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World class supercomputer to support COVID-19 recovery research

A new £3.8 million supercomputer commissioned by the N8 Research Partnership (N8) is being used by researchers to better understand COVID-19 and how to recover from the pandemic. It will also support research projects of the SARS-CoV-2 UK strain, energy storage and supply and therapeutic drug design.

Based at Durham University, the new high-performance computing (HPC) system, Bede, was designed, installed and is maintained by high performance compute, storage, cloud and AI integrator, OCF. Bede links the highest capability national and international supercomputers with local computers at individual research institutions.  

Its compute power enables researchers to accelerate projects and tackle larger problems and higher resolution imagery than has previously been possible in the North of England. 

Dr Chris Jewell, Senior Lecturer in Epidemiology, at Lancaster University, said: “In modelling the spread of COVID-19 around the UK, the power of GPU computing allows us to use Bayesian statistics to calibrate our models in real-time, providing up-to-date information on disease risk, reproduction numbers, and the effect of COVID-19 Alert Levels (local lockdowns) for the UK’s Scientific Advisory Group for Emergencies (SAGE).  Our advice currently feeds into SAGE reports as well as local authorities and is used to support important disease control decisions on a national scale.”

Bede has already been used in simulations to characterise the structural changes in the spike associated with the new SARS-CoV-2 UK strain. 

Professor Michele Vendruscolo, of the Centre for Misfolding Diseases, University of Cambridge, said: “We expect that these simulations will enable the development of a structure-based antibody discovery strategy for this strain, as well as for possible new strains that may arise in the future.” 

N8 is the largest research pooling partnership in the UK and is a strategic collaboration between the universities of Durham, Lancaster, Leeds, Liverpool, Manchester, Newcastle, Sheffield, and York.

Dr Annette Bramley, Director of the N8 Research Partnership, said: “The use of the facility will enable our researchers to undertake work that will address issues relating to the COVID-19 pandemic, including how our region can be the driving force behind a green recovery. Researchers will be able to undertake work that incorporates experimental activities underpinned by large data or modelling situations which are unable to be replicated in standard experiments.” 

N8 CIR Programme Director Professor Matt Probert said: “We are already seeing the benefits of Bede’s GPU-accelerated architecture to scientific research. Having ready access to a tier 2 HPC cluster for each of the N8 universities offers us a real competitive edge.” 

As part of the Bede project, each university is employing a full-time equivalent research software engineer to help researchers to work with Bede and encourage improvements in research code and coding habits. These members of the team will support researchers to access and utilise high performance computing in their work, a key goal of the group that manages Bede on behalf of the N8. 

This will mean that machine learning can be better used to analyse the vast data sets now being generated by experimentalists through national facilities such as Diamond Light Source in Harwell, Oxfordshire, and the Henry Royce Institute in Manchester, as well as international facilities such as the European Synchrotron Radiation Facility. 

This approach will enable scientists to, for example, advance the imaging techniques necessary to produce the next generation of X-ray instruments and to support the development of students working with deep learning techniques at the interface of algorithms and HPC. 

Andrew Dean, Sales Director at OCF, said: “Bede is a great example of how HPC is one of the most powerful tools we have in the fight and future protection against disease. The new facility at Bede will also give researchers in the North of England GPU capacity to support a wealth of different projects in scientific research.” 

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