Update on the ELIXIR UK node by Chris Ponting
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These slides were presented at the ELIXIR UK node update meeting in Hinton, Cambridge on 14th of October 2014
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Update on the ELIXIR UK node by Chris Ponting
- 1. European Life Sciences Infrastructure for Biological Information www.elixir-‐europe.org ELIXIR-‐UK the UK Node of the
- 2. Current Ac*vi*es and Future Plans of the ELIXIR UK Node Chris Pon*ng (30 mins)
- 3. Overall Mission To build strong and sustainable European infrastructure together with our ELIXIR partners. • Data • Standards • Tools • Compute • Training • Industry From now on, ELIXIR-‐UK will pursue its mission across all of these ELIXIR infrastructures
- 4. Training Mission To facilitate training of research scien*sts and infrastructure technologists in bioinforma*cs, compu*ng, sta*s*cs and biology, in partnership with UK centres, industry and other ELIXIR Nodes. Oxford University Computa*onal Genomics Analysis and Training (CGAT) University of Manchester European Bioinforma*cs Ins*tute (EMBL-‐EBI) University of Cardiff & NERC EOS Centre The Genome Analysis Centre (TGAC) The Oxford e-‐Research Centre University College London University of Birmingham University of Edinburgh Queen Mary, London University of Cambridge University of Liverpool Centre for Genomic Medicine
- 5. Training Spectrum TCRS Training Coordinator, Research Science 100% TCIT Training Coordinator, Infrastructure Technology 100% Lee Larcombe Aleks Pawlik Genomic Research Researchers Technical Infrastructure Service Providers
- 6. Mission: to establish an interacting ELIXIR wide training community & to ensure coherency in the delivery of training related to ELIXIR activities. TrCC members: Chair: Rita Hendricusdottir BE Katrijn Vannerum CZ Daniel Svozil DK Peter Longreen EE Hedi Peterson FI Eija Korpelainen FR Julie Thompson IL Michal Linial IT Allegra Via NL Celia van Gelder NO Ståle Nygård PT Pedro Fernandes SI Brane L. Leskosek & Peter Juvan ES Oswaldo Trelles SE Sara Light CH Patricia Palagi UK Rita Hendricusdottir & Lee Larcombe EMBL-‐EBI Sarah Morgan ELIXIR-‐UK working across Europe: Training Coordina*on CommiUee
- 7. 2012 Q2: Ini*al Mee*ng@MRC Q3: Subsequent Mee*ng@MRC Q4: Ini*al and subsequent submissions for ELIXIR-‐ UK Node status 2013 Q1: ELIXIR-‐UK Presubmission applica*on to RCs & Netherlands ELIXIR workshop Q2: Resubmission of applica*on to RCs a]er reviewers’ comments & ELIXIR Collabora*on Agreement mee*ng, Heathrow Q3: RCs applica*on accepted for Jan 1 2014 start & HoN mee*ng, Hinxton Q4: GOBLET/ELIXIR-‐UK mee*ng TGAC & ELIXIR is launched 2014 Q1: Recruitment round 1 & ELIXIR PoW5 Training dra]ed & ELIXIR Training Node Survey & Structural Bioinforma*cs Training Workshop & Industry workshop @ TGAC Q2: ELIXIR HoN and TCG mee*ng @Sandhamn & Lee, Aleks, Niall, Milo start & Advisory Group formed & TeSS mee*ng Manchester Q3: Industry CommiUee cons*tuted,& Kick-‐off mee*ng, Rita starts, ELIXIR/ELIXIR-‐UK Node mee*ng Hinxton, TrCC cons*tuted Q4:ELIXIR Innova*on and SME forum & ELIXIR SAB -‐ Heads of Nodes mee*ng, Hinxton, ELIXIR-‐UK ECA being nego*ated INFRADEV-‐3 prepara*on ABriefHistoryofELIXIR-UK Start
- 9. ELIXIR-‐UK: Current Ac*vi*es • Building a UK Training Community • Building a Training Community across Europe • Adding new missions, beyond Training • Iden*fying Training Needs • Delivering Training • Defining then ac*ng on Priori*es • Coordina*ng Training for ELIXIR Excelerate
- 10. Building a UK Community -‐ website
- 11. Building a Training Community -‐ TeSS ELIXIR-‐UK’s mission will be delivered, in part, by the development of a pilot training resource plagorm, termed TeSS. • Ready access to pre-‐exis*ng training materials, resources, ac*vi*es and events; • Links to training-‐relevant catalogues within and around the ELIXIR network. TeSS will ensure that all such informa*on is discoverable by trainers, trainees, researchers and technologists across ELIXIR’s training sectors, in academia and industry. The pilot phase, which will ul*mately inform the strategy for the long-‐term development and sustainability of the plagorm, will gather user requirements via surveys and workshops, perform regular gap analysis (regarding both training courses and resources), and run feasibility studies for developing content pipelines for ELIXIR stakeholders, portable plagorms containing open-‐source resources, etc. Carole Goble will talk more about this aLer lunch
- 12. Building a Training Community across Europe: the TrCC Rita HendricusdoMr will talk more about this aLer lunch The UK has led the forma*on of a Training Coordinator CommiUee with representa*ves from 17 ELIXIR nodes Chaired by Rita, this operates across Europe, repor*ng to the HoN Training has equal representa*on to the Exis*ng Technical Coordina*on Group (TCG)
- 13. Engaging with Industry • Audrey Kaufmann, Novar*s Ins*tutes for BioMedical Research • Samiul Hasan, GlaxoSmithKline • William Spooner, Eagle Genomics • Wendy Filsell, Unilever • Claus Bendtsen, Astra Zeneca • Mark Forster, Syngenta We have brought together a group of people from Industry to help us beUer understand industrial training priori*es Gabriella Rus*ci will talk more about the Industry Panel aLer lunch They have made themselves available for advice, and were important in helping distribute our industry survey
- 14. Iden*fying UK Training Needs Bioimaging Crop Genomics Data Cura*on & Standards Environmental Sciences Genomics Applica*ons Clinical Genomics ICT & So]ware Industry Engagement Metabolomics Proteomics Structural Bioinforma*cs Tess Industry & Sector-‐Specific Surveys Gabriella Rus*ci will talk more about the Industry Survey aLer lunch
- 15. Delivering Training: Data & So]ware Skills ElixirUKSectors ICT&SoftwareDataCuration&Standards Software Carpentry Essential Software Engineering for researchers: Data Carpentry Data literacy Q2: Establishing partnerships with DC and SWC Defining the strategy for data cura*on and standards delivery within DC Bidding for Microso] Azure for Research Award Q3: Development and improvement of the DC materials for life sciences (MSL Sprint) Elixir Pilot Ac*ons proposal for rolling out Carpentries in Elixir Europe Q4: SWC Train the Trainer @ TGAC Elixir SWC @ NHS MSc course in Manchester Start of materials development for DC modules on biosharing Elixir DC @ Manchester Elixir NL – establishing the demands for the curriculum for a life science data expert. (a series of “DTL Focus mee*ngs”)
- 16. TF: Service Registry Biomedbridges, Denmark, Sweden, EBI, UK • ELIXIR-‐UK contribu*on: – Ontologies: EDAM, So]ware Ontology (SWO) – Biocatalogue.org – Biosharing.org • Joint pilot proposal – EDAM development • Biotools registry Mee*ngs aUended: – Tool Registry, Imperial College London, April 17 2013 (Goble) – ELIXIR/BioMedBridges Workshop on Tool Registries, October 16-‐18, 2013, Technical University of Denmark (Beard) – January 2014 Aberdeen (Beard) – May ‘2014, Hinxton (Beard) – “A common vocabulary to classify resources in life sciences” Workshop Brussels 16th Oct 2014 (Goble, Beard, Sansone) – ELIXIR-‐DK three day hackathon to prime the ELIXIR Tools & Data Services Registry (forthcoming)
- 17. FAIRPORT The Netherlands, UK • Funded at four-‐day mee*ng hosted at The Netherlands. (Goble, Blomberg, Game aUended). • ELIXIR-‐UK Pilot • hUp://www.datafairport.org/ • Goble funded to run FAIRDOM (FAIRPORT for Systems Biology), working with ELIXIR-‐NL. • Strong links with the NIH BD2K Ini*a*ve • TF10: Data interoperability, vocabulary and ontology services
- 18. • Goble and Sansone aUended and presented at 4th Plenary, 22 -‐ 24 September 2014 -‐ Amsterdam, The Netherlands
- 19. Key Achievements Established partnerships with: • Data Carpentry (Aleksandra Pawlik on the Directors Board) • Software Carpentry (Carole Goble on the Advisory Board and transitional SWC Foundation Board) • Software Sustainability Institute • BioSharing community (led by Susanna Sansone) • International Society for Biocuration (Terri Attwood on Exec Board) • Research Data Alliance (ELIXIR Bridging IG, BioSharing IG, Sansone on RDA TAB) • NIH BD2K (Goble in ELIXIR delegation Data Science meeting, Sansone associated with first round projects). Breaking News "In order to foster So-ware Carpentry's con5nued growth, we are pleased to announce that we are crea5ng an independent So#ware Carpentry Founda1on (SCF). Like other non-‐profit open source founda5ons, it will decide So-ware Carpentry's overall scope and direc5on, manage finances hold its intellectual property." (Carole Goble on the Interim Board)
- 20. Upcoming ac*vi*es • ELIXIR UK & SSI SoLware Carpentry “Train the Trainer” Workshop at TGAC – 22nd&23rd October 2014 • ELIXIR UK So]ware Carpentry workshop for NHS Clinical Bioinforma*cs MSc @ Manchester – 9&14th November 2014 • ELIXIR UK Data Carpentry workshop – 27&28th November in Manchester including data cura*on & standards and tools module delivery • ELIXIR UK MicrosoL Azure for Research workshop – December 2014/ January 2015 in Manchester • ELIXIR UK & SSI So]ware Carpentry Course for EPSRC & MRC Centre for Doctoral Training in Regenera*ve Medicine – 3-‐4th February 2015
- 21. Defining Priori*es Lee Larcombe will talk more about this aLer coffee Clinical Genomics Structural Bioinforma*cs Advanced Scien*fic Skills Applied Genomics Metabolomics Five areas to develop as ELIXIR UK strategic training priori*es ELIXIR UK’s deliverables are *ed to the defini*on of five strategically-‐important areas of training need. The defini*on and pursuit of five strategic areas a]er consulta*on was described in the RC funding applica*on. Iden*fying the UK Training Needs is a cri*cal part of the process of selec*ng areas to focus on.
- 22. ELIXIR Excelerate (INFRADEV-‐3) 1. Excellence in Coordination, Operations and Governance 2. Strengthening Node Capacity 3. Excellence in User Services This is where training will sit The overall aim of ELIXIR-Excelerate is to ensure that Europe’s life scientists have access to world leading resources for bioinformatics. This will be done by accelerating the integration of Europe’s core bioinformatics resources, services and national centers into a single, distributed, infrastructure: ELIXIR.
- 23. Work Stream 5 -‐ Training Led by Chris Pon*ng as Work Stream Leader Objec*ves for: Strengthening Node Capacity Strengthen organisa*on of na*onal communi*es • Support in coordina*ng na*onal Nodes • Skills and Knowledge exchange between ELIXIR Nodes, i.e. staff exchanges, visits • Capacity building through accessing EU Structural Funds and Regional Partner Facili*es Build Europe wide capabili*es • Genome annota*on network? • Data management prac*ce ? Build Europe wide training network • Partner with goblet • Build elixir curriculum • Deliver training in core areas The 9 ELIXIR Objec*ves for Training 1. Link to individuals from all other ELIXIR programmes to ensure pan-‐ELIXIR coherency in the delivery of training related to ELIXIR infrastructures 2. Establish a common approach across ELIXIR to benchmark and evaluate diverse training ac*vi*es 3. Establish a coherent and interac*ng ELIXIR-‐wide training community 4. Disseminate relevant informa*on via a training portal 5. Iden*fy training gaps and priori*es by engaging with industry and other stakeholders 6. Expand high quality training ac*vi*es, and develop and deliver new training ac*vi*es, in order to fill iden*fied gaps and meet priori*es 7. Synchronise the development of ELIXIR data infrastructures with associated high quality training materials and ac*vi*es 8. Define core competencies of users and operators of ELIXIR infrastructure and map these competencies to training ac*vi*es 9. Capture and deliver ELIXIR training ac*vi*es in Open Educa*on Resources (OER) including videos and interac*ve training materials
- 24. Timeline WS5 – Training (TrCC) is feeding directly in at this stage HoN mee*ng Amsterdam, 23 Oct 14 Decisions taken on: • Overall shape of proposal • Budget • WPs • WPLs • Governance • Other Partners We are here
- 25. Future Ac*vi*es • Developing and Focussing on Priori*es • Delivering Training • Developing Funding Opportuni*es • Moving Beyond Training – Addi*onal Missions Con*nue Progress to
- 26. Funding Opportuni*es for Training • Lobbying for funding mechanisms for training • Training gap filling in Structural Bioinforma*cs Ready to go • Where is the funding to fill the yawning training gap between research scien*sts and data scien*sts? • Training is not just the preserve of the PhD student • MRC Training Lectureships Chris*ne Orengo will discuss this aLer coffee
- 27. MRC Training lecturers: Proposed job descrip*on • Full-‐*me, or Part-‐*me. • Adjacency to and interac*on with research science groups would be required • Part-‐*me will include those who wish to undertake both research and training roles • Lecturers should keep up-‐to-‐date with the fields in which they are training: this ensures that their training maintains its values and, importantly, that their careers in Training/Lecturing etc are sustained. • Applica*ons could include named individuals for the Lecturer posts, or else unnamed posts that will be filled through interna*onal compe**on. • Training is best done as a cohort – so smaller scale (one trainer, 1-‐2 trainees) will be less effec*ve than larger scale. This is unless the training is truly integrated in a research environment containing many FTEs/students. • Training should be available to individuals from any stage of their career from student to PI. • Training materials developed for these posts should be made freely available (open access). Training (not trainers) should be evaluated by the trainees to capture added-‐value. • Careers of Trainers need to be fostered by offering not less than 3 and op*mally 5 year Lecturer posts. • Overheads and associated capital will need to be part of the package. • Trainers should commit to training from across the MRC ‘family’ not just from the locality. • Trainers should be recognised for their contribu*ons when these are sufficient to warrant their inclusion as co-‐authors on scien*fic publica*ons etc.
- 28. • Training is the ini1al Mission of ELIXIR-‐UK • Nevertheless, the UK contains substan*al exper*se relevant to ELIXIR infrastructures • ELIXIR-‐UK seeks to capture this exper*se by appoin*ng representa*ves , of which the first two are • Carole Goble: Representa*ve for Data Interoperability, vocabulary & ontology • Susanna-‐Assunta Sansone: Representa*ve for Tools, Interoperability and Service Registry New Missions
- 29. ELIXIR-‐UK will: • Firmly establish Training, and its funding, as being essen*al for successful UK academic & industrial research, and for delivering ELIXIR infrastructures • Be strengthened by contribu*ons to ELIXIR infrastructures from individuals from across the UK Future Ques*ons: • How will ELIXIR-‐UK op*mally represent the UK (incl. industry) as a Distributed Node? • What should the Node look like in 2015, 2020 ...? Data Standards Tools Training Compute Industry Forecast
- 30. 30 Thank you