Bioinformatics with HPC Midlands

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Martin Hamilton

Tecnologia Educação

Themes
1. The Landscape
2. HPC Midlands

3. What’s in Scope?
4. Next Steps

HPC Midlands
– hpc-midlands.ac.uk
– Centre of Excellence in High
Performance Computing
• £1m seed funding from EPSRC/BIS

– Remit is to make Supercomputing
Accessible to Industry
• Working with startups and leading firms
such as Airbus, E.ON, Rolls-Royce,
RWE npower and Tata Steel
• Flexible licensing from ISVs including
ANSYS, CD-adapco and MSC Software

HPC Midlands
3,000 cores (48 Teraflops)
11 chassis (18 blades each)
15TB RAM
120TB Lustre storage
Non-blocking QDR Infiniband
188 compute node blades:
2 x 2.0GHz (8 core) Sandy Bridge
140 with 64GB RAM (4GB/core)
48 with 128GB RAM (8GB/core)

What’s in Scope?
– Bias towards industrially
linked R&D work
– Majority of use to date has
been science and engineering
– Interest from biotech sector

– Links to big pharma and
startups/spinouts

Next Steps
– Use cases
• “Conventional” MPI codes and
off-the-shelf parallel apps
• High Throughput Computing /
embarassingly parallel codes

– Bioinformatics applications
• BLAST/CS-BLAST/CSIBLAST, Bowtie, Cufflinks, FAST
A, GATK, …
• HPC plugin for i2b2?

Next Steps
– Collaborators sought!
– Local or remote i2b2 database?
• NHS infosec requirements
• Redaction/anonymization/consent

– Combining sources, e.g. Mosaic
• Machine Learning

• Big Innovation Centre: “Data
Switzerland” etc

– New or existing project?

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