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Enhancing Life Sciences Training through Cloud-Based Bioinformatics at The Genome Analysis Centre

The Genome Analysis Centre emphasizes the critical need for enhanced training in bioinformatics, recognizing that training bottlenecks significantly hinder progress in life sciences. Utilizing cloud computing, we provide flexible, scalable bioinformatics training solutions that overcome traditional barriers. Participants can use their own laptops for a familiar learning experience while accessing advanced tools seamlessly online. This innovative approach accommodates various learning styles and technical skills, fostering a more competent workforce in genomic research and data analysis.

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Enhancing Life Sciences Training through Cloud-Based Bioinformatics at The Genome Analysis Centre

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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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