Life-saving medical discoveries don’t only require visionary scientists within world-class research institutes, they also need IT infrastructure to power the possibilities.
Transforming the way genomic research is conducted in Australia, the Garvan Institute of Medical Research has implemented a new Dell EMC high-performance computing system to allow its researchers to push scientific boundaries.
The Garvan’s Data Intensive Computer Engineering group’s new system has been designed to underpin several genomic datasets – including the Sydney Genomics Collaborative and the Medical Genome Reference Bank – and help drive the Australian Genomic Cancer Medicine Program.
With the new infrastructure, Garvan researchers are able to harness big-data analytics and deep-learning capabilities, providing them with accelerated findings that can be applied to patient treatment faster and at lower cost.
The technology has transformed the way the Garvan does science, according to Dr Warren Kaplan, the institute’s Chief of Informatics.
“It’s given us the ability to transform Garvan into a data-driven medical research institute, and the more genomes we sequence, the more we’re able to use that information to inform future studies,” Kaplan said.
When the first whole human genome was sequenced, the project took over 10 years and cost almost US$3 billion but extraordinary advances in technology have meant the Garvan is able to sequence up to 50 genomes a day at a base price of around US$1000. So far, it has sequenced more than 10,000.
The world-renowned institute’s genomic research unearths revelations into how variations in people’s DNA sequences contribute to health and disease, and has achieved significant success in identifying changes that lead to cancer, and immune, cardiac, mitochondrial and other diseases.
To store, analyse and use genomic information, the Garvan requires considerable computational resources and data storage.
Each person’s genomic data contains over six billion bases and around five million genetic variants, taking up to 700 hours to process.
“We want to change the direction of medicine and have a life-changing impact on people’s health,” Kaplan said.
“We see genomics as the key to driving this transformative change, and we couldn’t achieve this without the computing infrastructure to make it possible. Genomics requires significant computational power to analyse the data and that’s why we partnered with Dell EMC.”
The Dell EMC HPC infrastructure expands on the Garvan’s existing on-premises system to provide researchers with architecture that can handle scientific workloads.
“The advent of genomic sequencing has played a critical role in understanding the underlying pathways of disease,” Andrew Underwood, High Performance Computing, Dell EMC Australia and New Zealand said.
“The heterogeneous high-performance computing platform will allow scientists to quickly discover effective treatments, prolonging the life of thousands of Australians living with life-altering illness. With genome research fast becoming more accessible to scientists, Garvan needed a solution that could handle its fast-growing research needs. The unique design means that the HPC will continue to grow as it is required.”
The new computational superpower servicing the Garvan’s genome sequencing capability is also core to the Kinghorn Centre for Clinical Genomics, the Garvan Weizmann Centre for Cellular Genomics, and is crucial to precision cancer medicine initiatives such as the Lions Kids Cancer Genome Project.
- Across 47 Dell EMC PowerEdge servers, the solution provides clinical researchers with the genomics processing capacity of 1632 Intel Xeon Scalable Processor cores
- 10 Intel Arria 10 GX FPGAs
- 122,880 NVIDIA Tesla V100 CUDA cores
- 15,360 NVIDIA Tensor cores to accelerate HPC and AI techniques
- 744TB of NVMe to accelerate in memory processing of genome data sets
- 41TB DDR4 RAM Memory
- 530TB usable capacity CephFS storage
- The HPC cluster is connected by 25 GbE and 100 GbE.
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