1. Bioinformatics with HPC Midlands
Martin Hamilton, Centre Manager

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

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

4. The Landscape

5. The Landscape

6. The Landscape

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

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. HPC Midlands

10. HPC Midlands

11. HPC Midlands

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. HPC Midlands

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

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

17. Next Steps

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. Next Steps

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. Bioinformatics with HPC Midlands
Martin Hamilton, Centre Manager