This presentation was delivered at the ELIXIR Board meeting in November 2014 as an update of UK node activities

1. European
Life
Sciences
Infrastructure
for
Biological
Information
www.elixir-­‐europe.org
ELIXIR-­‐UK
the UK Node of the
elixir-­‐uk.org

2. Establishing
a
fresh
UK
ac2vity
Oxford
University
Computa5onal
Genomics
Analysis
and
Training
(CGAT)
The
University
of
Manchester
The
Oxford
e-­‐Research
Centre
European
Bioinforma2cs
Ins2tute
(EMBL-­‐EBI)
University
of
Cardiff
&
NERC
EOS
Centre
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
€1.6million
Seed
fund
in
kind
funding

3. Establishing
a
fresh
UK
ac2vity
Core
Staff
TeSS
Staff

4. Ac2vi2es
Research
scien2sts
and
Infrastructure
technologists
bioinforma2cs,
compu2ng,
sta2s2cs
and
biology,
service
deployment
Mul2plier
effects
Training
Partnerships
12
UK
centres,
Na2onal
Centres
SoUware
Sustainability
Ins2tute,
Digital
Cura2on
Centre.
ELIXIR
Nodes
SIB,
NL,
Slovenia,
Sweden,
EBI
Interna2onal
ini2a2ves
GOBLET,
SoUware
Carpentry,
Data
Carpentry,
FOSTER,
Intl
Soc
BioCura2on
Industry

5. Ac2vi2es
Research
scien2sts
and
Infrastructure
technologists
bioinforma2cs,
compu2ng,
sta2s2cs
and
biology,
service
deployment
Mul2plier
effects
Training
Data
Interoperability,
vocabularies
and
ontology
services
Tools
Interoperability
&
Service
Registry
Cloud
Technical
Services
EDAM,
SWO
€32,000

6. Ac2vi2es
Research
scien2sts
and
Infrastructure
technologists
bioinforma2cs,
compu2ng,
sta2s2cs
and
biology,
service
deployment
Mul2plier
effects
Training
Data
Interoperability,
vocabularies
and
ontology
services
Tools
Interoperability
&
Service
Registry
Cloud
Technical
Services
NETHERLANDS
Bring Your Own Data
DENMARK
SWEDEN
EBI
€32,000

7. Research
scien2sts
and
Infrastructure
technologists
bioinforma2cs,
compu2ng,
sta2s2cs
and
biology,
service
deployment
Training
Genomic
Research
Researchers
Technical
Infrastructure
Infostructure
Providers
Lee Larcombe Aleks Pawlik

8. Structural
Bioinforma2cs
represen2ng
the
sector
at
ini2al
Training
the
Trainers
events
training
gap
analysis
and
training
workflow
workshop
fund-­‐raising
to
plug
these
training
gaps.
Protein
structure
classifica5on/analysis
Alexey
Murzin
–
LMB
(Cambridge)
-­‐
SCOP
Chris2ne
Orengo
–
UCL
-­‐
CATH
Structural
annota5on
of
genome
sequences
and
3D
models
Tom
Blundell
–
Cambridge
University
-­‐
FUGUE
Chris2ne
Orengo
–
Gene3D
Julian
Gough
–
Bristol
University
-­‐
SUPERFAMILY
David
Jones
–
UCL
-­‐
pDomThreader
Michael
Sternberg
–
Imperial,
London
-­‐
PHYRE
-­‐
hHp//:genome3d.eu

9. protein
network Search protein(s) and interactions
Database Integration
Specific applications
3D structure
tutorial
tutorial
tutorial
link
link
link
tutorial
STRING
with
structure
/
model?
Interactome3D
Yes
No
Visualisation &
Functional annotation
tutorial
Complex prediction
Interface analysis
tutorial
tutorial
tutorial
Protein-protein interaction network analysis
link
PDBePISA HOTREGION
BLAST
Structural analysis
Output
*BLAST: Basic Local Alignment Search Tool (sequence similarity)

11. soKware-­‐carpentry.org
Teach
the
“95%
researchers”
basic
lab
skills
for
scien2fic
compu2ng:
the
tools
and
techniques
that
will
help
them
get
more
done
in
less
2me,
and
with
less
pain.
Volunteer
instructors
/
Bootcamps
/
Train
the
trainers
/
Free
lesson
materials

12. • Essen2al
SoUware
Engineering
for
researchers
• SoUware
Sustainability
Ins2tute,
UK
• UK
and
European
workshops
– Train
researchers.
Train
the
trainers.
– Suppor2ng
other
SW
workshops
• Establishing
SC
Founda2on
– ELIXIR
representa2on
on
interim
board
soKware-­‐carpentry.org
• Data
literacy
for
researchers
• Expert
data
cura2on/integra2on
• Establishing
Data
Carpentry
– ELIXIR
representa2on
on
board
• First
European
Data
Carpentry
Workshop
Nov
27-­‐28,
2014,
UK
– Applica2ons
to
FOSTER
open
science
training
awards
to
scale
up
train
the
trainers
datacarpentry.org

13. • 22&23
October
2014
– ELIXIR
UK
&
SSI
SoKware
Carpentry
“Train
the
Trainer”
Workshop
@TGAC
–ELIXIR
UK
• 6&7
November
2014
– Advanced
R"
SoUware
Carpentry
bootcamp
at
UZH/ETHZ
in
Zurich
• 9&14
November
2014
– SoUware
Carpentry
workshop
for
NHS
Clinical
Bioinforma5cs
MSc
@
Manchester
• 17&18
November
2014
– CGR
&
GARNet
SoUware
Carpentry
for
the
2nd
Plant
Scien2sts
Bootcamp
@Liverpool
• 27&28
November
2014
– ELIXIR
UK
Data
Carpentry
workshop
in
Manchester
(data
cura2on
&
standards
and
tools
module)
• December
2014/
January
2015
– ELIXIR
UK
MicrosoK
Azure
for
Research
workshop
in
Manchester
• 3-­‐4
February
2015
– ELIXIR
UK
&
SSI
SoUware
Carpentry
Course
for
EPSRC
&
MRC
Centre
for
Doctoral
Training
in
Regenera5ve
Medicine
soKware-­‐carpentry.org
datacarpentry.org

14. 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
• Coopera2on
with
eLearning
Platorm,
ELIXIR-­‐Slovenia
• Pilo2ng
with
Structural
Biology

15. Industry
• Industry
board
• Two
surveys:
– bioinforma2cians,
– wet
lab
scien2sts
• ELIXIR-­‐Netherlands
use
same
survey
0 10 20 30 40 50 60 70 80
Novartis
GlaxoSmithKline
Illumina
Eagle Genomics
Sanofi
NIBR
Bayer Pharma AG
Bayer
AstraZeneca
Unilever
UCB
Pfizer Inc.
OP
Heptares
Eli Lilly & Company
Bayer Healthcare
Astellas Pharma Inc.
Roche
Redoxis AB
Omixon Biocomputing LTD
Novo Nordisk
MedImmune
Lundbeck
Life Technologies - Thermo Fisher
LGC
Instem Scientific
Ina Harrow Consulting
Genentech
Euformatics Oy
EMD Serono (Merck Serono)
Dupont
DNAnexus
DNAdigest.org
Databiology
Bioindustry Park Silvano Fumero
Biogen Idec

16. 0 10 20 30 40 50 60 70 80
Novartis
GlaxoSmithKline
Illumina
Eagle Genomics
Sanofi
NIBR
Bayer Pharma AG
Bayer
AstraZeneca
Unilever
UCB
Pfizer Inc.
OP
Heptares
Eli Lilly & Company
Bayer Healthcare
Astellas Pharma Inc.
Roche
Redoxis AB
Omixon Biocomputing LTD
Novo Nordisk
MedImmune
Lundbeck
Life Technologies - Thermo Fisher
LGC
Instem Scientific
Ina Harrow Consulting
Genentech
Euformatics Oy
EMD Serono (Merck Serono)
Dupont
DNAnexus
DNAdigest.org
Databiology
Bioindustry Park Silvano Fumero
Biogen Idec
Use of data standards in curation and/or data integration practices
Bioinforma2cians:
Which
bioinforma2cs
training
would
you
most
value
in
rela2on
to
your
work?
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
Statistical methodologies
Programming skills
Data analysis skills
Basic computing skills
Sta2s2cs
is
a
major
weakness,
regardless
of
the
user
group
Industry
• Industry
board
• Two
surveys:
– bioinforma2cians,
– wet
lab
scien2sts
• ELIXIR-­‐Netherlands
use
same
survey

17. Iden2fying
UK
Training
Needs
Bioimaging
Crop
Genomics
Data
Cura5on
&
Standards
Environmental
Sciences
Genomics
Applica5ons
Clinical
Genomics
ICT
&
SoKware
Industry
Engagement
Metabolomics
Proteomics
Structural
Bioinforma5cs
Tess
Industry
&
Sector-­‐Specific
Surveys

18. Bioimaging
Crop
Genomics
Data
Cura2on
&
Standards
Environmental
Sciences
Genomics
Applica2ons
Genomics
Methods
ICT
&
SoUware
Industry
Engagement
Metabolomics
Proteomics
Structural
Bioinforma2cs
Tess
Five
areas
to
develop
as
ELIXIR
UK
strategic
training
Clinical
Genomics
Structural
Bioinforma2cs
Advanced
Scien2fic
Skills
Applied
Genomics
Metabolomics
Transla2onal
Engagement
Community
Support
(TeSS)
C u r r e n t
E L I X I R
U K
t r a i n i n g
s e c t o r
a c 5 v i 5 e s
Important
suppor2ng
ac2vi2es
to
develop
further
as
ELIXIR
UK
priori2es
Sta2s2cs

19. ELIXIR-­‐UK
working
across
Europe:
Training
Coordina2on
Commivee
Establish
an
interacting
ELIXIR
wide
training
community
&
to
ensure
coherency
in
the
delivery
of
training
related
to
ELIXIR
activities.
TrCC
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
TeSS
Carole
Goble
(invited
for
INFRADEV3)

20. TrCG
facilita2ng
training
in
UK/Europe
Form
a
strong
training
community
within
ELIXIR
• F
orm
strong
training
community
within
ELIXIR
• Drive
partnerships
• Coordinate
development
of
training
– Training/workshops:
Related
to
ELIXIR
infrastructure
– Train
the
trainers:
Universities
and
Industry
– E-­‐learning:
improve
E-­‐learning
training
• Increase
accessibility
for
training
– TeSS:
ELIXIR
training
portal
• 11
Nov
2014:
First
TrCG
Face
to
Face
meeting
• EXCELERATE
Training
WP.
Encourage
collaboration
within
UK
and
Europe
Partnership
with
training
professionals
Enhance
quality
of
training
Enhance
impact
of
training
Funding
opportunities
Promote
UK
training
in
Europe

21. Summary
Training
Cloud
Technical
Services
Data
Interoperability,
vocabularies
and
ontology
services
Tools
Interoperability
&
Service
Registry
NETHERLANDS
SWITZERLAND
DENMARK EBI SWEDEN SLOVENIA
EDAM,
SWO

22. Summary
Training
Cloud
Technical
Services
Data
Interoperability,
vocabularies
and
ontology
services
Tools
Interoperability
&
Service
Registry
NETHERLANDS
SWITZERLAND
DENMARK EBI SWEDEN SLOVENIA
EDAM,
SWO

23. 23
Thank
you
http://elixir-uk.org/

24. 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
ELIXIR
countries
with
their
own
governance
and
healthcare
regulations.
• (serious
local
customisation
needed)
• How
do
we
get
help
to
run
a
SC
bootcamp
in
our
node?
• (we
need
to
have
core
information
on
the
web
site).
24

25. Additional
thoughts
• We
should
consider
the
ELIXIR-­‐UK
activities
in
terms
of
Additional
and
Commissioned
Services,
in
line
with
the
Consortium
Agreement.
25

26. ELIXIR
UK
node
Mission: To facilitate training of research scientists and infrastructure technologists in
bioinformatics, computing, statistics and biology, in partnership with UK centres, industry and
other ELIXIR Nodes.
Oxford University Computational Genomics
Analysis and Training (CGAT)
University of Manchester
European Bioinformatics Institute (EMBL-EBI)
University of Cardiff & NERC EOS Centre
The Genome Analysis Centre (TGAC)
The Oxford e-Research Centre
University College London
University of Birmingham
University of Edinburgh
Queen Mary, London
University of Cambridge
University of Liverpool Centre for Genomic
Medicine
2014
Q1: Recruitment round 1
& ELIXIR PoW5 Training
drafted & ELIXIR Training
Node Survey & Structural
Bioinformatics Training
Workshop & Industry
workshop @ TGAC
Q2: ELIXIR HoN and
TCG meeting
@Sandhamn & Lee,
Aleks, Niall, Milo start &
Advisory Group formed &
TeSS meeting
Manchester
Q3: Industry Committee
constituted,& Kick-off
meeting, Rita starts,
ELIXIR/ELIXIR-UK Node
meeting Hinxton, TrCC
constituted
Q4:ELIXIR Innovation and
SME forum & ELIXIR
SAB - Heads of Nodes
meeting, Hinxton, ELIXIR-UK
ECA being negotiated
INFRADEV-3 preparation
Bringing together
an ELIXIR-wide
Training
Coordination
Group
Key achievements
in Software & Data
Carpentry delivery
and International
engagement
(BD2K, SCF, RDA
etc)
Strategic Focus on:
Clinical Genomics
Structural Bioinformatics
Advanced Scientific Skills
Applied Genomics
Metabolomics