Aust-US biosoftware alliance touted

Top-ranked computational biologists in Australia and the US are looking at joining forces to produce better software for bioscience researchers.

The world's number one expert on folded RNA structures, US researcher Robin Gutell, is holding preliminary discussions on the issue with Queensland bioinformatics specialists Prof Kevin Burrage and Prof Mark Ragan.

Gutell, 46, heads the Gutell Lab at the Institute for Cellular and Molecular Biology at the University of Texas where his work straddles the fields of structural, computational and comparative biology.

Burrage is director of the Advanced Computational Modelling Centre in Queensland while Ragan leads the computational biology and bioinformatics section at the Institute for Molecular Bioscience.

Gutell says public and commercially-available biosoftware continues to lack the flexibility needed by leading-edge researchers.

"We've always had to develop our own software tools to do the analysis we want because if we waited for the right tools [from commercial vendors] we wouldn't be on the cutting edge of research anymore," he says.

"What appals me is that so many researchers use existing tools which only allow them to ask the kind of questions that are dictated by the capabilities of the programs. They aren't free to ask the types of questions that they really want to ask."

His goal is to develop is a suite of more user-friendly software programs embedded in an infrastructure that will also cater for small, plug-in modules written in Java or C++.

The plug-in modules would give researchers the flexibility to handle specific types of analysis which aren't catered for by the off-the-shelf tools. The infrastructure would contain pathways for exchange of information between all the programs in the suite as well as the plug-in modules.

The project could proceed as collaborative venture with Queensland co-workers if a research grant can be found to support it, Gutell said.

But he is not ruling out involvement from commercial vendors: "I thought it might be easier to write a grant proposal and do this with academic sources, but if a (commercial software) company has any interest, I would welcome it."

A self-taught programmer, Gutell has helped develop software tools for sequence alignments and RNA structural analysis over the past 20 years as well as a database system for his research lab in Texas.

He's had to build bioinformatics skills because he's never found an off-the-shelf program that does everything he wants it to, Gutell says.

While he "enjoys interacting with professional programmers" he maintains that all bio-software development requires continuous exchanges between software programmers and bio-research users.

"The biologists are needed to find the bugs and to optimise the program so that it does what they want it to do."

Gutell may be moving toward a much closer involvement with Australian bioinformatics.

The IMB is talking with him about the possibility of moving to the institute from his Texas base. Interviewed this week during a visit to the IMB, Gutell characterised the discussions as "early stage."