Genomics Applications in the Cloud with the DNAnexus Platform


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The bioinformatics community faces numerous challenges in developing research and clinical software for analyzing genomic data. The DNAnexus Platform enables solutions to these problems. This presentation will cover its features: massively scalable ondemand cloud infrastructure, fully configurable and scriptable genomics API, commandline interface and SDKs, collaboration and community support, visualization and publication tools, enterprise-grade security, compliance with clinical and diagnostic standards.

Published in: Technology

Genomics Applications in the Cloud with the DNAnexus Platform

  1. 1. Powering the genomics revolutionGenomics applications in the cloudwith the DNAnexus PlatformAndrey  Kislyuk  SFAF  2013  
  2. 2. What drives DNAnexus?Grad  students,  industry  scien9sts,  researchers.  We  kept  hi>ng  bioinforma9cs  roadblocks.  – Don’t  know  how  much  compute  we’ll  need  – Resource  conten9on  – I/O  boKlenecks  – Storage  shortages  – Bad  interfaces  – Byzan9ne  IT  – Overpriced  and  underu-lized  – Blocks  clinical  applica-ons  
  3. 3. What if there was a way to…Break IT limitationsPublish your toolsWork together
  4. 4. Powering the genomics revolutionIt’s here.
  5. 5. The DNAnexus PlatformConfigurable  cloud  infrastructure  for  genomics  
  6. 6. The DNAnexus PlatformOpen  and  comprehensive  API  
  7. 7. The DNAnexus PlatformOpen  and  comprehensive  SDK  Linux  OS  X  Windows    Upload  agents  (Dropbox-­‐like)  
  8. 8. Powering the genomics revolutionBatteries are included
  9. 9. The DNAnexus PlatformPowerful  visualiza9on  tools  built  in  
  10. 10. The DNAnexus PlatformPowerful  visualiza9on  tools  built  in  
  11. 11. The DNAnexus PlatformPowerful  visualiza9on  tools  built  in  
  12. 12. The DNAnexus PlatformQuality  control  reports  
  13. 13. Your visualization engine here(there’s an API for that)
  14. 14. Yes, we have Circos
  15. 15. Powering the genomics revolutionDNAnexus is readyfor clinical data
  16. 16. Secure, compliant, audited
  17. 17. Those are not just acronyms…• All  data  encrypted  with  full-­‐disk  AES-­‐256  at  rest,  SSL  on  the  move  • Produc9on  access  controls  • Third-­‐party  security  audits  • Op9onal  2-­‐Factor  Auth  • LXC  (Linux  Containers)  hypervisor  • Auditable  by  user  
  18. 18. Your data is yoursWe  will  never  hold  your  data  hostage  – Always  exportable  – Always  downloadable  – We’re  not  allowed  to  look  at  it  
  19. 19. The DNAnexus PlatformReliability  • Triple  data  redundancy  • Geographically  distributed  • Job-­‐level  hardware  fault  tolerance  • Reproducible  and  auditable  results  for  6+  years  DNAnexus  is  ready  for  clinical  data  
  20. 20. Powering the genomics revolutionBlazing fast development
  21. 21. Open-source stackApp  wizard  walks  you  through  app  crea1on  Learn  by  example  fork  our  repos  Collaborate  deploy  apps  from  GitHub    
  22. 22. Debug quickly•  SDK  tools  for  debugging  •  Jobs  start  in  5  seconds  under  most  circumstances  •  Real-­‐9me  job  logs  
  23. 23. Data standards•  GTable:  Columnar  indexed  data  store  for  genome  data  – Suitable  for  storing  SAM,  GFF/GTF,  BED,  VCF,  etc.  •  I/O  specifica9ons  – Contracts  between  apps  enable  composi9on  •  Data  type  defini9ons  and  validators  Foundations forInteroperability
  24. 24. Powering the genomics revolutionMassive on-demand compute
  25. 25. Instant-on supercomputerat your fingertips……only when you need itSpin up thousands of instancesSpecify instance typesPay by the second
  26. 26. Powering the genomics revolutionCommunityCollaboration
  27. 27. DNAnexus AnswersA  community  working  together  
  28. 28. Instant collaboration•  Eliminate  data  transfer  headaches  •  Collaborate  on  data,  tools,  workflows  in  one  environment  •  Enable  bioinforma9cs  experts  to  deliver  tools  to  biologists  
  29. 29. So how do I add my app?
  30. 30. 1. Run App Wizard
  31. 31. So how do I add my app?
  32. 32. app spec
  33. 33. 2. Add entry point code
  34. 34. 3. Build, test, publish
  35. 35. done
  36. 36. ReproducibilityEver  try  to  reproduce  results  from  a  bioinforma9cs  paper?  How  about  CLIA  compliance?    All  objects  are  versioned  Analysis  I/O  is  read-­‐only  Jobs  enter  into  project’s  permanent  record  
  37. 37. PublishingAuthors  who  publish  their  sohware  •  Don’t  worry  about  suppor9ng  diverse  installs  – You  installed  my  package  on  WHAT?  •  Leverage  all  Plajorm  features  – Accessible  UI  •  Compose  with  other  apps  – It’s  an  ecosystem  – Publish  your  workflows  as  apps,  too  
  38. 38. RecognitionUsers  are  encouraged  to  cite  app  authors  One-­‐click  bibliographies  coming  soon  
  39. 39. Powering the genomics revolutionWe care aboutdevelopers
  40. 40. DNAnexus developer program•  $1000  credit  •  App  Boun9es  •  Featured  Apps  
  41. 41. Powering the genomics revolutionVision
  42. 42. DNAnexus roadmap•  App  mone9za9on  (Summer  2013)  •  Channels  for  organiza9ons  •  AWS  Glacier  –  cheap  data  archival  •  Projects  as  publica9ons  Supplementary  materials!    And  of  course…  •  More  apps  
  43. 43. DNAnexus roadmapAlways  improving…  …And  so  are  our  cloud  providers  We  pass  on  the  savings  to  you  
  44. 44. DNAnexus visionUnlock the potential for DNA-basedmedicine and biotechnologywith a collaborative and scalabledata platform
  45. 45. DNAnexus is the platform forpublishing your algorithms
  46. 46. DNAnexus is the platform fordelivering genomics results to users
  47. 47. Powering the genomics revolutionAcknowledgmentsDNAnexus isAndreas SundquistArend SidowSerafim BatzoglouEvan WorleyGeorge AsimenosJoseph DaleLee BendekgeyMike FurnessMichael Kawai
  48. 48. Powering the genomics revolutionThank
  49. 49. Pricing: Individuals
  50. 50. InstitutionsVolume  pricing  for  genome  centers    20-­‐30%  cheaper  than  TCO  of  your  average  neighborhood  cluster