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Bioinformatics with HPC Midlands
Martin Hamilton, Centre Manager
Themes
1. The Landscape
2. HPC Midlands

3. What’s in Scope?
4. Next Steps
Themes
1. The Landscape
2. HPC Midlands

3. What’s in Scope?
4. Next Steps
The Landscape
The Landscape
The Landscape
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
HPC Midlands
HPC Midlands
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)
HPC Midlands
Themes
1. The Landscape
2. HPC Midlands

3. What’s in Scope?
4. Next Steps
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
Themes
1. The Landscape
2. HPC Midlands

3. What’s in Scope?
4. Next Steps
Next Steps
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
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?
Bioinformatics with HPC Midlands
Martin Hamilton, Centre Manager

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