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Medical researchers at King's College London cut analysis time with HPC

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Medical researchers at the National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London are for the first time using a High Performance Computer (HPC system). The system is being used by researchers to analyse, store and archive vast quantities of data generated through work on understanding the role of genetics in a range of common health issues, such as the development of cancer.

The two sequencing machines in use in the King's College London and NIHR Biomedical Research Centre's genomics facility collectively generate up to 50 billion base pairs of usable DNA sequence data every 10 days. The HPC system can reduce the time necessary to analyse this data 20-fold or more, reducing the time scales for analysis from days to hours.

'The sequence of the human genome has been known for 10 years now so we are using new sequencing technologies to sequence specific regions of the genome in large numbers of people in order to help understand the contributory factors to a variety of common complex disorders and developmental defects,' said Dr Rebecca Oakey, reader in epigenetics, Department of Medical and Molecular Genetics, School of Medicine, King's College London. 'These include skin diseases such as psoriasis, inflammatory bowel disease and the step by step development of vascular disorders, psychiatric disorders, diabetes, infection and immune disease as well as genetic components in cancer development.'

Dr Oakey added: 'To do so we need innovative sequencing technology to generate the data and the processing power to analyse, store and archive the data.'

The HPC system's bespoke design, implementation, configuration, ongoing support and user training is handled by OCF. 'Data generated and stored by organisations around the world is growing at an alarming rate,' said Julian Fielden, managing director, OCF. 'According to IBM, worldwide data volumes are doubling every two years and IDC puts the total worldwide data figure at 281 billion Gigabytes.

'Sequencing machines specifically - similar to those in use in the NIHR Biomedical Research Centre’s funded genomics facility at King’s College London - are generating vast quantities of data on a regular basis. The Comprehensive Biomedical Research Centre is a great example of an organisation that acknowledges data on its own delivers little or no value; organisations must analyse and take value from their data so that the findings can be translated to improved patient care at the earliest opportunity. In many cases this analysis is best performed using an HPC system.'

The HPC System design includes: IBM's iDataplex server hardware, which includes ultra-low latency, 10Gb Ethernet switching modules from Blade Network Technologies; Panasas plug-and-play ActiveStor Series 8 clustered storage with capacity of up to 180TB of raw data; and an IBM TS3310 Tape Library Unit with Tivoli Storage Manager to enable long-term, secure, off-site data back-up.

Fielden continued: 'By using well configured and innovative technologies from companies like IBM and Panasas, it is now possible for companies of any size in any industry to own a practical, economical, environmentally friendly HPC.'