The document outlines the current activities and future plans of the ELIXIR UK node, focusing on building a robust European life sciences infrastructure for biological information. It emphasizes training initiatives for researchers and technologists in bioinformatics and related fields, detailing collaborations across various UK institutions and industry engagement. Key aspects include the establishment of a training community, addressing training needs, and coordinating efforts to enhance the delivery and effectiveness of bioinformatics training across Europe.

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

2. Current
Ac*vi*es
and
Future
Plans
of
the
ELIXIR
UK
Node
Chris
Pon*ng
(30
mins)

3. Overall
Mission
To
build
strong
and
sustainable
European
infrastructure
together
with
our
ELIXIR
partners.
• Data
• Standards
• Tools
• Compute
• Training
• Industry
From
now
on,
ELIXIR-­‐UK
will
pursue
its
mission
across
all
of
these
ELIXIR
infrastructures

4. Training
Mission
To
facilitate
training
of
research
scien*sts
and
infrastructure
technologists
in
bioinforma*cs,
compu*ng,
sta*s*cs
and
biology,
in
partnership
with
UK
centres,
industry
and
other
ELIXIR
Nodes.
Oxford
University
Computa*onal
Genomics
Analysis
and
Training
(CGAT)
University
of
Manchester
European
Bioinforma*cs
Ins*tute
(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

5. Training Spectrum
TCRS
Training
Coordinator,
Research
Science
100%
TCIT
Training
Coordinator,
Infrastructure
Technology
100%
Lee Larcombe Aleks Pawlik
Genomic
Research
Researchers
Technical
Infrastructure
Service Providers

6. Mission:
to
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
ELIXIR-­‐UK
working
across
Europe:
Training
Coordina*on
CommiUee

7. 2012
Q2:
Ini*al
Mee*ng@MRC
Q3:
Subsequent
Mee*ng@MRC
Q4:
Ini*al
and
subsequent
submissions
for
ELIXIR-­‐
UK
Node
status
2013
Q1:
ELIXIR-­‐UK
Presubmission
applica*on
to
RCs
&
Netherlands
ELIXIR
workshop
Q2:
Resubmission
of
applica*on
to
RCs
a]er
reviewers’
comments
&
ELIXIR
Collabora*on
Agreement
mee*ng,
Heathrow
Q3:
RCs
applica*on
accepted
for
Jan
1
2014
start
&
HoN
mee*ng,
Hinxton
Q4:
GOBLET/ELIXIR-­‐UK
mee*ng
TGAC
&
ELIXIR
is
launched
2014
Q1:
Recruitment
round
1
&
ELIXIR
PoW5
Training
dra]ed
&
ELIXIR
Training
Node
Survey
&
Structural
Bioinforma*cs
Training
Workshop
&
Industry
workshop
@
TGAC
Q2:
ELIXIR
HoN
and
TCG
mee*ng
@Sandhamn
&
Lee,
Aleks,
Niall,
Milo
start
&
Advisory
Group
formed
&
TeSS
mee*ng
Manchester
Q3:
Industry
CommiUee
cons*tuted,&
Kick-­‐off
mee*ng,
Rita
starts,
ELIXIR/ELIXIR-­‐UK
Node
mee*ng
Hinxton,
TrCC
cons*tuted
Q4:ELIXIR
Innova*on
and
SME
forum
&
ELIXIR
SAB
-­‐
Heads
of
Nodes
mee*ng,
Hinxton,
ELIXIR-­‐UK
ECA
being
nego*ated
INFRADEV-­‐3
prepara*on
ABriefHistoryofELIXIR-UK
Start

8. Current
Organisa*onal
Chart

9. ELIXIR-­‐UK:
Current
Ac*vi*es
• Building
a
UK
Training
Community
• Building
a
Training
Community
across
Europe
• Adding
new
missions,
beyond
Training
• Iden*fying
Training
Needs
• Delivering
Training
• Defining
then
ac*ng
on
Priori*es
• Coordina*ng
Training
for
ELIXIR
Excelerate

10. Building
a
UK
Community
-­‐
website

11. Building
a
Training
Community
-­‐
TeSS
ELIXIR-­‐UK’s
mission
will
be
delivered,
in
part,
by
the
development
of
a
pilot
training
resource
plagorm,
termed
TeSS.
•
Ready
access
to
pre-­‐exis*ng
training
materials,
resources,
ac*vi*es
and
events;
•
Links
to
training-­‐relevant
catalogues
within
and
around
the
ELIXIR
network.
TeSS
will
ensure
that
all
such
informa*on
is
discoverable
by
trainers,
trainees,
researchers
and
technologists
across
ELIXIR’s
training
sectors,
in
academia
and
industry.
The
pilot
phase,
which
will
ul*mately
inform
the
strategy
for
the
long-­‐term
development
and
sustainability
of
the
plagorm,
will
gather
user
requirements
via
surveys
and
workshops,
perform
regular
gap
analysis
(regarding
both
training
courses
and
resources),
and
run
feasibility
studies
for
developing
content
pipelines
for
ELIXIR
stakeholders,
portable
plagorms
containing
open-­‐source
resources,
etc.
Carole
Goble
will
talk
more
about
this
aLer
lunch

12. Building
a
Training
Community
across
Europe:
the
TrCC
Rita
HendricusdoMr
will
talk
more
about
this
aLer
lunch
The
UK
has
led
the
forma*on
of
a
Training
Coordinator
CommiUee
with
representa*ves
from
17
ELIXIR
nodes
Chaired
by
Rita,
this
operates
across
Europe,
repor*ng
to
the
HoN
Training
has
equal
representa*on
to
the
Exis*ng
Technical
Coordina*on
Group
(TCG)

13. Engaging
with
Industry
• Audrey
Kaufmann,
Novar*s
Ins*tutes
for
BioMedical
Research
• Samiul
Hasan,
GlaxoSmithKline
• William
Spooner,
Eagle
Genomics
• Wendy
Filsell,
Unilever
• Claus
Bendtsen,
Astra
Zeneca
• Mark
Forster,
Syngenta
We
have
brought
together
a
group
of
people
from
Industry
to
help
us
beUer
understand
industrial
training
priori*es
Gabriella
Rus*ci
will
talk
more
about
the
Industry
Panel
aLer
lunch
They
have
made
themselves
available
for
advice,
and
were
important
in
helping
distribute
our
industry
survey

14. Iden*fying
UK
Training
Needs
Bioimaging
Crop
Genomics
Data
Cura*on
&
Standards
Environmental
Sciences
Genomics
Applica*ons
Clinical
Genomics
ICT
&
So]ware
Industry
Engagement
Metabolomics
Proteomics
Structural
Bioinforma*cs
Tess
Industry
&
Sector-­‐Specific
Surveys
Gabriella
Rus*ci
will
talk
more
about
the
Industry
Survey
aLer
lunch

15. Delivering
Training:
Data
&
So]ware
Skills
ElixirUKSectors
ICT&SoftwareDataCuration&Standards
Software Carpentry
Essential Software Engineering for
researchers:
Data Carpentry
Data literacy
Q2:
Establishing
partnerships
with
DC
and
SWC
Defining
the
strategy
for
data
cura*on
and
standards
delivery
within
DC
Bidding
for
Microso]
Azure
for
Research
Award
Q3:
Development
and
improvement
of
the
DC
materials
for
life
sciences
(MSL
Sprint)
Elixir
Pilot
Ac*ons
proposal
for
rolling
out
Carpentries
in
Elixir
Europe
Q4:
SWC
Train
the
Trainer
@
TGAC
Elixir
SWC
@
NHS
MSc
course
in
Manchester
Start
of
materials
development
for
DC
modules
on
biosharing
Elixir
DC
@
Manchester
Elixir
NL
–
establishing
the
demands
for
the
curriculum
for
a
life
science
data
expert.
(a
series
of
“DTL
Focus
mee*ngs”)

16. TF:
Service
Registry
Biomedbridges,
Denmark,
Sweden,
EBI,
UK
• ELIXIR-­‐UK
contribu*on:
– Ontologies:
EDAM,
So]ware
Ontology
(SWO)
– Biocatalogue.org
– Biosharing.org
• Joint
pilot
proposal
– EDAM
development
• Biotools
registry
Mee*ngs
aUended:
– Tool
Registry,
Imperial
College
London,
April
17
2013
(Goble)
– ELIXIR/BioMedBridges
Workshop
on
Tool
Registries,
October
16-­‐18,
2013,
Technical
University
of
Denmark
(Beard)
– January
2014
Aberdeen
(Beard)
– May
‘2014,
Hinxton
(Beard)
– “A
common
vocabulary
to
classify
resources
in
life
sciences”
Workshop
Brussels
16th
Oct
2014
(Goble,
Beard,
Sansone)
– ELIXIR-­‐DK
three
day
hackathon
to
prime
the
ELIXIR
Tools
&
Data
Services
Registry
(forthcoming)

17. FAIRPORT
The
Netherlands,
UK
• Funded
at
four-­‐day
mee*ng
hosted
at
The
Netherlands.
(Goble,
Blomberg,
Game
aUended).
• ELIXIR-­‐UK
Pilot
• hUp://www.datafairport.org/
• Goble
funded
to
run
FAIRDOM
(FAIRPORT
for
Systems
Biology),
working
with
ELIXIR-­‐NL.
• Strong
links
with
the
NIH
BD2K
Ini*a*ve
• TF10:
Data
interoperability,
vocabulary
and
ontology
services

18. • Goble
and
Sansone
aUended
and
presented
at
4th
Plenary,
22
-­‐
24
September
2014
-­‐
Amsterdam,
The
Netherlands

19. Key
Achievements
Established partnerships with:
• Data Carpentry (Aleksandra Pawlik on the Directors Board)
• Software Carpentry (Carole Goble on the Advisory Board and transitional
SWC Foundation Board)
• Software Sustainability Institute
• BioSharing community (led by Susanna Sansone)
• International Society for Biocuration (Terri Attwood on Exec Board)
• Research Data Alliance (ELIXIR Bridging IG, BioSharing IG, Sansone on
RDA TAB)
• NIH BD2K (Goble in ELIXIR delegation Data Science meeting, Sansone
associated with first round projects).
Breaking
News
"In
order
to
foster
So-ware
Carpentry's
con5nued
growth,
we
are
pleased
to
announce
that
we
are
crea5ng
an
independent
So#ware
Carpentry
Founda1on
(SCF).
Like
other
non-­‐profit
open
source
founda5ons,
it
will
decide
So-ware
Carpentry's
overall
scope
and
direc5on,
manage
finances
hold
its
intellectual
property."
(Carole
Goble
on
the
Interim
Board)

20. Upcoming
ac*vi*es
• ELIXIR
UK
&
SSI
SoLware
Carpentry
“Train
the
Trainer”
Workshop
at
TGAC
–
22nd&23rd
October
2014
• ELIXIR
UK
So]ware
Carpentry
workshop
for
NHS
Clinical
Bioinforma*cs
MSc
@
Manchester
–
9&14th
November
2014
• ELIXIR
UK
Data
Carpentry
workshop
–
27&28th
November
in
Manchester
including
data
cura*on
&
standards
and
tools
module
delivery
• ELIXIR
UK
MicrosoL
Azure
for
Research
workshop
–
December
2014/
January
2015
in
Manchester
• ELIXIR
UK
&
SSI
So]ware
Carpentry
Course
for
EPSRC
&
MRC
Centre
for
Doctoral
Training
in
Regenera*ve
Medicine
–
3-­‐4th
February
2015

21. Defining
Priori*es
Lee
Larcombe
will
talk
more
about
this
aLer
coffee
Clinical
Genomics
Structural
Bioinforma*cs
Advanced
Scien*fic
Skills
Applied
Genomics
Metabolomics
Five
areas
to
develop
as
ELIXIR
UK
strategic
training
priori*es
ELIXIR
UK’s
deliverables
are
*ed
to
the
defini*on
of
five
strategically-­‐important
areas
of
training
need.
The
defini*on
and
pursuit
of
five
strategic
areas
a]er
consulta*on
was
described
in
the
RC
funding
applica*on.
Iden*fying
the
UK
Training
Needs
is
a
cri*cal
part
of
the
process
of
selec*ng
areas
to
focus
on.

22. ELIXIR
Excelerate
(INFRADEV-­‐3)
1. Excellence in Coordination, Operations and
Governance
2. Strengthening Node Capacity
3. Excellence in User Services
This
is
where
training
will
sit
The overall aim of ELIXIR-Excelerate is to ensure that Europe’s life scientists have
access to world leading resources for bioinformatics.
This will be done by accelerating the integration of Europe’s core bioinformatics
resources, services and national centers into a single, distributed, infrastructure:
ELIXIR.

23. Work
Stream
5
-­‐
Training
Led
by
Chris
Pon*ng
as
Work
Stream
Leader
Objec*ves
for:
Strengthening
Node
Capacity
Strengthen
organisa*on
of
na*onal
communi*es
• Support
in
coordina*ng
na*onal
Nodes
• Skills
and
Knowledge
exchange
between
ELIXIR
Nodes,
i.e.
staff
exchanges,
visits
• Capacity
building
through
accessing
EU
Structural
Funds
and
Regional
Partner
Facili*es
Build
Europe
wide
capabili*es
• Genome
annota*on
network?
• Data
management
prac*ce
?
Build
Europe
wide
training
network
• Partner
with
goblet
• Build
elixir
curriculum
• Deliver
training
in
core
areas
The
9
ELIXIR
Objec*ves
for
Training
1. Link
to
individuals
from
all
other
ELIXIR
programmes
to
ensure
pan-­‐ELIXIR
coherency
in
the
delivery
of
training
related
to
ELIXIR
infrastructures
2. Establish
a
common
approach
across
ELIXIR
to
benchmark
and
evaluate
diverse
training
ac*vi*es
3. Establish
a
coherent
and
interac*ng
ELIXIR-­‐wide
training
community
4. Disseminate
relevant
informa*on
via
a
training
portal
5. Iden*fy
training
gaps
and
priori*es
by
engaging
with
industry
and
other
stakeholders
6. Expand
high
quality
training
ac*vi*es,
and
develop
and
deliver
new
training
ac*vi*es,
in
order
to
fill
iden*fied
gaps
and
meet
priori*es
7. Synchronise
the
development
of
ELIXIR
data
infrastructures
with
associated
high
quality
training
materials
and
ac*vi*es
8. Define
core
competencies
of
users
and
operators
of
ELIXIR
infrastructure
and
map
these
competencies
to
training
ac*vi*es
9. Capture
and
deliver
ELIXIR
training
ac*vi*es
in
Open
Educa*on
Resources
(OER)
including
videos
and
interac*ve
training
materials

24. Timeline
WS5
–
Training
(TrCC)
is
feeding
directly
in
at
this
stage
HoN
mee*ng
Amsterdam,
23
Oct
14
Decisions
taken
on:
• Overall
shape
of
proposal
• Budget
• WPs
• WPLs
• Governance
• Other
Partners
We
are
here

25. Future
Ac*vi*es
• Developing
and
Focussing
on
Priori*es
• Delivering
Training
• Developing
Funding
Opportuni*es
• Moving
Beyond
Training
–
Addi*onal
Missions
Con*nue
Progress
to

26. Funding
Opportuni*es
for
Training
• Lobbying
for
funding
mechanisms
for
training
• Training
gap
filling
in
Structural
Bioinforma*cs
Ready
to
go
• Where
is
the
funding
to
fill
the
yawning
training
gap
between
research
scien*sts
and
data
scien*sts?
• Training
is
not
just
the
preserve
of
the
PhD
student
• MRC
Training
Lectureships
Chris*ne
Orengo
will
discuss
this
aLer
coffee

27. MRC
Training
lecturers:
Proposed
job
descrip*on
• Full-­‐*me,
or
Part-­‐*me.
• Adjacency
to
and
interac*on
with
research
science
groups
would
be
required
• Part-­‐*me
will
include
those
who
wish
to
undertake
both
research
and
training
roles
• Lecturers
should
keep
up-­‐to-­‐date
with
the
fields
in
which
they
are
training:
this
ensures
that
their
training
maintains
its
values
and,
importantly,
that
their
careers
in
Training/Lecturing
etc
are
sustained.
• Applica*ons
could
include
named
individuals
for
the
Lecturer
posts,
or
else
unnamed
posts
that
will
be
filled
through
interna*onal
compe**on.
• Training
is
best
done
as
a
cohort
–
so
smaller
scale
(one
trainer,
1-­‐2
trainees)
will
be
less
effec*ve
than
larger
scale.
This
is
unless
the
training
is
truly
integrated
in
a
research
environment
containing
many
FTEs/students.
• Training
should
be
available
to
individuals
from
any
stage
of
their
career
from
student
to
PI.
• Training
materials
developed
for
these
posts
should
be
made
freely
available
(open
access).
Training
(not
trainers)
should
be
evaluated
by
the
trainees
to
capture
added-­‐value.
• Careers
of
Trainers
need
to
be
fostered
by
offering
not
less
than
3
and
op*mally
5
year
Lecturer
posts.
• Overheads
and
associated
capital
will
need
to
be
part
of
the
package.
• Trainers
should
commit
to
training
from
across
the
MRC
‘family’
not
just
from
the
locality.
• Trainers
should
be
recognised
for
their
contribu*ons
when
these
are
sufficient
to
warrant
their
inclusion
as
co-­‐authors
on
scien*fic
publica*ons
etc.

28. • Training
is
the
ini1al
Mission
of
ELIXIR-­‐UK
• Nevertheless,
the
UK
contains
substan*al
exper*se
relevant
to
ELIXIR
infrastructures
• ELIXIR-­‐UK
seeks
to
capture
this
exper*se
by
appoin*ng
representa*ves
,
of
which
the
first
two
are
• Carole
Goble:
Representa*ve
for
Data
Interoperability,
vocabulary
&
ontology
• Susanna-­‐Assunta
Sansone:
Representa*ve
for
Tools,
Interoperability
and
Service
Registry
New
Missions

29. ELIXIR-­‐UK
will:
• Firmly
establish
Training,
and
its
funding,
as
being
essen*al
for
successful
UK
academic
&
industrial
research,
and
for
delivering
ELIXIR
infrastructures
• Be
strengthened
by
contribu*ons
to
ELIXIR
infrastructures
from
individuals
from
across
the
UK
Future
Ques*ons:
• How
will
ELIXIR-­‐UK
op*mally
represent
the
UK
(incl.
industry)
as
a
Distributed
Node?
• What
should
the
Node
look
like
in
2015,
2020
...?
Data
Standards
Tools
Training
Compute
Industry
Forecast

30.
30
Thank
you