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

[egi.edu] The Genome Analysis Centre The Genome Analysis

The Genome Analysis Centre The Genome Analysis

Bottleneck is NOT Production of data Technology Budget The Genome Analysis Centre The Genome Analysis

Bottleneck IS TRAINING! The Genome Analysis Centre The Genome Analysis

Bottleneck IS TRAINING! – Bioinformatics The Genome Analysis Centre The Genome Analysis

Bioinformatics Training The Genome Analysis Centre The Genome Analysis

Mick Watson Roslin Institute The Genome Analysis Centre The Genome Analysis

1.Most bioinformaticians are bad scientists The Genome Analysis Centre The Genome Analysis

1.Most bioinformaticians are bad scientists 2.Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics The Genome Analysis Centre The Genome Analysis

1.Most bioinformaticians are bad scientists 2.Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics 3.Short courses benefit no-one The Genome Analysis Centre The Genome Analysis

Carole Goble University of Manchester The Genome Analysis Centre The Genome Analysis

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

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 The Genome Analysis

How can we bridge the gap? The Genome Analysis Centre The Genome Analysis

Bioinformatics Learning Tools iPython (analytics learning) Sanbox resources (galaxy instance with data) Repository of training machines Suite of VMs

Titus Brown Michigan State University The Genome Analysis Centre The Genome Analysis

1.Participants bring their laptops The Genome Analysis Centre The Genome Analysis

1.Participants bring their laptops 2.Pre installed machines The Genome Analysis Centre The Genome Analysis

1.Participants bring their laptops 2.Pre installed machines 3.Cloud computing The Genome Analysis Centre The Genome Analysis

Cloud + Bioinformatics + Training = The Genome Analysis Centre The Genome Analysis

Why Bioinformatics Training in the Cloud? The Genome Analysis Centre The Genome Analysis

3 Advantages The Genome Analysis Centre The Genome Analysis [Adapted from Titus Brown]

1.Participants can use own – Computers – Web browser 2.Graphical interaction via – X Windowes – IPython – Knitr 3.Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre The Genome Analysis

1.Participants can use own – Computers – Web browser 2.Graphical interaction via – X Windows – IPython – Knitr 3.Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre The Genome Analysis

1.Participants can use own – Computers – Web browser 2.Graphical interaction via – X Windowes – IPython – Knitr 3.Compute can be scaled up/down depending on what it’s being taught The Genome Analysis Centre The Genome Analysis

3 Challenges The Genome Analysis Centre The Genome Analysis [Adapted from Titus Brown]

1.Institutional resistance – Privacy of clinically sensitive data 2.Reliable network access and servers needed – > 30 people clicking at the same time! 3.Cost The Genome Analysis Centre The Genome Analysis

1.Institutional resistance – Privacy of clinically sensitive data 2.Reliable network access and servers needed – > 30 people clicking at the same time! 3.Cost The Genome Analysis Centre The Genome Analysis

1.Institutional resistance – Privacy of clinically sensitive data 2.Reliable network access and servers needed – > 30 people clicking at the same time! 3.Cost The Genome Analysis Centre The Genome Analysis

NM Trainee Trainer Registry The Genome Analysis Centre The Genome Analysis National eResearch Collaboration Tools and Resources (NeCTAR) Watson-Haigh et al. 2013

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

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

Cloud + Bioinformatics + Training = The Genome Analysis Centre The Genome Analysis

The Genome Analysis Centre The Genome Analysis Rafael Jiménez Titus Brown Mick Watson Carole Goble Nick Loman Vicky Schneider