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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

...
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 Infinib...
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
– ...
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 /
embarassin...
Next Steps
Next Steps
– Collaborators sought!
– Local or remote i2b2 database?
• NHS infosec requirements
• Redaction/anonymization/c...
Bioinformatics with HPC Midlands
Martin Hamilton, Centre Manager
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Transcript of "Bioinformatics with HPC Midlands"

  1. 1. Bioinformatics with HPC Midlands Martin Hamilton, Centre Manager
  2. 2. Themes 1. The Landscape 2. HPC Midlands 3. What’s in Scope? 4. Next Steps
  3. 3. Themes 1. The Landscape 2. HPC Midlands 3. What’s in Scope? 4. Next Steps
  4. 4. The Landscape
  5. 5. The Landscape
  6. 6. The Landscape
  7. 7. Themes 1. The Landscape 2. HPC Midlands 3. What’s in Scope? 4. Next Steps
  8. 8. 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
  9. 9. HPC Midlands
  10. 10. HPC Midlands
  11. 11. HPC Midlands
  12. 12. 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)
  13. 13. HPC Midlands
  14. 14. Themes 1. The Landscape 2. HPC Midlands 3. What’s in Scope? 4. Next Steps
  15. 15. 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
  16. 16. Themes 1. The Landscape 2. HPC Midlands 3. What’s in Scope? 4. Next Steps
  17. 17. Next Steps
  18. 18. 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?
  19. 19. Next Steps
  20. 20. 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?
  21. 21. Bioinformatics with HPC Midlands Martin Hamilton, Centre Manager
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