VPAC offers software access to life science and biotech

A new service has been established to give researchers and biotechnology companies access to drug discovery and bioinformatics tools.

The BioPlatform service includes access to both commercial and open-source tools, including the Tripos Discovery suite, the Lion Bioscience suite, IBM Discovery Link Solutions and others.

It was developed by the Victorian Partnership for Advanced Computing (VPAC) in collaboration with the Victorian Bioinformatics Consortium (VBC), Bio21, the Victorian Infectious Diseases Reference Laboratory (VIDRL), and the Victorian Department of Primary Industry.

Access to the BioPlatform will be free to academic researchers, while small biotech companies will pay a nominal cost to use it. "The entry cost [for bioinformatics packages] is prohibitive for many companies, so we're providing an entry point," said VPAC CEO, Prof Bill Appelbe.

The organisation not only provides access to the bioplatform, but also assists with training and technical support, and has become the local agent and service provider for many of the packages to which it offers access.

"We have technical people in-house who understand scientific problems and can help groups to get up to speed more quickly," said Bill Yeadon, VPAC's business development manager.

Yeadon said that companies interested in using the platform could use the platform via a proof-of-concept model to drive their research projects to proof-of-concept stage at a nominal cost. Once that step has been achieved, companies are then required to enter into an agreement to use VPAC's infrastructure for a pilot project of a specified time period and a negotiated token fee shared by VPAC and the software vendor. Following that, companies would be able to either buy the vendor solution for further use or use VPAC's platforms on a project-defined basis.

"The real benefits are the low costs and the ease of access," Yeadon said.

Among the companies and organisations which have used VPAC's services to date are biotech companies Biota and Kinacia (now Cerylid), as well as Melbourne Health and the Victorian Infectious Diseases Reference Laboratory (VIDRL).

VBC director Prof Ross Coppel said the BioPlatform would free up VBC and other providers to focus on providing custom solutions. "You have to appropriately target the solution to the question being asked. The VPAC BioPlatform fills the gap in access to commercial software that does particular tasks very efficiently," he said.

VPAC was the recipient of a Victorian government STI grant in 2000, which provided AUD$6 million to a consortium -- comprising La Trobe University, Monash University, RMIT, Swinburne University of Technology, University of Ballarat and University of Melbourne -- to set up high-performance computing facilities. The organisation is also a founding partner of the Australian Partnership for Advanced Computing (APAC). According to Appelbe, the organisation is now fully self-sustaining and even generates a modest profit.

The software packages available through the BioPlatform include:

• Tripos Discovery software -- molecular modelling and visualisation, chemical informatics, bioinformatics, desktop modelling and data analysis.
• Lion Bioscience software -- comparative genomics, data and tool integration.
• Schrodinger software -- structure based drug design, lead optimisation and docking.
• IBM DiscoveryLink solutions -- including genes@work, Tieresias, biodictionary.
• Swiss-PDB Viewer and Modeller -- protein structure and function and interactions.
• Gromacs -- high-performance biochemical molecular dynamics analysis.
• NAMD -- high-performance simulations of biomolecular systems.
• Bio-Mirror-APAC -- conduit to global bio-mirror to GenBank and EMBL databases, and other software tools.