cloud infrastructure for training in life sciences manuel corpas the genome analysis centre

Cloud infrastructure for training in Life Sciences

Manuel Corpas

The Genome Analysis Centre

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

@manuelcorpas

The Genome Analysis CentreThe Genome Analysis Centre@manuelcorpas

Bottleneck is NOT

• Production of data• Technology• Budget


Bottleneck IS

•TRAINING!


Bottleneck IS

•TRAINING!–Bioinformatics


Bioinformatics Training



Mick Watson

Roslin Institute

The Genome Analysis Centre@manuelcorpas

1. Most bioinformaticians are bad scientists



2. Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics



2. Most biologists are bad bioinformaticians: poor computer skills, bad at maths/statistics

3. Short courses benefit no-one



Carole Goble

University of Manchester


• Students and trainers don’t like learning how to use new things


• Students and trainers don’t like learning how to use new things

• Trainees need to be eased in by using familiar stuff


How can we bridge the gap?



Titus BrownMichigan State University


1. Participants bring their laptops


1. Participants bring their laptops2. Pre installed machines


1. Participants bring their laptops2. Pre installed machines3. Cloud computing


Cloud + Bioinformatics + Training

=


Why Bioinformatics Training in the Cloud?


3 Advantages


[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



2. Graphical interaction via– X Windows– IPython– Knitr




2. Graphical interaction via– X Windowes– IPython– Knitr



3 Challenges


[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


Materials

Data

NM

Trainee Trainer

Registry

Genomics

VMs+tools


National eResearch Collaboration Tools and Resources (NeCTAR)

Watson-Haigh et al. 2013

MRC UK Microbial Genomicshttp://climb.ac.uk

• Open Stack• Each VM 32Gb RAM, 8 cores, 1Tb• Biolinux


Nick Loman, University of Birmingham

Why Cloud?

• Very little technical knowledge required

• Snapshot ready for replication• User can take instance home


Cloud + Bioinformatics + Training

=



Rafael Jiménez

[email protected]

• Titus Brown

• Mick Watson

• Carole Goble

• Nick Loman

• Vicky

Schneider

cloud infrastructure for training in life sciences manuel corpas the genome analysis centre

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