity throughout Europe Implemented through National ELIXIR Nodes ELIXIR consolidates Europe’s national centres, services, and core bioinformatics resources into a single, coordinated infrastructure.
- Creating a robust infrastructure for biological information is a bigger task than any individual organisation or nation can take on alone These are issues of such complexity that no single institution or country can tackle alone ELIXIR Nodes ensures local bioinformatics capacity throughout Europe
- To represent the UK’s strengths in computational biology and bioinformatics within ELIXIR to benefit the UK community seen broadly as: computational biology and bioinformatics researchers and developers, life scientists who use the data resources, and industry who wish to benefit from the data infrastructure; To support the development of a training infrastructure in this area, for example through Software and Data Carpentry and Clinical Bioinformatics training; To nucleate specialist areas within the UK community to facilitate their integration and build their links with ELIXIR and related international consortia; To reflect the strategic emphases developed by our major funders, for example in human health and disease, agridata, and environmentally contextualised data, in our interactions with ELIXIR.
- The benefits of UK participation in ELIXIR are two-way: From a UK perspective, ELIXIR provides leading UK researchers the opportunity to participate in and shape the development of a major global player, allowing UK innovation in this area to have maximum impact in laying down future technologies and data standards. At the same time it provides access to training across the national nodes, providing the opportunity to raise skills levels in an area critical for future economic development. From a European and global perspective, it provides access to UK expertise in data resources, tools and training expertise which is world class. ELIXIR and ELIXIR-UK engage four communities: the national (UK), European (ELIXIR) and global RDI communities and industry, which has a need for integrated infrastructures to provide optimised access to data to drive innovation from the pharmaceutical industry to agritech.
- Improve – use map
- Node Coordination Leads, analogous to an Institute’s Division Heads. Coordinator leads are Node standing positions covering Training (CTrO), Technical (CTO), Data (CIO) in the first instance. Node Working Group Leads, analogous to an Institute’s Group Leads. Working Groups are ad-hoc, fluid and can be chartered and sunset in consultation with the Management Committee.
- Add Earlham EXCELERATE Staff
- Nodefunded Services are: Technical and administrative services that fall under the administrative and financial responsibility of the Node. Included in the Service Delivery Plan, approved by the ELIXIR Board and attached as an Annex 1 of the Node Collaboration Agreement. Commissioned Services are: Technical and administrative services that fall under the responsibility of the ELIXIR Hub, funded through the ELIXIR Budget and carried out by ELIXIR Nodes pursuant to a Collaboration Agreement or by EMBL pursuant to a Work Programme. Commissioned Services are regulated via a contract that is approved by the ELIXIR Board and attached as an Annex 2 to the Node Collaboration Agreement (in case of 1 see ELIXIR founding documents: ELIXIR Consortium Agreement and Node Collaboration Agreement ELIXIR Nodes) or via a document approved by the ELIXIR Board and attached as Annex 2 to EMBL Work Programme (in case of EMBL acting as ELIXIR Node). Commissioned Services can be divided into two distinct categories: 1. ELIXIR Implementation Studies2 consist of specific, time limited (usually less than 18 months) studies; 2. ELIXIR Infrastructure Services established through an excellence driven tender process3. They are assumed to be a mature, stable services, with the underlying contract being regularly reviewed and renewed conditional on regular performance reviews.
- 14 out of 20 1. Alignment with the five ELIXIR infrastructure themes (data, tools, compute, interoperability, training) 2. Strong complementarity to 2014-18 ELIXIR programme 3. Complementarity to ELIXIR-UK strategic themes 4. Potential for cross-node collaborations 5. Provide comparable impact to existing ELIXIR resources from other Nodes already accepted by the ELIXIR SAB 6. Resource contribution to wider EU infrastructures and integration 7. Ability to interoperate with other ELIXIR resources 8. Evidence of community outreach and adoption 9. Leadership in data stewardship within a community 10. Evidence of long-term sustainability Training Bioinformatics Training Program (Cambridge) Birmingham Metabolomics Training Centre (BMTC) Edinburgh Genomics Advanced Training in Bioinformatics TeSS Interoperability ISA Tools & Commons (Oxford) BioSharing (Oxford) InterMine (Cambridge) Protein Structure and Function Phyre2 (Imperial) CATH-Gene3D (UCL) Jalview and the Dundee Resource for Sequence Analysis and Structure Prediction (Dundee) Biomedical Atlases Biomedical Atlas Centre (Edinburgh, Newcastle, potentially others) Human Health and Disease IUPHAR/BPS Guide to PHARMACOLOGY (Edinburgh) Farmed Animals & Plants Pathogen Host Interactions Database (PHI-base) (Rothamsted)
- Provide your dataset or tool on a stable (sustainable) basis Work towards closer integration with ELIXIR interoperability standards Participate in ELIXIR activities
- Technical infrastructure for training (TeSS) Develop training expertise Training quality Fill training gaps (e.g. Software and Data Carpentry) Descriptive Metadata for Datasets - DATS model Identifiers & (meta)data descriptions, linked to Use Case packages Consolidate existing services Implement interoperability between priority resources BYOD bootcamps Bioschemas.org semantic search