Research Impact

Cloud Computing Enables Genomics Researchers To Devote More Time And Resources To Research

Thom Cuddihy (left), a QCIF/RCC bioinformatician and software developer, demonstrates the cloud compute environment to Microbial Genomics Lab student Budi Permana. (Photo: Rhys White, Beatson Lab.)Summary

In a bid to reduce time and financial constraints, the University of Queensland’s Microbial Genomics Lab is increasingly using free cloud computing resources, such as QCIF’s, for a range of ARC and NHMRC-funded projects that use genomics to investigate multi-drug resistant superbugs.
 
For the lab, QCIF developed a customised version of a virtual laboratory compute cluster on QRIScloud, QCIF’s cloud computing service. This infrastructure will support rapid investigation of healthcare-associated bacterial outbreaks as part of the Queensland Genomics Health Alliance project.
 
The Microbial Genomics Lab previously relied on in-house IT hardware to run bioinformatics analyses, which require high-performance compute environments. However, increased computational demands, and associated administrative overheads, led the lab’s team to seek alternatives to obtaining and maintaining their own expensive HPC hardware.

Full article

11 August 2017

The University of Queensland’s Microbial Genomics Lab is increasingly using QCIF and Research Computing Centre (RCC)-managed cloud computing resources in a bid to reduce time and financial constraints.

The lab, in UQ’s School of Chemistry and Molecular Biosciences, is using cloud computing for a range of ARC and NHMRC-funded projects that use genomics to investigate multi-drug resistant superbugs. The custom-built compute infrastructure will also support rapid investigation of healthcare-associated bacterial outbreaks through a recently announced Queensland Genomics Health Alliance project.

The Microbial Genomics Lab previously relied on in-house IT hardware to run bioinformatics analyses, which require high performance compute environments. However, increased computational demands, and associated administrative overheads, led the lab’s team to seek alternatives to obtaining and maintaining their own expensive HPC hardware.

Lab head Associate Professor Scott Beatson said using QCIF and RCC’s shared resources is more efficient, leaving his team to focus on research rather than IT administration. “Working with QCIF and RCC enables us to future-proof our research by drawing on a team of IT experts and making better use of local and national compute facilities,” he said.

Instead of maintaining physical servers in-house, the lab’s researchers are now able to leverage the HPC cluster infrastructure of QCIF and RCC to provide the computational resources they need to produce world-class research.

With QCIF and RCC’s on-demand and scalable resources, the lab is supported in a flexible manner that deals with changes in requirements across studies, ranging from smaller pilots to large-scale analyses.

Combined with powerful, cloud-based biological analysis platforms, such as the RCC-supported Genomics Virtual Lab (GVL), this cloud computing approach offers numerous benefits to both biologists and bioinformaticians. RCC Director Professor David Abramson said cloud resources are ideal for this type of work because RCC and QCIF can provision solutions quickly without needing dedicated hardware.

QCIF/RCC bioinformatician and software developer Thom Cuddihy has spent the last three months working with the Microbial Genomics Lab to develop a customised version of a GVL compute cluster on QRIScloud. Thom's work included porting existing workflows and software to take advantage of the virtual cluster environment. He also established versioned tool environments available on both the GVL cluster and lab computers, to assist in the seamless transition from exploratory analysis on desktop machines to large-scale processing on the cloud.

QCIF is happy to help all researchers with their high throughput compute needs. Please contact the QRIScloud support team to discuss your project: This email address is being protected from spambots. You need JavaScript enabled to view it..

This article was first published on the QRIScloud website in August 2017.