Ace bio-IT team formed to spearhead phenome research

By Pete Young
Thursday, 19 September, 2002

A star-studded cast of researchers strongly seasoned with Australians has launched an ambitious bid to develop the next-generation bioinformatics needed to unravel the complexities of the phenome.

The group, whose participants include researchers from IBM Life Sciences, has applied for an Australian Research Council grant to create a centre of excellence from which to mount the attempt.

They want to build ultra-sophisticated tools that will do for research into entire cells what the current generation of tools has done for gene sequencing.

Part of their vision involves techniques permitting researchers to stand inside a cell via immersive visual modelling and watch in real-time as changes ripple through it when a gene expression is altered.

Their application straddles the boundaries between genome/phenome research and complex/intelligent systems which are two of the four priority research areas targeted for ARC funding in 2003. The other two are nano/bio materials and photonics.

Starting in 2003, the ARC will support winning applicants with up to $2 million annually for the next five years.

Those judged to have performed exceptionally well could receive funding.

The bioinformatics application is backed by a diverse group of Australian and US participants, including IBM's Thomas J Watson Research Centre in New York, the University of Colorado, Newcastle University, and Australian National University. However, the centre of gravity is in Queensland with University of Queensland, Queensland University of Technology and James Cook University all involved. The physical focus of the centre would be located at the new Institute for Molecular Bioscience building due to open on UQ's campus in December.

An impressive team of bioinformatics luminaries in the US and Australia are involved in the proposal. They include Prof Mike Waterman of the University of Southern California, a central figure in genomics and bioinformatics research. He is also co-inventor of the Smith-Waterman algorithm, used for searching out similarities and changes in DNA or protein sequences and the standard against which other sequence alignment tools are measured.

He also helped create the Lander-Waterman method, a tool vital to the success of the Human Genome Project, as well as much of the early software used in genomic and bioinformatic analysis of databases.

Two other high-profile bioinformatics researchers from the US east coast are also involved.

So is Australian researcher Prof Mark Ragan, head of the computational biology and bioinformatics section at the Institute for Molecular Bioscience, and a key figure in organising the ARC application.

Ragan describes the proposal as one that would put Australia in the front ranks of the effort to generate 3D modelling of cells which is now attracting huge investments particularly in the US and Japan.

Up to this point, bioinformatics has focused on discrete processes such as assembling sequences and searching gene databases for particular gene features, he says.

Ahead of it is the massively more sophisticated task of "getting our minds and our software around looking at cells and organisms as networks and systems." Researchers need to create a new algorithmic space that is equal to the job of handling the gigantic databases which have been developed.

An integrated database environment must be developed so bioscientists can ask questions across the range of new data types which are popping up.

"And we need high-throughput methods that let us understand cell phenotypes directly, so you can plug in a gene change and see what happens to the cell," says Ragan.

In its ARC funding application, the group makes the case that research into how genomic information is turned into phenomic structure and function makes a natural fit with research into complex intelligent systems.

Says Ragan: "Analysing biological systems of molecules as complex systems helps us understand the phenome and, conversely, complex systems research can use biology as a rich applications area."

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