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Cloud infrastructure for training in Life Sciences

Cloud infrastructure for training in Life Sciences. The Genome Analysis Centre. Manuel Corpas. [ egi.edu ]. The Genome Analysis Centre @ manuelcorpas. The Genome Analysis Centre @ manuelcorpas. Bottleneck is NOT. Production of data Technology Budget.

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Cloud infrastructure for training in Life Sciences

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  1. Cloud infrastructure for training in Life Sciences The Genome Analysis Centre Manuel Corpas

  2. [egi.edu] The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  3. The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  4. Bottleneck is NOT • Production of data • Technology • Budget The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  5. Bottleneck IS • TRAINING! The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  6. Bottleneck IS • TRAINING! • Bioinformatics The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  7. Bioinformatics Training The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  8. Mick Watson Roslin Institute The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  9. Most bioinformaticians are bad scientists The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  10. Most bioinformaticians are bad scientists • Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  11. Most bioinformaticians are bad scientists • Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics • Short courses benefit no-one The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  12. Carole Goble University of Manchester The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  13. Students and trainers don’t like learning how to use new things The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  14. Students and trainers don’t like learning how to use new things • Trainees need to be eased in by using familiar stuff The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  15. How can we bridge the gap? The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  16. Titus Brown Michigan State University The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  17. Participants bring their laptops The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  18. Participants bring their laptops • Pre installed machines The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  19. Participants bring their laptops • Pre installed machines • Cloud computing The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  20. Cloud + Bioinformatics + Training= The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  21. Why Bioinformatics Training in the Cloud? The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  22. 3 Advantages The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  23. Participants can use own • Computers • Web browser • Graphical interaction via • X Windowes • IPython • Knitr • Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  24. Participants can use own • Computers • Web browser • Graphical interaction via • X Windows • IPython • Knitr • Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  25. Participants can use own • Computers • Web browser • Graphical interaction via • X Windowes • IPython • Knitr • Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  26. 3 Challenges The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  27. Institutional resistance • Privacy of clinically sensitive data • Reliable network access and servers needed • > 30 people clicking at the same time! • Cost The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  28. Institutional resistance • Privacy of clinically sensitive data • Reliable network access and servers needed • > 30 people clicking at the same time! • Cost The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  29. Institutional resistance • Privacy of clinically sensitive data • Reliable network access and servers needed • > 30 people clicking at the same time! • Cost The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  30. National eResearch Collaboration Tools and Resources (NeCTAR) Registry Materials Data Genomics Watson-Haighet al. 2013 VMs+tools NM Trainer Trainee The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  31. MRC UK Microbial Genomics • Open Stack • Each VM 32Gb RAM, 8 cores, 1Tb • Biolinux Nick Loman, University of Birmingham The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  32. Why Cloud? • Very little technical knowledge required • Snapshot ready for replication • User can take instance home The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  33. Cloud + Bioinformatics + Training= The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

  34. Rafael Jiménez rafael@elixir-europe.org The Genome Analysis Centre @manuelcorpas The Genome Analysis Centre

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