CLIMB project receives honours for supporting COG-UK alongside other computing teams
HPCwire has presented the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project, alongside other computing teams across COG-UK, with the Readers’ Best High Performance Computing Collaboration award, after providing COG-UK with vital computing infrastructure and bioinformatics analysis.
CLIMB, alongside other computing teams across COG-UK, was presented with the Readers’ Best High Performance Computing Collaboration award during the virtual International Conference for High Performance Computing, Networking, Storage and Analysis (SC20) via HPCwire.com.
CLIMB has proved pivotal to COG-UK in providing the computing infrastructure and bioinformatics analysis capability that has so far helped sequence over 110,000 virus genomes — to help understand the spread of SARS-CoV-2 and advise local and national control strategies.
“In COG-UK we were incredibly lucky to be able to make use of the existing CLIMB-BIG-DATA infrastructure,” said Dr Ewan Harrison from the Wellcome Sanger Institute and University of Cambridge, and the Director of Strategy for COG-UK.
“This combined with the exceptional talent and hard work of the CLIMB-COVID team and other COG-UK members has enabled COG-UK to build a national infrastructure for COVID-19 genomics virtually overnight, and has allowed us to analyse over 100,000 genomes linked with epidemiological data. Arguably, CLIMB-COVID has been a principal component in the success of the COG-UK effort.”
What is CLIMB?
CLIMB was launched in 2014, supported by a grant from the Medical Research Council (MRC) to meet the needs of medical microbiologists handling vast amounts of data coming from high-throughput genomics. It is an open, cloud-based computing infrastructure for developing and sharing datasets and bioinformatics software, tools and methods to interpret ‘big data’.
CLIMB represents a partnership between the Universities of Bath, Birmingham, Cardiff, Leicester, Swansea and Warwick, the London School of Hygiene and Tropical Medicine and Quadram Institute Bioscience.
How has CLIMB supported the COG-UK consortium?
After the UK Government and Chief Scientific Adviser announced a £20 million initiative to map how COVID-19 spreads and evolves on March 23rd 2020 — the COG-UK consortium — CLIMB’s pre-existing infrastructure and expertise allowed the consortium to launch quickly and deliver rapid genome sequencing data of SARS-CoV-2.
Insights from these data have informed national decision-making of the Scientific Advisory Group for Emergencies (SAGE) as well as the local public health level, including monitoring outbreaks in real-time.
“The CLIMB-BIG-DATA infrastructure exists to support the bioinformatics needs of the UK microbiology community,” said Professor Mark Pallen from the Quadram Institute, and director of the CLIMB-BIG-DATA project.
“It’s been great to see how our infrastructure and our team have been able to respond so quickly and effectively to the national and international challenge of understanding and controlling the spread of COVID-19”.
“When we first conceived CLIMB we had the idea that it could provide a revolutionary place to bring together data and researchers to fight infectious disease,” said Professor Tom Connor from Cardiff University and technical architect of CLIMB.
“With COVID-19, CLIMB has proved its worth, providing us with the platform to be able to rapidly develop and scale up an analysis infrastructure to support the COVID-19 pandemic response. CLIMB COVID has had a massive impact, from supporting outbreak analysis in our hospitals all the way up to providing analyses that inform government policy. The impact of CLIMB and this award is a testament to both the hard work of the team and the broader vision of the CLIMB and CLIMB-BIG-DATA projects.”
A special thanks to a dedicated team
COG-UK would like to give a special thanks to Dr Sam Nicholls, Radoslaw Poplawski, and Simon Thompson from the University of Birmingham, and Dr Matt Bull and Dr Christine Kitchen from the University of Cardiff for their continued hard work on the CLIMB project and support in hosting the equipment.
COVID-19 Genomics UK (COG-UK)
The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.
Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/
COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. For more information, visit: https://www.cogconsortium.uk
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