New OCF Supercomputer at the University of Aberdeen Supports Ground Breaking Genomics Research

July 7, 2020

July 7, 2020 — Researchers at the University of Aberdeen are benefitting from an investment in High Performance Computing (HPC). The new HPC cluster, called Maxwell, is supporting ground breaking research at the University’s Centre for Genome-Enabled Biology and Medicine (CGEBM) and provides a centralized HPC system for the whole University with applications in medicine, biological sciences, engineering, chemistry, maths and computing science. The new HPC system is designed, integrated and managed by high performance compute, storage, cloud and AI integrator, OCF. The supercomputer is part of the University’s expansion to improve facilities for staff and students.

Image courtesy of the University of Aberdeen

With Maxwell, the University’s CGEBM is able to rapidly analyze complex genomics datasets from known and novel organisms and help researchers to revolutionize the study of the Earth’s biodiversity and complex ecosystems important to health and disease, agriculture or the environment. It is estimated that only around 1 percent of the Earth’s biodiversity is easily culturable in a laboratory, and there is little knowledge on most living organisms on the planet.

With the use of HPC, University researchers can analyze microbiomes associated with a diverse array of ecosystems, such as the human gut, fish important to Scottish aquaculture, glaciers, deep-sea sediments, soil and bioreactors for the production of sustainable and environmentally friendly biofuels. These state-of-the-art studies provide new understanding of important and diverse biological processes such as antimicrobial drug resistance; pathogen detection, evolution and virulence; mechanisms of drug efficacy and toxicity; development; inflammation; tumorigenesis; nutrition and satiety; and degradation of hydrocarbons.

Scotia Biologics, a SME research company, is working with the University’s CGEBM, using Maxwell’s capacity to speed up its existing pipeline and generating a more comprehensive dataset using genomics compared to traditional methods typically used in its field.

The new HPC system is also being used to teach graduates and post-graduate students in specialist subjects such as AI and bioinformatics, fields important to modern research and STEM careers, providing them with a unique opportunity to access HPC capacity. With 300 users, the cluster is providing a centralized HPC system to support all researchers and post-graduate students across the University.

With twenty times more storage than the University’s previous HPC system, Maxwell comprises four Lenovo ThinkSystem SD530 servers, 40 compute nodes, ThinkParkQ supported BeeGFS Parallel FileSystem hosted on Lenovo Servers and Storage and NVIDIA GPUs. OCF is also providing an OpenSource Software Stack and its OCF Remote HPC Admin Managed Service to support the in-house HPC team.

Image courtesy of the University of Aberdeen

Dean Phillips, Assistant Director, Digital and Information Services of the University of Aberdeen says: “Aberdeen is a research-intensive university and we’ve already seen an increase of 50 percent in registered users of our Maxwell HPC cluster. Having our own HPC system helps the University to attract new researchers, research funding and expand on existing programs of research and teaching. It is highly beneficial for our researchers to have on-site access to HPC infrastructure, particularly when securing start-up funds.”

Phillips continues: “OCF’s Remote Admin Service is an extension of our team and really helps to ensure the smooth day to day running of our HPC cluster and dealing with support issues, user requests and keeping on top of software and security updates.”

Dr Elaina Collie-Duguid, Manager, Centre for Genome Enabled Biology & Medicine at the University of Aberdeen says: “Genomics is a dynamic discipline that rapidly evolves into new applications and approaches to interrogate complex systems. The new HPC cluster, with its expanded capacity and advanced GPU capabilities, enables us to use new analysis methods and work at a much quicker rate than before. It really is an exciting time for genomics, which is revolutionizing the study of organisms and complex ecosystems to address issues of global importance, and HPC is a critical tool for analysis of these data.”

Russell Slack, Managing Director of OCF comments: “The new HPC cluster helps the University remain ahead of a fiercely competitive market. It attracts researchers, students and grants to its facility. Aberdeen’s investment in its HPC is a credit to its foresight in the importance of HPC in research that impacts people and everyday lives.”

Keith Charlton, CEO of Scotia Biologics, says, “As part of our drive to introduce new services to offer to the life sciences sector, Scotia is developing phage display library capabilities based around a growing number of animal species. With access to Maxwell, we’ve been able to quickly generate a large volume of data relatively inexpensively whilst significantly advancing our R&D program.”


Source: University of Aberdeen

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