ELIXIR and ELIXIR-UK Training Activities
August 2016
Rita Hendricusdottir [email protected] of the ELIXIR Training Coordinator groupTraining Outrech Manager ELIXIR-UK
Data
Interoperability
Tools
Compute
Training
Technical platforms
User communities Marine metagenomics
Human data
Crop and forest plants
Rare diseases
data for life!
Target Audience
ELIXIR Training Coordination in 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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Delivering training to the 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
Building an ELIXIR Training 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)
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.
The Training platform and its external liaisons
ELIXIR Training builds on pre-existing activities in the national NodesSurvey
ELIXIR Training builds on pre-existing activities in the national Nodes
ELIXIR-UKCoordinating the
DC/SWC; Statistics training & TeSS
ELIXIR-FR110 courses in bioinformatics, NGS, Cloud & Galaxy; (2400
trainees)
ELIXIR-FITraining in NGS data analysis, HPC, clouds
and VMs All nodes provide node specific training and training activities - highlights
ELIXIR-ESHPC Workshop
Galaxy Workshop
ELIXIR-CHOver 50 courses per year; over
70 SIB and international trainers
ELIXIR-EE Training in RNAseq, HPC,
Python, R, ELIXIR-EE tools
ELIXIR-NLBYOD; Bioinformatics
training, NGS, SWC/DC, Galaxy
ELIXIR-ITLeading TtT; Training in
NGS, Galaxy, Metagenomics & HPC
ELIXIR-CZE-learning platform
testing
ELIXIR-NOTraining in NGS, Galaxy
pipelines, HPC
ELIXIR-SIeLearning platform
(Galaxy, Cloud and HPC); SWC/DC
ELIXIR-PTTtR lead; GTPB Training; Plants/ Marine Metagenomics
ELIXIR-EBITraining in
Bioinformatics, tools, resources; TtT
ELIXIR-UK training
Lee LarcombeELIXIR-UK Training [email protected]
Consider Strategic Training Priorities
• Talking to research communities
• Surveys (both ours and others)
• Engaging with Industry
• Listening to experts (sector leads and others)
• Observing funding trends/initiatives
ELIXIR-UK training priorities
Core Bioinformatics Skills
Applied Genomics
Metabolomics
Clinical Genomics
Structural Bioinformatics
ELIXIR-UK is addressing these 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
Named ELIXIR training centres
Edinburgh GenomicsMick Watson. Edinburgh University
Cambridge Bioinformatics Training CentreGabriella Rustici. Cambridge University
Birmingham Metabolomics Training CentreMark Viant & Rick Dunn. University of Birmingham
Earlham Institute training (soon)
Edinburgh GenomicsCore Bioinformatics Skills
Applied Genomics
Named ELIXIR training centres
Cambridge Bioinformatics
Named ELIXIR training centresCore Bioinformatics Skills
Applied Genomics
MetabolomicsBirmingham Metabolomics Centre
Named ELIXIR training centre
Earlham InstituteNamed ELIXIR training centre
Core Bioinformatics Skills
Applied Genomics
Core Bioinformatics SkillsSoftware & Data CarpentryCollaborating with other Institutes & Initiatives
Core Bioinformatics Skills
Applied Genomics
FARR Institute
Clinical GenomicsFARR InstituteCollaborating with other Institutes & Initiatives
Structural BioinformaticsBioExcelWorking with other infrastructure projects
www.statschoices.org.uk
Core Bioinformatics Skills
Developing new projects to fill gaps
Core Bioinformatics Skills
Statistics Training Signposting (StaTS) project
25
If you want to be involved please contact:Rita Hendricusdottir [email protected] [email protected]
Thank you Lee Larcombe. Edinburgh University Chris Ponting. Edinburgh University Mick Watson. Edinburgh University Gabriella Rustici. Cambridge UniversityMark Viant & Rick Dunn. University of BirminghamNiall Beard. University of ManchesterAleksandra Nenadic. University of Manchester
And everyone involved….
ELIXIR Training workshops Sept 2015- June 2016
Overview of previous workshops
ELIXIR Training workshops May 2016- Dec 2016
Overview of currently planned workshops There are many more workshops in the nodes, see some highlights in the following slide
The Training platform liaison - externalELIXIR 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