About
Molecular Modelling of the drug Zanamivir (trade name: Relenza) binding into a pocket of the Influenza neurminisda. Credit: Mike Kuiper PhD

About

Victorian researchers using this supercomputer facility have access to a powerful tool to help them solve some of the biggest challenges facing the State’s health system and impacting on our quality of life. Life scientists and computer scientists are forming exciting collaborations to improve diagnostics, find new drug targets, refine treatments and further our understanding of the major diseases affecting our community: cancer, epilepsy, genetic disorders, infectious diseases and eye disease, among others. The collaboration with IBM further enhances Victoria’s reputation as a global centre for excellence in life sciences research capabilities. Read more about Victoria's Technology Plan for the Future - Biotechnology.

Scaling-up life science research to operate on high performance computers cannot be realised without sound technical and scientific advice and collaboration. Facility staff, Life Sciences Computation Centre staff and IBM Research Collaboratory for Life Sciences, Melbourne experts provide these services, along with formal training and documentation.

Background

The Victorian Government is committed to providing 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. To sustain and grow Victoria’s standing as a world leader in life science research, it is vital to keep ahead in the new fields of Computational Biology, Bioinformatics, and Computational Imaging. To do this we must have high performance computation capacity and expertise. These computation resources have the potential to transform basic and clinical research and lead to major improvements in public health outcomes in the areas such as cancer, cardiovascular and neurological disease, chronic inflammatory diseases, bone diseases and diabetes.

Life science 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 modelling. These advancements are not only driving the frontier of research but are also providing major computing challenges and it will take significant expertise and computational infrastructure to make full advantage of these opportunities. Computational expertise is especially important to allow improvements in technology to flow through to research outcomes.

The VLSCI is 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. It exists for all Victorian Life Sciences researchers and their collaborators.

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 staffed by technical experts who will maximise the user experience. The Facility is now operating at over 855 teraflops.
  • A Life Sciences Computation Centre operating from three research 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 provide skills to scale up projects to efficiently use the processing power being delivered.
  • Ongoing skills development and training to nurture 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.

Milestones

2008

June - Victorian Premier John Brumby announces the $100 million Victorian Life Sciences Computation Initiative, including $50 million in State funding for peak computing infrastructure at the BIO2008 conference in California on 17 June 2008.

September - At The University of Melbourne, key Victorian Universities and research institutions across Victoria were briefed about the project.

2009

Business Plan developed in consultation with potential partners such as Monash and LaTrobe Universities, the Victorian Partnership for Advanced Computing (VPAC), the Victorian eResearch Strategic Initiative (VeRSI), Ludwig Institute for Cancer Research, Howard Florey Institute, Peter MacCallum Cancer Centre, and St Vincent's Institute.

November - Call made for a Key Partner to help deliver the Life Sciences Computation Centre and Peak Computing Facility (PCF).

November - Twenty early-stage projects were selected from researchers at The University of Melbourne, Monash University, VPAC, VeRSI, NICTA and WEHI.

November - Six postgraduate students sponsored to attend Supercomputing Conference (SC09).

December - First call for Resource Allocation Grant Scheme.

December - Announcement of postgraduate intern program developed in association with Australian Mathematical Sciences Institute.

2010

February - IBM becomes the Key Partner and included in the agreement is the establishment of the first IBM Research Collaboratory for Life Sciences at VLSCI along with the provision of an IBM Blue Gene/P supercomputer and an IBM iDataplex x86 system. SGI were awarded a contract to provide an SGI Altix x86 system for the PCF also.

March - SGI Altix x86 goes live. Professor Peter Taylor appointed as Director. Professor Justin Zobel appointed as Interim Director until Professor Taylor’s arrival in September.

April - Key IBM technical staff start work at VLSCI, joining growing staff in PCF.

May - Second call for Resource Allocation Scheme, with accompanying information sessions run at major Universities.

July - Undergraduate Research Opportunities Program Conference Day, includes presentations by eight VLSCI-supported students working in a biomedical research laboratory on current bioinformatics projects.

August - IBM Blue Gene/P goes live. Launch event held on August 10 featured the Victorian Premier, John Brumby, Minister for Innovation, Gavin Jennings, UOM Vice Chancellor Glyn Davis and Senior US and Australian IBM personnel.

August - IBM host a workshop: High performance computing: Thinking big! From desktop to supercomputer: Enabling scientific computing

September - IBM Dataplex x86 goes live. Stage 1 completed.

November - Six postgraduate students sponsored to attend Supercomputing Conference (SC10).

November - Data storage facilities fully implemented.

December - Dr Andrew Lonie appointed as Head, LSCC.

2011

March - Life Sciences Computation Centre officially opens for business.

March - Annual Report notes in-kind contributions far in excess of budget.

May -  VLSCI announces three-year sponsorship of Bio21 Cluster’s UROP program.

June -  Launch of VLSCI Exhibition and video – Things Change When You’ve Got the Power.

July - new bioinformaticians start arriving at LSCC.

October – Resource Allocation Scheme oversubscribed for 2012.

November - VLSCI announces Ph.D. top-ups, travel and conference grants and releases new story on cancer research in the Science Stories series. November – new video released, High Performance Computing Reveals New Drug Targets. Six students supported to attend SC11 in Seattle.

December – 5 LSCC and 3 IBM summer interns arrive.

2012

February – Announcement of decision to proceed to Stage 2 and purchase IBM Blue Gene/Q supercomputer.

March – LSCC Expressions of Interest attract projects from across the Victorian research community.

May-July - Over May/July, VLSCI's Peak Computing Facility had four racks of the IBM Blue Gene/Q supercomputer installed as part of the Stage 2 upgrade, delivering petascale computing for Life Science researchers in Victoria. The upgrade also included other add-ons to existing systems.

July – VLSCI is biggest supercomputer in Australia, the largest in the world devoted to life sciences research and the Blue Gene/Q ranks as the greenest supercomputer in the world.

Beyond 2013

The objectives for 2013 and beyond are to:

  • Achieve a strong user base extending throughout Victorian research institutions and beyond into national and international collaborations.
  • Enable excellent research outputs (of both quality and quantity).
  • Embed the operation of the completed facility.
  • Employ at least 30 expert staff on the program.
  • Plan for sustainability beyond the life of the initial contract.
  • Identify and move into other research areas.