Introduction to ELIXIR-UK's training activities presented by Rita Hendricusdottir at the ELIXIR-UK Workshop during Genome Science 2016 in Liverpool on 31st August 2016

1. ELIXIR and ELIXIR-UK Training 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
Marine metagenomics
Human data
Crop and forest plants
Rare diseases
data for life!

3. Target Audience

4. 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.

5. BuildinganELIXIR
TrainingInfrastructureELIXIR Training Platform
Deliveringtrainingtothe
ELIXIRCommunity

6. 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

7. 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)

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 platform and its external liaisons

10. ELIXIR Training builds on pre-existing activities in the
national Nodes
Survey

11. ELIXIR Training builds on 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-UK Training Coordinator
Lee.Larcombe@igmm.ed.ac.uk

13. 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

14. ELIXIR-UK training priorities
Core Bioinformatics Skills
Applied Genomics
Metabolomics
Clinical Genomics
Structural Bioinformatics

15. 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

16. Named ELIXIR training centres
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 Bioinformatics Skills
Applied Genomics
Named ELIXIR training centres

18. Cambridge Bioinformatics
Named ELIXIR training centres
Core Bioinformatics Skills
Applied Genomics

19. MetabolomicsBirmingham Metabolomics Centre
Named ELIXIR training centre

20. Earlham Institute
Named ELIXIR training 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
Collaborating with other Institutes & Initiatives

23. Structural Bioinformatics
BioExcel
Working with other infrastructure projects

24. www.statschoices.org.uk
Core Bioinformatics Skills
Developing new projects to fill gaps
Core Bioinformatics Skills
Statistics Training Signposting (StaTS) project

25. 2
5
If you want to 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 workshops Sept 2015- June 2016
Overview of previous workshops

27. 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

28. The Training platform liaison - 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