European  Life  Sciences  Infrastructure  for  Biological  Information  www.elixir-­‐europe.org  

ELIXIR-­‐UK   the UK Node of the

Current  Ac*vi*es  and  Future  Plans  of  the  ELIXIR  UK  Node  

Chris  Pon*ng  (30  mins)  

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        

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  

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

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  

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  

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Current  Organisa*onal  Chart  

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  

Building  a  UK  Community  -­‐  website  

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  

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)  

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  

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  

Delivering  Training:  Data  &  So]ware  Skills  

Elixir U

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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”)      

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)  

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  

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

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)  

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        

         

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.  

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.

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    

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  

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  

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  

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.  

•  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  

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  

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Thank  you