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ELIXIR and ELIXIR-UK training activities
The document outlines Elixir's training activities and infrastructure, aimed at creating a unified training community across Europe for bioinformatics and related fields. It details the various training initiatives and coordinated efforts among member countries, including specific training programs, workshops, and the development of an e-learning strategy. The initiative targets different audiences, including developers, trainers, and researchers to enhance bioinformatics skills and collaboration among national nodes.
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ELIXIR and ELIXIR-UK training activities
- 1. ELIXIR and ELIXIR-UKTraining Activities August 2016 Rita Hendricusdottir rita.hendricusdottir@igmm.ed.ac.uk Chair of the ELIXIR Training Coordinator group Training Outrech Manager ELIXIR-UK
- 2. Data Interoperability Tools Compute Training Technical platforms User communities Marinemetagenomics Human data Crop and forest plants Rare diseases data for life!
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- 4. ELIXIR Training Coordinationin Europe Mission: To establish an interactive ELIXIR wide training community across all member states that coherently delivers ELIXIR-related training. Platform lead: Chris Ponting (ELIXIR-UK), Patricia Palagi (ELIXIR-CH), Rita Hendricusdottir (ELIXIR-UK), Celia van Gelder (ELIXIR-NL) Training Coordinators Group (TrCG): One Training Coordinator of each ELIXIR node plus the subtask leaders of EXCELERATE.
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- 6. Delivering training tothe ELIXIR Community Train the Developer (EE, EBI, SE, IL) Developing the Virtual Coffee room, a forum for developer and infrastructure operator Train the Trainer (IT, EBI, FI, SE, CH, UK) Build a highly skilled and coherent community of trainers Train the Researcher (PT, CH, UK, NL, SI, NO, ES, GR, FI, FR) Provide training for researchers: • Software and Data Carpentry • Galaxy & Chipster • High Performance Computing • Driven by use case needs
- 7. Building an ELIXIRTraining Infrastructure Quality/Impact (UK, EBI) Defining and delivering framework of best practices, specifications, standards, metrics for ELIXIR Training. eLearning (SI, NL, CH, PT, IL, FI) Provide ELIXIR with a e-Learning strategy, guidelines and recommendations for standard and interoperable ELIXIR e-Learning resources TeSS Training Portal (UK, CH, PT, NL)
- 8. ELIXIR Training Portal– TeSS for browsing & discovering training events, courses, materials… https://tess.elixir-uk.org/ Aims to give a snapshot of the ELIXIR training landscape and beyond • automatically aggregating data from Nodes & 3rd-party providers • making events & resources discoverable, surfacing information in ways that support user decisions & choices via training packages & workflows Allows Nodes to contribute their training resources • to showcase their latest news, events, activity highlights, etc.
- 9. The Training platformand its external liaisons
- 10. ELIXIR Training buildson pre-existing activities in the national Nodes Survey
- 11. ELIXIR Training buildson pre-existing activities in the national Nodes ELIXIR-UK Coordinating the DC/SWC; Statistics training & TeSS ELIXIR-FR 110 courses in bioinformatics, NGS, Cloud & Galaxy; (2400 trainees) ELIXIR-FI Training in NGS data analysis, HPC, clouds and VMs All nodes provide node specific training and training activities - highlights ELIXIR-ES HPC Workshop Galaxy Workshop ELIXIR-CH Over 50 courses per year; over 70 SIB and international trainers ELIXIR-EE Training in RNAseq, HPC, Python, R, ELIXIR-EE tools ELIXIR-NL BYOD; Bioinformatics training, NGS, SWC/DC, Galaxy ELIXIR-IT Leading TtT; Training in NGS, Galaxy, Metagenomics & HPC ELIXIR-CZ E-learning platform testing ELIXIR-NO Training in NGS, Galaxy pipelines, HPC ELIXIR-SI eLearning platform (Galaxy, Cloud and HPC); SWC/DC ELIXIR-PT TtR lead; GTPB Training; Plants/ Marine Metagenomics ELIXIR-EBI Training in Bioinformatics, tools, resources; TtT
- 12. ELIXIR-UK training Lee Larcombe ELIXIR-UKTraining Coordinator Lee.Larcombe@igmm.ed.ac.uk
- 13. Consider Strategic TrainingPriorities • Talking to research communities • Surveys (both ours and others) • Engaging with Industry • Listening to experts (sector leads and others) • Observing funding trends/initiatives
- 14. ELIXIR-UK training priorities CoreBioinformatics Skills Applied Genomics Metabolomics Clinical Genomics Structural Bioinformatics
- 15. ELIXIR-UK is addressingthese training priorities through: • Named ELIXIR-UK training centres • Collaborating with other institutes and initiatives • Working with other infrastructure projects • Developing new projects to fill gaps
- 16. Named ELIXIR trainingcentres Edinburgh Genomics Mick Watson. Edinburgh University Cambridge Bioinformatics Training Centre Gabriella Rustici. Cambridge University Birmingham Metabolomics Training Centre Mark Viant & Rick Dunn. University of Birmingham Earlham Institute training (soon)
- 17. Edinburgh Genomics Core BioinformaticsSkills Applied Genomics Named ELIXIR training centres
- 18. Cambridge Bioinformatics Named ELIXIRtraining centres Core Bioinformatics Skills Applied Genomics
- 19. MetabolomicsBirmingham Metabolomics Centre NamedELIXIR training centre
- 20. Earlham Institute Named ELIXIRtraining centre Core Bioinformatics Skills Applied Genomics
- 21. Core Bioinformatics Skills Software& Data Carpentry Collaborating with other Institutes & Initiatives Core Bioinformatics Skills Applied Genomics
- 22. Clinical Genomics FARR Institute Collaboratingwith other Institutes & Initiatives
- 23. Structural Bioinformatics BioExcel Working withother infrastructure projects
- 24. www.statschoices.org.uk Core Bioinformatics Skills Developingnew projects to fill gaps Core Bioinformatics Skills Statistics Training Signposting (StaTS) project
- 25. 2 5 If you wantto be involved please contact: Rita Hendricusdottir rita.hendricusdottir@igmm.ed.ac.uk Lee Larcombe lee.Larcombe@igmm.ed.ac.uk Thank you Lee Larcombe. Edinburgh University Chris Ponting. Edinburgh University Mick Watson. Edinburgh University Gabriella Rustici. Cambridge University Mark Viant & Rick Dunn. University of Birmingham Niall Beard. University of Manchester Aleksandra Nenadic. University of Manchester And everyone involved….
- 26. ELIXIR Training workshopsSept 2015- June 2016 Overview of previous workshops
- 27. ELIXIR Training workshopsMay 2016- Dec 2016 Overview of currently planned workshops There are many more workshops in the nodes, see some highlights in the following slide
- 28. The Training platformliaison - external ELIXIR has representative in EDISON External Liaison Group (ELG) Discuss and align ELIXIR’s training plans with those of the BD2K Training Coordination Center (TCC) GOBLET-ELIXIR Collaboration in place (April 2015) Explore collaboration regarding RDA-CODATA Data Science Summer Schools Collaboration agreement in preparation with Software Carpentry/Data Carpentry foundation (pilot already ongoing). Build SWC/DC capacity in the ELIXIR nodes Galaxy , ELIXIR strategy under development