Shannon Lindsay

Shannon Lindsay

Shannon Lindsay

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

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.

QRIScloud delivers satellite data to Australian farmers, govt and the public

Dan Burnham, a fifth-generation cattle grazier, is happy. Ground cover on his certified organic 2,500-hectare property, near Thangool in central Queensland, is up approximately 10 per cent.

Good ground cover — earth with grass or other plants — is essential not only for grazing, but also to minimise flood damage and polluting runoff. Healthy paddocks result in healthier livestock and better financial returns for the grazier.

Mr Burnham’s increased ground cover is partly thanks to Vegmachine — a free, fast online tool providing Australians with world-class, detailed ground cover analysis to help with grazing and land management decisions.

DustWatch Australia: wind erosion modelling for sustainable land management

During the last decade, wind erosion of soils has removed millions of tonnes of valuable topsoil from Australia’s agricultural and pastoral lands, reducing capacity to produce food and affecting the economy. The loss of topsoil can also negatively affect biodiversity, the climate and air and water quality.

During an Australian dust storm on 23 September 2009, more than 2.5 million tonnes of soil was blown off the Australian coast. The economic impact of this event on the NSW economy alone was conservatively estimated to be almost $300 million.

TERN, RCC and QCIF develop portal for reproducing scientific workflows and results

Reproducibility of research results has long been a hot topic amongst scientists.

As science becomes more data and computationally intensive, the harder it has become to reproduce others’ research. Not only is access to the data required, but also access to the same software, operating systems and other tools used.

A Queensland-based team led by the Terrestrial Ecosystem Research Network (TERN) has taken a step towards addressing this issue by developing infrastructure for reproducible science in the form of a virtual desktop, accessed by a web-browser, called CoESRA: Collaborative Environment for Ecosystem Science Research and Analysis.

Researchers seek to solve the complex puzzle of Chardonnay

In the 1980s and 1990s big, buttery Chardonnay was the white wine to drink. A backlash eventually occurred and some drinkers began to ask for “ABC — anything but Chardonnay”.

Since then, the styles of Chardonnay available in Australia have broadened significantly and Chardonnay is making a deserved comeback. This is a testament to the great malleability of the variety and to the improved quality and diversity of available plant material. Plantings of this grape in Australia far outweigh any other white grape variety — in part because Chardonnay is an important component of sparkling wine.

As the world's fourth largest exporter of wine, Australia’s wine industry is very important to the nation’s economic health. With 18 per cent of all grape plantings in Australia being Chardonnay, the variety contributes significantly to the economy and viability of the wine industry.

The Australian Wine Research Institute (AWRI) in South Australia and Canada’s BC Genome Sciences Centre at the University of British Columbia are investigating the genetic make-up of the Chardonnay grape to help the industry better understand the variety.

Cloud Power Users

Rowland Mosbergen is a power user of the Nectar Research Cloud, managing five production-ready virtual machines (VMs) as lead developer for Stemformatics.

After meeting other power users of the Nectar Research Cloud at a meeting hosted by QCIF, the Queensland node of the Research Cloud, Rowland established a power users group. According to Rowland, a power user wants to build things that are “maintainable, extensible, scalable, reliable.”

QRIScloud's large memory node helps QBI gain advantage

The use of one of QRIScloud’s large memory nodes has given the Queensland Brain Institute a competitive edge in the prototyping of new research domain specific information technology facilities.

Jake Carroll (pictured), QBI’s Senior Information Technology Manager (Research), said QBI used the node as a deconvolution pipeline prototype for its high throughput microscopy facilities.

Deconvolution is a computationally-intensive image processing technique that is being increasingly used to improve the contrast and resolution of digital images captured via high-end microscopy facilities.

Deep learning: A QRIScloud GPU node experience

QRIScloud’s special compute service has enabled a Griffith University PhD student to run document image retrieval experiments faster and with greater flexibility.

Ranju Mandal, at Griffith’s Gold Coast School of Information and Communication Technology, Is applying QRIScloud’s GPU (Graphics Processing Unit) node in his experiments. Together with a deep learning technique, his GPU algorithms can retrieve relevant documents by image queries into document repositories.

The goal of Mr Mandal’s research is to make querying and document retrieval based on images (e.g. a handwritten signature, seal or logo) in administrative documents a lot faster, making possible an automated process, rather than manual document scans. For example, a bank or other company could use the application to search its databases for documents featuring a particular signature.

The biodiversity and climate change ‘one stop modelling shop’

The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is enabling researchers to tackle data modelling without needing technical skills.

According to Professor Brendan Mackey, Director of Griffith University’s Climate Change Response Program, who helped shape BCCVL, it is a “one stop modelling shop to simplify the process of modelling species responses to climate change and enable more efficient investigation of related problems in the fields of conservation biology, ecology, and vector-borne diseases."

What researchers won’t see is QRIScloud, the NeCTAR research cloud, and National Computational Infrastructure (NCI) all working away behind the scenes, providing cloud compute and data storage for the virtual lab.

About QRIScloud

QRIScloud is a large-scale cloud computing and data storage service.  It is aimed at stimulating and accelerating research use of computing across all disciplines. 

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