Bioinformatics with HPC Midlands

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  • 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