Biotechnology
mechanism. It takes an active part in the drug binding process. Including water molecules demands more computer power and slows the simulation down, but now we’re no longer sacrificing accuracy for speed.” Enhanced computer resources also mean that Kuiper can run his simulations over longer periods of time. They are dynamic, and the molecules and their components jiggle and move with respect to one another. “When I started postgraduate research, I would be running what happened in a few hundred picoseconds (trillionths of a second), and I thought that was giving us a pretty good indication of what was going on,” Kuiper says. “A couple of years ago I would have told you that 10 nanoseconds (billionths of a second) was a long simulation, and that was the benchmark then. Now I’m
thinking more in terms of 500 nanoseconds to a few microseconds (millionths of a second).” The point is that the longer the simulation, the more time you have to work out what is occurring and what is significant. In his simulation of the anti-flu drug Relenza, for
instance, Kuiper has not yet reached the point at which the drug has docked into its protein target, neuraminidase, but already he has zeroed in on a part of the molecule near the receptor which appears to usher Relenza into the docking area. This has stimulated him to think that a mutation changing the structure of this part of the target molecule may be what confers resistance to Relenza’s action. At all times Kuiper is aware that he is working with a model on a computer, not a real molecule – which
AS WE BUILD IT, HERE THEY COME
It took less than one year of operation for applications to use the supercomputers at the Victorian Life Sciences Computation Initiative to be oversubscribed. In the latest competitive grant round to gain access to these resources, over 50 research groups submitted such high-quality applications that most had their allocations reduced to ensure everyone could either continue or make a start with their work and keep their research globally competitive. Most of these Victorian-led projects involved collaborations across a number of research organisations from a number of regions, both in Australia and beyond. This success confirms the Victorian government’s decision in 2009 to establish a Life Sciences Computation facility as part of its plan to create a world-class infrastructure base upon which it is building Victoria as a world biotechnology hub. The Australian Synchrotron, the Victorian Comprehensive Cancer Centre, the AgriBio Centre, Bio21, the Australian Regenerative Medicine Institute, the Melbourne Centre for Nanofabrication and the Victorian Life Sciences Computation Initiative (VLSCI) are key infrastructure projects as laid out in the Victorian Biotechnology Action Plan 2011. Life Sciences researchers today have the
understanding and technologies to investigate life at all levels. Medical imaging, genomics, structural biology, integrated biological systems, bioinformatics and health informatics are providing powerful and versatile tools for life sciences researchers to investigate the structure and interaction of molecules, complex biological systems (from proteins, cells, tissues, organs, up to organisms), the nature of disease and more.
In each of these areas, the technologies are
advancing: higher quality medical imaging, increasingly cost-effective gene sequencing, better access to protein crystallography facilities and refinements in computer simulation and modeling. These advancements are not only driving the frontier of research but are also providing major computing challenges and it will require significant expertise and computational infrastructure to take full advantage of these opportunities. Computational expertise
80 Australia China: BEYOND TOMORROW
is especially important to allow improvements in technology to flow through to research outcomes. The VLSCI is a A$100m initiative of the Victorian
government in partnership with The University of Melbourne and the IBM Life Sciences Research Collaboratory, Melbourne. Other major stakeholders include key Victorian health and medical research institutions, major universities and public research organisations. VLSCI aims to be one of the top five life science computation facilities in the world by 2013. This important project is enhancing Victoria’s
international standing in life sciences by positioning researchers at the cutting edge of this growing discipline, nurturing future leaders in these fields and creating a magnet to attract industry to Victoria. The outcomes for the broader Victorian community will be the generation of new knowledge leading to improved medical and health outcomes.
KEY RESOURCES:
A high performance computation facility accessible to all Victorian Life Sciences researchers and their collaborators, staffed by technical experts who will maximise the user experience. Stage 1 is now performing at a peak capacity of 46 teraflops. Stage 2, by 2013, will see the delivery of petascale computing.
A Life Sciences Computation Centre operating from three hubs based in Melbourne’s Central (Parkville), South East (Clayton) and North (Bundoora) precincts. These hubs have been created to meet the skills gaps in research teams, build the necessary cross-disciplinary research collaborations and assist with scaling-up projects to make the most of the processing power being delivered.
Ongoing training to develop computational biology, computational imaging and bioinformatics expertise for research and industry.
A communications strategy for highlighting the benefits of such research to the public, industry and government.
AUSTRALIA
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