bioinformatics with hpc midlands
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Bioinformatics with HPC MidlandsMartin Hamilton, Centre Manager
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
Themes
The Landscape
The Landscape
The Landscape
1. The Landscape
2. HPC Midlands
3. What’s in Scope?
4. Next Steps
Themes
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
3,000 cores (48 Teraflops)11 chassis (18 blades each)15TB RAM120TB Lustre storageNon-blocking QDR Infiniband188 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
HPC Midlands
1. The Landscape
2. HPC Midlands
3. What’s in Scope?
4. Next Steps
Themes
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
1. The Landscape
2. HPC Midlands
3. What’s in Scope?
4. Next Steps
Themes
Next Steps
– Use cases• “Conventional” MPI codes
and off-the-shelf parallel
apps
• High Throughput Computing /
embarassingly parallel codes
– Bioinformatics applications• BLAST/CS-BLAST/CSI-BLAST,
Bowtie, Cufflinks, FASTA,
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?
Next Steps
Bioinformatics with HPC MidlandsMartin Hamilton, Centre Manager