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Australian BioCommons
Published October 15, 2021 | Version v1
Presentation Open

Australian BioCommons ToolFinder: discovery of bioinformatics software in an Australian infrastructure context

Creators

  • 1. Australian BioCommons, Australia; Melbourne Bioinformatics, University of Melbourne, Australia
  • 2. Australian BioCommons, Australia; Queensland Cyber Infrastructure Foundation (QCIF), Australia
  • 3. Australian BioCommons, Australia
  • 4. National Computational Infrastructure (NCI), Australia
  • 5. Pawsey Supercomputing Research Centre, Australia
  • 6. Sydney Informatics Hub, University of Sydney, Australia
  • 7. Queensland Cyber Infrastructure Foundation (QCIF), Australia

Description

This presentation took place during a session at the eResearch Australasia 2021 Conference 11-15 October 2021. A recording of this presentation is available on the Australian BioCommons YouTube Channel.

Abstract

Introduction

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.

Methods

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.

Results

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.

Conclusions

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.

Files

2021_eResearch_Gustafsson_ToolFinder.pdf

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