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2013	
  Winter	
  School	
  
Mark	
  Crowe,	
  July	
  2013	
  
Genomics infrastructure for NGS
Expertise infrastructure
•  What	
  is	
  your	
  experimental	
  goal?	
  
•  Is	
  NGS	
  really	
  the	
  right	
  tech...
When to ask advice
BEFORE	
  	
  
you	
  start	
  your	
  project	
  
Sequencing infrastructure
agrf.org.au www.ramaciotti.unsw.edu.au
•  ACRF	
  centres	
  
•  Local	
  (department/insFtute)	...
Bioinformatics infrastructure
•  ‘Support’	
  rather	
  than	
  research	
  
– Accessible	
  to	
  biologists	
  
– Stable...
The challenges of
Bioinformatics support
In	
  house	
  
Outsource	
  
Collabora1on	
  
Cloud	
  
Infrastructure	
  
So5wa...
Going it alone
•  Networking	
  and	
  community	
  for	
  
bioinformaFcians	
  
•  Yammer	
  channel	
  
•  Conference	
  and	
  naFonal...
•  Training	
  
– 3	
  day	
  NGS	
  analysis	
  workshops	
  
•  Embedded	
  bioinformaFcians	
  
– Associated	
  with	
 ...
Genomics Virtual Lab
www.genome.edu.au
Galaxy: simplifying bioinformatics
GVL on the cloud
•  NeCTAR	
  research	
  cloud	
  –	
  a	
  free	
  resource	
  
for	
  Australian	
  researchers	
  
•  ...
•  The	
  NCI	
  NaFonal	
  Facility	
  supports	
  
Australian	
  research	
  through	
  the	
  use	
  of	
  
high-­‐end	...
NCI-SF infrastructure
•  Computer	
  scienFsts,	
  bioinformaFcians,	
  and	
  
IT	
  professionals	
  
•  High	
  Perform...
Access to NCI-SF
•  Directly,	
  through	
  Partner	
  shares:	
  
–  UQ	
  
–  CSIRO	
  
–  QCIF	
  (CQU,	
  GU,	
  JCU,	...
•  BioinformaFcs	
  Resource	
  Australia	
  –	
  EMBL	
  
	
  
•  Developed	
  out	
  of	
  the	
  EBI	
  mirror	
  proje...
BRAEMBL resources
•  FTP	
  site	
  –	
  mirror	
  of	
  13TB	
  of	
  EBI	
  data	
  
•  Local	
  ENSEMBL	
  browser	
  
...
Most useful thing?
About QFAB
QFAB	
  delivers	
  bioinformaFcs	
  
services	
  to	
  analyse	
  and	
  
manage	
  large-­‐scale	
  datasets	...
ComputaFonal	
  Biology	
  
K.	
  Le	
  Cao	
   X.	
  Chua	
   R.	
  Legaie	
   J.	
  Straube	
  
Organisation
IT/GRID
Spe...
Other bioinformatics providers
•  Victorian	
  Life	
  Science	
  ComputaFonal	
  IniFaFve	
  
(VLSCI)	
  and	
  Life	
  S...
Useful links
•  qfab.org
•  agrf.org.au
•  www.ramaciotti.unsw.edu.au
•  australianbioinformatics.net
•  bioplatforms.com....
QFAB Genomics Infrastructure for NGS - Mark Crowe
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QFAB Genomics Infrastructure for NGS - Mark Crowe

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As high-throughput DNA sequencing continues to become cheaper and more widely accessible, the bottleneck in genomics research has become one of bioinformatics rather than data generation. Sequencing service providers and equipment manufacturers are attempting to address this by providing a range of analysis options, but ultimately most researchers using genomics technologies will need support and resources beyond these standard offerings.

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QFAB Genomics Infrastructure for NGS - Mark Crowe

  1. 1. 2013  Winter  School   Mark  Crowe,  July  2013   Genomics infrastructure for NGS
  2. 2. Expertise infrastructure •  What  is  your  experimental  goal?   •  Is  NGS  really  the  right  technology?   •  How  will  you  manage:   – Data  collecFon?  Data  storage?   Analysis?  StaFsFcs?  
  3. 3. When to ask advice BEFORE     you  start  your  project  
  4. 4. Sequencing infrastructure agrf.org.au www.ramaciotti.unsw.edu.au •  ACRF  centres   •  Local  (department/insFtute)  services  
  5. 5. Bioinformatics infrastructure •  ‘Support’  rather  than  research   – Accessible  to  biologists   – Stable  and  documented   •  SoWware,  hardware  and  experFse   EMBLBRAustralia
  6. 6. The challenges of Bioinformatics support In  house   Outsource   Collabora1on   Cloud   Infrastructure   So5ware   Training   Sta1s1cs   Exper1se   Cost  
  7. 7. Going it alone
  8. 8. •  Networking  and  community  for   bioinformaFcians   •  Yammer  channel   •  Conference  and  naFonal  bioinformaFcs  society   •  Web,  twiZer   australianbioinformatics.net @ausbionet
  9. 9. •  Training   – 3  day  NGS  analysis  workshops   •  Embedded  bioinformaFcians   – Associated  with  BPA  infrastructure   •  Reference  datasets   – Dedicated  bioinformaFcs  support   www.bioplatforms.com.au
  10. 10. Genomics Virtual Lab www.genome.edu.au
  11. 11. Galaxy: simplifying bioinformatics
  12. 12. GVL on the cloud •  NeCTAR  research  cloud  –  a  free  resource   for  Australian  researchers   •  GVL  provides  Galaxy  and  CloudBioLinux   NeCTAR  instances   hZp://nectar.org.au  
  13. 13. •  The  NCI  NaFonal  Facility  supports   Australian  research  through  the  use  of   high-­‐end  computaFonal  resources   •  The  NCI  Specialised  Facility  in   BioinformaFcs  offers  NCI  support  tailored   for  the  life  science  community   www.ncisf.org
  14. 14. NCI-SF infrastructure •  Computer  scienFsts,  bioinformaFcians,  and   IT  professionals   •  High  Performance  CompuFng   –  384  compute  nodes   –  3144  CPU  cores   –  11.5TB  RAM   –  24  Teraflops  of  performance   –  280TB  shared  disk     •  35TB  of  BioinformaFcs     databanks   •  >150  bioinformaFcs  tools  and  applicaFons  
  15. 15. Access to NCI-SF •  Directly,  through  Partner  shares:   –  UQ   –  CSIRO   –  QCIF  (CQU,  GU,  JCU,  QUT,  UQ,  USQ,  USC)   –  QCMG   –  QFAB   •  Through  NaFonal  Merit  ApplicaFon  Scheme   h=p://nf.nci.org.au/accounts/    
  16. 16. •  BioinformaFcs  Resource  Australia  –  EMBL     •  Developed  out  of  the  EBI  mirror  project   •  Enable  opFmal  exploitaFon  of  the  tools  and  data   of  bioinformaFcs  by  Australian  scienFsts   •  Contribute  to  the  global  biomolecular  informaFon   infrastructure  in  a  way  which  showcases   Australian  science   EMBLBRAustralia braembl.org.au
  17. 17. BRAEMBL resources •  FTP  site  –  mirror  of  13TB  of  EBI  data   •  Local  ENSEMBL  browser   •  ProgrammaFc  access  to  data  and  tools  via   Web  Services  technologies   •  Survey  on  bioinformaFcs  needs  
  18. 18. Most useful thing?
  19. 19. About QFAB QFAB  delivers  bioinformaFcs   services  to  analyse  and   manage  large-­‐scale  datasets   Our  support  includes   experimental  design  and  data   capture  through  to  NGS  and   ‘omics  analyses.     qfab.org @QFAB_Bioinfo
  20. 20. ComputaFonal  Biology   K.  Le  Cao   X.  Chua   R.  Legaie   J.  Straube   Organisation IT/GRID Specialist IT/GRID Infrastructure     Research & Support Specialist Research Community Bioinformatics/Statistics Tools, Data & Skills Senior  Management  Team   J.  Barker   D.  Gorse   M.  Desselle   S.  Rudd   M.  Crowe   Data  Specialists   J.  Parsons   P.  Chaumeil   A.  Kunert   N.  Rhodes   Currently  recrui1ng  a  Computa1onal  Biologist  to  join  the  team    
  21. 21. Other bioinformatics providers •  Victorian  Life  Science  ComputaFonal  IniFaFve   (VLSCI)  and  Life  Science  ComputaFon  Centre     •  Centre  for  ComparaFve  Genomics,  WA   www.vlsci.org.au ccg.murdoch.edu.au
  22. 22. Useful links •  qfab.org •  agrf.org.au •  www.ramaciotti.unsw.edu.au •  australianbioinformatics.net •  bioplatforms.com.au •  genome.edu.au •  ncisf.org •  braembl.org.au •  vlsci.org.au •  ccg.murdoch.edu.au •  m.crowe@qfab.org •  @QFAB_Bioinfo

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