Australian BioCommons ToolFinder: discovery of bioinformatics software in an Australian infrastructure context
Dr Ove Gustafsson1,2, Dr Jeffrey Christiansen1,3, Dr Tiffanie Nelson1, Dr Nigel Ward1,3, Dr Dale Roberts4, Brian Davis4, Dr Marco De La Pierre5, Dr Tracy Chew6, Dr Dominique Gorse3, Dr Gareth Price3, A/Prof Andrew Lonie1,2
1Australian BioCommons, Australia
2Melbourne Bioinformatics, University of Melbourne, Australia
3Queensland Cyber Infrastructure Foundation (QCIF), Australia
4National Computational Infrastructure (NCI), Australia
5Pawsey Supercomputing Centre, Australia
6Sydney Informatics Hub, University of Sydney, Australia
The discovery of bioinformatics software for a particular purpose, and where it can be accessed to support research, can be challenging for both bench/wet-lab life scientists and bioinformaticians. Multiple Australian BioCommons community consultations highlighted a need for resource discoverability, and so we have created a searchable compendium of bioinformatics software (ToolFinder) that also highlights availability across major Australian research focused compute infrastructures including QRIScloud, the National Computational Infrastructure (NCI), Pawsey Supercomputing Centre (Pawsey) and Galaxy Australia.
The BioCommons maintains a central register of bioinformatics software, sourced from consultations with Australian life science researchers. Supported by collaborations with the Queensland Cyber Infrastructure Foundation (QCIF), NCI, Pawsey, Galaxy Australia and the ELIXIR Tools Platform in Europe, this register includes (a) metadata sourced from the global bio.tools registry and (b) facility supported software versions installed across Australian infrastructures. The register is publicly available: https://australianbiocommons.github.io/2_tools.html.
ToolFinder provides rich descriptions of software use and features, links to international registries (bio.tools, biocontainers, Galaxy toolshed) for more information, and connects this to a landscape view of installation across Australian computational infrastructures. ToolFinder currently has more than 400 entries.
ToolFinder makes the Australian bioinformatics software ecosystem more tangible for researchers. It integrates with global software registries, and presents pathways for software discovery and use on Australian infrastructures. A similar WorkflowFinder is being planned.
Dr Johan Gustafsson is a Bioinformatics Engagement Officer with the Australian BioCommons. He works with the Australian BioCommons communities, national science drivers (including the Bioplatforms Australia Framework Initiatives) and infrastructure partners to define community bioinformatics requirements and establish fit-for-purpose solutions. He has a background in mass spectrometry and proteomics, with a PhD in Biochemistry from the University of Adelaide.