ISC HPC Blog
Looking for Healthy Outcomes for Australians? Computer Experts Wanted
March 2014 saw the launch of yet another venture by American biologist and entrepreneur J. Craig Venter. Having created the Human Genome project, the Global Ocean Sampling Expedition and Synthetic genomics he has now added Human Longevity Inc.(HLI). With start-up funding of US $70 million, the aim of HLI is to develop tools and techniques aimed at bringing better health to the world’s increasingly ageing population. On their website, HLI’s goals are “to build the world’s most comprehensive database on human genotypes and phenotypes to tackle the diseases associated with aging-related human biological decline.”
And what kind of people are they employing? On May 18 they announced that Yaron Turpaz has left his position as Vice President, IT Research and Development at AstraZeneca to become HLI’s chief information officer. His job is to create and develop their genomic and phenotypic database business, lead their various bioinformatics and software engineering initiatives, and build a computing facility in Singapore as well as expand the informatics program at its existing facility in California.
How are they creating the database? One way is to contract others to supply important parts, such as the California-based CorTechs Labs who will be supplying imaging data for HLI’s database, enabling them to join up magnetic resonance imaging data with other sources of information to create a more comprehensive picture of aging.
Venter’s new venture isn’t alone in focussing on improving the lives of the ageing. Australian researchers are playing their role in the International Cancer Genomics Consortium (ICGC) whose aim is to generate comprehensive catalogues of genomic abnormalities in tumors from 50 different cancer types and/or subtypes. These tumors are of clinical and societal importance across the globe and the genomic data will be made available to the entire research community as rapidly as possible, and with minimal restrictions, to accelerate research into the causes and control of cancer.
Whether public or private, these enterprises are just a snapshot of the immense changes occurring in health and medical research. What unites them however is – firstly – that the tools and techniques they rely on are increasingly sophisticated, complicated and developing rapidly. Secondly, and perhaps even more importantly, the skills-base needed for these are other similar projects are being found outside of the traditional medical school graduation lists.
While the problems are biological and medical, the enormity of the size of the databases that are being used to solve these ageing problems are only manageable using supercomputers. So the people needed to run these projects have to have expertise not only in the life sciences but in computing, maths and engineering.
With the US, China and Japan planning to develop exaflop-capable machines by around 2020, where does Australia stand in all this? Last year Raijin was launched at the National Computational Infrastructure facility (NCI) in Canberra and at over 1.2 petaflops, hit the Top 500 rankings at 24.
Australia tends to lag about four years behind the main players in the supercomputer stakes. So we need to be ready by 2024. If we want to deliver these more sophisticated understandings of disease by using some of the techniques arising from genomic research, then we need supercomputers that are at least somewhere in the Top 500 in size, preferably in the Top 50.
We can’t just sit back and contract other countries to do our number crunching. We may use some of the tools HLI develop, we may contract to share some of our de-identified data with them if it brings us some benefits, but it is unlikely that we will be willing to hand over to other countries or companies most of our own health data to mine.
No, we will need to own these computers. But more importantly, what we will need is people to run them. Other countries are already targeting those people – currently in early high school – to develop the expertise to run, program, decipher, maintain and develop the information going into and coming out of these supercomputers. The UK has identified that it will need 830,000 new science, engineering and technology professionals and 450,000 technicians between now and 2020. In the new world of the super-supercomputer, life scientists, mathematicians and engineers will be working together to deliver better health outcomes.
Australia’s Prime Minister encourages us to see this period of time in Australia’s history as one of infrastructure growth. I would argue that this should be half of the plan: the other half should be to promote students into mathematics, bioinformatics and computer science from a young age. Encourage them to see these fields as potentially making a very valuable contribution to future health outcomes in our community, arguably a very socially rewarding career.
Professor Peter R. Taylor is Director of the Victorian Life Sciences Computation Initiative (VLSCI). Funded by the Victorian Government and contributing institutions and hosted by the University of Melbourne it includes the first IBM Research Collaboratory for Life Sciences and an extensive outreach program attracting students and researchers into the exciting new world of computational biology. Based in Victoria’s world-leading biomedical research precinct, as at May 2014 it remains the biggest supercomputer facility devoted to life sciences in the world.