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How to choose compute resources for your team

Presenters: Lee LarcombeHost: Adam Carter

BioExcel Webinar Series

8 March, 201714:00 GMT / 15:00 CET

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Today’s PresenterLee Larcombe began his scientific career in the lab, with an undergrad degree in Genetics from QMUL and later, a PhD studying Chlamydia trachomatis at Cranfield University from where he worked himself up to the post of Lecturer in Genetics and Computational biology. Here he was the course director of the University's MSc in Applied Bioinformatics. He subsequently made the move to industry: first as bioinformatics lead for Lonza Biologics, and then most recently as an independent consultant.

His research has focused mainly on functional genomics, and data integration for the study of oncology and the discovery of novel biomarkers and targets.

He’s currently ELIXIR-UK's Training Coordinator for Research Science based at the MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh with Prof. Chris Ponting.

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CHOOSING COMPUTE RESOURCES FOR YOUR TEAMDR LEE LARCOMBE

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Resources – first thoughts

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• Before thinking about the technical resources, best to consider the people

• Who do you have – who do you need – is recruitment or collaboration the best way forward

• Most important …

Working with IT• You will probably decide you need to buy a computer (or

maybe re-purpose one)• Talking to your IT department may not be the best way to

do this (although you might not have an option)

• Do not:

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Expect them to understand your requirements

Expect them to install your software

Offer end-user support

Treat this as scientific equipment!• Computers often have some special purchasing

arrangements – that might not suit you

• Departing from this normal route can be a fight – both with the IT dept and Accounting dept!

• You need to make people understand that this is not just a computer – it is a piece of scientific equipment

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Data transfer & storage

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1TB over 100Mbps = 22 hours

Many tasks do not need huge storage – although you should have plenty for backups and long-term archiving

Molecular dynamics simulations and genomic analysis can involved large files

You might need to look into options like RAID

You need to be mindful of your networking!

Platform considerations

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A basic laptop/desktop

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What is possible?• Quite a lot!

• Everything web-based. Eg EBI resources – integrated

data and huge amounts of information

• Basic coding – PERL, Python, R etc

• A window to another more powerful system!

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A workstation

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What is possible?• Everything we had for the smaller machine, plus…• More & faster – analysis that can use multiple CPUs• Simulation – particularly molecular simulation• Some genome analysis – differential expression/RNAseq,

microarrays, limited metagenomics, re-sequencing, perhaps some prokaryotic de-novo assembly

• Data visualisation – molecular modelling, image analysis (microscopy etc)

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Something bigger

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Question why you think you need this?

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What is really the bottleneck to your research? ie.

• Simple job but lots of data

• Complex job but simple data

• Simple job – but many repetitions

• Is time the key factor? Is this need or convenience?

• (sometimes getting more resource can be slower than getting monkeys to do the job on typewriters)

Accessing local HPC resource

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You might have local HPC…

Have you checked?

There is a significant chance though that it is not running the software you want!

Accessing alternative resource

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The key to this challenge is not computing – it’s people

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Understanding computers and your computational need is important – so you can communicate that need

Most of the battle of acquiring more compute resource is working with those who can support you in getting/using it

Making the most of the resources you have or acquire means having a team who know how to use it

Questions?

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