Repurposed hardware boosts national capacity and powers innovation
This story is co-published with QCIF Ltd
After successfully completing a previous project, QCIF Ltd donated high-performance hardware to the Australian BioCommons, giving the hardware a second life in science and uplifting national capacity for the benefit of the scientific community.
Well suited for running AlphaFold 2 jobs, the five General-Purpose Graphics Processing Units (GPGPUs) are now being used to enhance the national compute network behind the Galaxy Australia service.
The impact of this donation goes beyond infrastructure improvements. It has significantly expanded Galaxy Australia's capacity to support innovation by enabling the use of other GPU-enabled tools that offer major benefits to the scientific community. GPU processing can provide massive improvements in computational efficiency, decreasing processing times to less than 5% of conventional equivalents.
Dr Cameron Hyde, a bioinformatician at QCIF who supports the development of national software platforms like Australian BioCommons' Galaxy and Apollo services, co-authored the original AlphaFold 2 wrapper that enabled the tool to run within Galaxy Australia, ensuring both a friendly user-interface as well as instant access to the GPU clusters required to power the tool. He shared his enthusiasm for the new possibilities unlocked by the donated hardware, which directly enhances the bioinformatics services he helps deliver to Australian researchers, “Now that we have five GPU nodes of our own, we have room to experiment and explore new GPU-enabled tools. This gives us room to innovate beyond AlphaFold and accelerate scientific discovery in other research domains.”
For example, Galaxy Australia’s lead Bioinformatician Michael Thang has been using the hardware to explore running Nanopore’s “Dorado” on Galaxy Australia. Dorado is a high-performance basecaller for Oxford Nanopore Technology sequencing data. This innovation would enable researchers to conduct their entire analysis, from raw sequencing data through to assembled genome, all within the Galaxy Australia service.
Collaboration driving innovation
Developed by Google DeepMind, AlphaFold is an AI system that predicts a protein’s 3D structure from its amino acid sequence with accuracy comparable to experimental methods. In 2020, Australian BioCommons identified an opportunity to democratise access to this powerful tool by making AlphaFold 2 available through Galaxy Australia. This gave Australian researchers much greater accessibility to AlphaFold 2, allowing life scientists to easily visualise proteins in a manner inaccessible to all but dedicated structural biology researchers. This advance has supported research into protein-protein interactions, activation and inhibition mechanisms, and drug design.
By 2025, use of AlphaFold 2 has surged, evolving from an analytical tool for individual proteins into a routine screening tool for studying protein-protein interactions. To support this shift, Dr Hyde collaborated closely with Australian Structural Biology Computing Community to develop extensions to the AlphaFold Galaxy tool, including new output formats, input parameters, and an option to re-use intermediate files for improved efficiency.
Supported by the Australian BioCommons, AARNnet, QCIF Ltd, and The University of Melbourne, the optimised system now provides fully subsidised access for all Australian researchers via the Australian Alphafold Service.