eResearch Centre Monash University’s microscope of the future

Melbourne is fast building a reputation as a world-leading medical technology hub. Academic researchers, startups and large corporations in the medical technology space are increasingly choosing the city as their base, not least because of the cutting-edge technological infrastructure it is home to, such as the Australian Synchrotron.

The eResearch Centre is one example of Melbourne’s internationally recognised medical technology facilities. Based at Monash University, it is a world leader in advanced computing and IT services to support medical research. Yet centre director Professor Paul Bonnington uses the analogy of a much older scientific instrument to describe what the centre does.

“We provide the world’s most advanced computing technologies to help solve research challenges, but I like to think of our facility as a 21st century microscope,” says Bonnington.

Big screen

A microscope comprises three key components: a light source, focusing knobs and a viewfinder.

“In our case, the light source is a range of scientific equipment that produces massive volumes of digital data,’’ says Bonnington.

“The focusing knob is a high-performance supercomputer that we use to isolate out the things that really interest us in that vast sea of data.

“And our viewfinder is a computer screen. Although ours is a rather special screen,’’ he says, referring to Monash’s CAVE2 Immersive Visualisation Platform, which is 8 metres in diameter by 2.2 metres high, consisting of 84 million pixels that can be used to project 2D or 3D images.

“It’s the highest-quality microscope lens available and the largest of its type in the world,’’ says Bonnington.

International recognition

Bonnington says the eResearch Centre is unique in that it is the first in the world to take these highly sophisticated tools and stitch them together seamlessly so that researchers can engage with them in a very simple way.

“This is complex and hard to do well,’’ he says. “But our partners around the world are looking at us and saying that we have got it right.’’

One of the many Australian medical researchers grateful for the services of the eResearch Centre is Professor Gary Egan, director of the Australian Research Council Centre of Excellence for Integrative Brain Function, also based at Monash University.

“We collect huge amounts of data using MRI, CT and PET scanners with a focus on brain research,’’ says Egan.

“The eResearch Centre team provide us with advanced imaging analysis on a high-performance computer system that can handle our large data sets.

“For example, as part of our longitudinal study of healthy ageing, we scan the brains of over 500 people who are return each year. As people age, our brain capacity diminishes. This happens faster for some people than others, and we’d like to learn why. Our goal is to one day be able to help people in cognitive decline.’’

Each subject in the longitudinal study undergoes a 40 minute MRI brain scan each year. As the study has been running for some years now, the sheer volume of digital data generated is a challenge to store and analyse.

Key to the eResearch Centre’s services is its ability to process and store such huge amounts of information as those generated by Egan’s ageing study.

“Here in the Clayton precinct we have the largest campus of Australia’s largest research intensive university, and the largest campus of the CSIRO,’’ says Bonnington.

“There is also Australia’s largest scientific instrument, the Australian Synchrotron (a facility about the size of a football field that creates beams of extremely bright light used for research), and other major instrumentation such as those at Monash Biomedical Imaging, as well as some of the most powerful electron microscopes.

“All of these instruments are producing vast amounts of digital data into our computing system.

“A single electron microscope can produce up to two terabytes of data a day, and that is just one of the many instruments connected. Fortunately, we currently have capacity to store and process 10 petabytes (10,000 terabytes) of data.’’

In addition Monash University also hosts MASSIVE (Multi-modal Australian ScienceS Imaging and Visualisation Environment), a high performance computing facility designed specifically to process complex data. It leads in coordinating imaging informatics infrastructure across Australia and has played a key role in driving discoveries across many disciplines including biomedical sciences, materials research, engineering and geosciences.

New scanner

Earlier this year, Egan’s ARC Centre commissioned a new simultaneous Magnetic Resonance and Positron Emission Tomography scanner – financed with grants from CSIRO and Monash.

“This new machine has the extraordinary ability to do both MRI and PET scans simultaneously,’’ says Egan.

“The key advantage of this is that the MRI looks at brain function (blood flow), while the PET scan looks at metabolism – for example how glucose is used within the brain, or how drugs or neurotransmitters are metabolised.

“Analysing all the new data this scanner is providing will be fascinating, and it will be so much easier thanks to Paul (Bonnington) and his eResearch team, who provide us with the advanced tools we need.’’

Access to this world class high performance computing infrastructure is not only allowing Victorian researchers for the first time to visualise data in ways not previously possible but also through partnerships with industry is driving the discovery of new drugs and products.