ELIXIR and ELIXIR-UK Training Activities

August 2016

Rita Hendricusdottir rita.hendricusdottir@igmm.ed.ac.ukChair 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 CoordinatorLee.Larcombe@igmm.ed.ac.uk

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 rita.hendricusdottir@igmm.ed.ac.ukLee Larcombelee.Larcombe@igmm.ed.ac.uk

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