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ELIXIR UK Node ELIXIR‐UK the UK Node of the European Life Sciences Infrastructure for Biological Information www.elixir‐europe.org elixir‐uk.org The USA 2 EUROPE 3 UK: Poor data quality hindering government open data programme • “A Computer Weekly analysis of 50 spending data releases by the Cabinet Office since May 2010 has shown they were so marred by "dirty data" and inconsistent computer encoding, systematic scrutiny would require advanced computer programming skills.” Thursday 28 August 2014 http://www.computerweekly.com/news/2240227682/Poor‐data‐quality‐ hindering‐government‐open‐data‐transparency‐programme 4 Establishing a fresh UK activity Oxford University Computational Genomics Analysis and Training (CGAT) €1.6million The University of Manchester Seed fund The Oxford e‐Research Centre European Bioinformatics Institute (EMBL‐EBI) in kind University of Cardiff & NERC EOS Centre funding The Genome Analysis Centre (TGAC) University College London University of Birmingham University of Edinburgh Queen Mary, London University of Cambridge University of Liverpool Centre for Genomic Medicine Harness existing expertise Core Staff TeSS Staff Train across the Spectrum Technical Life Science Infrastructure Researchers Service Providers TCRS TCIT Training Training Coordinator, Coordinator, Research Infrastructure Science Technology Lee Larcombe Aleks Pawlik ELIXIR‐UK working across Europe: Training Coordination Group Mission: to establish an interacting ELIXIR wide training community & to ensure coherency in the delivery of training related to ELIXIR activities. TrCG 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 TrCG facilitating training in UK/Europe Form a strong training community within ELIXIR • Form strong training community Encourage within ELIXIR collaboration within • Drive partnerships UK and Europe • Coordinate development of training – Training/workshops: Related to Partnership with training professionals ELIXIR infrastructure – Train the trainers: Universities and Enhance quality of training Industry – E‐learning: improve E‐learning Enhance impact of training training • Increase accessibility for training – TeSS: ELIXIR training portal Funding opportunities • 11 Nov 2014: First TrCG Face to Face meeting Promote UK training in Europe • EXCELERATE Training WP. Reaching out to Europe The ELIXIR Training Coordinator Group is key to this ENGAGING WITH INDUSTRY 11 Appointed an Industry Engagement advisory committee Confirmed members: • Claus Bendtsen, AstraZeneca • Mark Forster, Syngenta • Samiul Hasan, GSK • Wendy Filsell, Uniliver • William Spooner, Eagle Genomics • Audrey Kauffmann, Novartis 12 Two Surveys Technical Life Science Infrastructure Researchers Service Providers • To help us understanding the bioinformatics‐related training needs of industry and • consequently to ensure that suitable training activities are developed and honed to target such needs. 13 Novartis Respondents GlaxoSmithKline Illumina Eagle Genomics Sanofi NIBR Bayer Pharma AG Bayer AstraZeneca 90 Unilever UCB 80 Pfizer Inc. OP 70 Heptares 60 Eli Lilly & Company Bayer Healthcare 50 Astellas Pharma Inc. 40 Roche Redoxis AB 30 Omixon Biocomputing LTD 20 Novo Nordisk MedImmune 10 Lundbeck Life Technologies - Thermo Fisher… 0 LGC Bioinformaticians Wet lab Instem Scientific Large company Small-to-medium enterprise Ina Harrow Consulting Genentech Euformatics Oy EMD Serono (Merck Serono) Dupont DNAnexus DNAdigest.org Databiology Bioindustry Park Silvano Fumero… Biogen Idec 0 1020304050607080 14 Disciplines Bioanalytics Biochemistry/Biophysics Bioinformatics Biomedical Sciences Cell biology Chemistry Computational chemistry Computer Science Drug development Epidemiology Genomics/epigenomics Immunology Infectious diseases Medicine Microbiology Molecular Biology Neurobiology Oncology Plant Sciences Proteomics Systems biology Toxicology Virology 0 102030405060 Bioinformaticians Wet lab 15 Lab‐based scientists and statistics How confident are you Do you collaborate with a with statistics? bioinformatician/statistician? Yes, I have a bioinformatician in the group that helps me to design experiments and 32.4% Very also provides support for the data analysis confident 6% 6% Yes, occasionally I interact with a Confident bioinformatician/statistician at my Institute, 32.4% particularly when I get stuck and I don’t 29% know how to proceed. Not so confident No, the data analysis is carried out by 59% someone else. I just receive a file with the 1.5% I am not even results. sure of what statistics I need to know No, I do not have any support. I am responsible for analyzing the data that I 34.0% generate. 16 Programming experience, languages Wet lab – programming Bioinformaticians - experience Programming languages SQL sparql Scala PL/SQL MySQL 26 HTML bash Unix % Yes Javascript No Ruby Matlab 74 C++ Java % Perl R/BioConductor Python 0 5 10 15 20 17 TRAINING STRATEGY 18 UK: How have we prioritised training need? • Talking to research communities • Surveys (both ours and others) • Engaging with Industry • Listening to experts (sector leads and others) • Observing funding trends/initiatives Bioimaging Statistics Crop Genomics Data Curation & Standards Five areas to develop as ELIXIR UK strategic training priorities Environmental Sciences Clinical Genomics (TeSS) sector Genomics Applications Structural Bioinformatics Genomics Methods Engagement Advanced Scientific Skills Support training ICT & Software Applied Genomics UK Industry Engagement Translational Metabolomics Community Metabolomics ELIXIR Important supporting activities to develop Proteomics further as ELIXIR UK activities Current Structural Bioinformatics Tess Structural Bioinformatics representing the sector at initial Training the Trainers Protein structure classification/analysis events Alexey Murzin – LMB (Cambridge) ‐ SCOP Christine Orengo – UCL ‐ CATH Structural annotation of genome sequences and 3D training gap analysis models and training Tom Blundell – Cambridge University ‐ FUGUE workflow workshop Christine Orengo – Gene3D Julian Gough –Bristol University ‐ SUPERFAMILY David Jones –UCL ‐ pDomThreader fund‐raising to plug Michael Sternberg – Imperial, London ‐ PHYRE these training gaps. ‐ http//:genome3d.eu protein network Search protein(s) and interactions Protein-protein interaction network analysis Structural analysis Database Integration STRING Complex prediction tutorial tutorial tutorial Interface analysis tutorial No BLAST tutorial Specific applications with structure / link model? Yes tutorial link link Interactome3D Output 3D structure link PDBePISA HOTREGION tutorial Visualisation & Functional annotation tutorial *BLAST: Basic Local Alignment Search Tool (sequence similarity) Identifying UK Training Needs Bioimaging Crop Genomics Data Curation & Standards Environmental Sciences Genomics Applications Clinical Genomics Industry & Sector‐Specific ICT & Software Surveys Industry Engagement Metabolomics Proteomics Structural Bioinformatics Tess TRAINING DELIVERY 24 software‐carpentry.org Teach the “95% researchers” basic lab skills for scientific computing: the tools and techniques that will help them get more done in less time, and with less pain. Volunteer instructors / Bootcamps / Train the trainers / Free lesson materials • Essential Software Engineering for researchers • Software Sustainability Institute, UK • UK and European workshops – Train researchers. Train the trainers. – Supporting other SW workshops software‐carpentry.org • Establishing SC Foundation – ELIXIR representation on interim board • Data literacy for researchers • Expert data curation/integration • Establishing Data Carpentry datacarpentry.org – ELIXIR representation on board • First European Data Carpentry Workshop Nov 27‐28, 2014, UK – Applications to FOSTER open science training awards to scale up train the trainers TeSS Portal • Registering and discovering training materials • Standard metadata • Aggregated & Sourced from ELIXIR‐UK, ELIXIR nodes and externals, Branding • Packaging, VMs & linking • Training workflows • Progressively deliver forms of training online • Cooperation with eLearning Platform, ELIXIR‐Slovenia • Piloting with Structural Biology Summary NETHERLANDS SWITZERLAND Training DENMARKEBI SWEDEN SLOVENIA ESTONIA ITALY Cloud Technical Services Data Interoperability, vocabularies and ontology services Tools Interoperability & Service Registry Thank you http://elixir-uk.org/ 29 Summary NETHERLANDS SWITZERLAND Training DENMARKEBI SWEDEN SLOVENIA Cloud Technical Services Data Interoperability, vocabularies and ontology services Tools Interoperability & Service EDAM, SWO Registry Questions from the floor • How many people will be trained, or can we aim to train? Scalability and multipliers • (the model of train the trainers, coordinated materials and bootcamps is a scalable approach. The addressing of scale of training was appreciated.) • How do we relate to EMTRAIN, Coursera, ROSALIND (http://rosalind.info) • (we feed from and to these as resources for TeSS, but we need more formal links). • How will we measure the impact of the training? • (follow‐up metrics needed. Hard problem. Manny in a metrics TF). • How will our training be applied to clinical and medical training, esp in different
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