Powering discovery: diverse outputs from ABLeS-enabled research

The Australian BioCommons Leadership Share (ABLeS) has been providing access to infrastructure and computational resources for over 5 years, enhancing the capacity of life scientists to readily harness national infrastructure to accelerate their discoveries. Working with Australia’s Tier 1 high-performance computing facilities, Pawsey and NCI, this Australian BioCommons program provides computational resources, specialist expertise, and a shared repository of tools and software, tailored to support life science research communities.

The publications generated by 73 projects involving 471 ABLeS users provide a fascinating insight into the diversity of research requiring large-scale computational power for bioinformatics. Project leads have shared outputs from the first half of the year, offering a snapshot of how ABLeS is supporting research across a diverse range of areas. 

As part of the Australian Amphibian and Reptile Genomics initiative (AusARG), Dr Ian Brennan, ANU, leveraged Pawsey compute to document the phylogenomics of native animals:

• Sphenomorphini unravelled: a phylogenomic framework and generic reassessments for Australia’s most species-rich vertebrate radiation

• Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia

• Generalists link peaks in the shifting adaptive landscape of Australia’s dragon lizards

• Aridification and habitat shifts are associated with diversification in Australian diplodactylid geckos. 

Prof Benjamin Schwessinger (ANU) from the Plant Pathogen Omics Initiative has used NCI to create outputs that report on the economically significant pathogen of barley and wheat, stripe rust:

• Sexual recombination under tetrapolar mating can alter host-specialization boundaries between wheat- and barley-adapted stripe rust lineages

• The variable wheat stripe rust effector AvrYr7 evades Yr7 recognition through sequence and expression polymorphisms

• A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei.

Over the years, access to the right national facilities has underpinned the ability of research groups to analyse and process their data. Dr Patricia Agudelo-Romero, and her team The Kids Research Institute, have been utilising their Pawsey resources to great effect, with publications across domains:

• Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia.

• Exploring the complexity of the human respiratory virome through an in silico analysis of shotgun metagenomic data retrieved from public repositories  Conservation of gene expression patterns between the amniotic and nasal epithelium at birth

• Programming of the respiratory epithelium in utero — insight from the amniotic epithelial methylome

• Conservation of gene expression patterns between the amniotic epithelium at birth and a newborn's nasal epithelium.

Dr Agudelo-Romero remarked:

“Through ABLeS computing resources, the research I lead at The Kids Research Institute Australia has enabled multi-omics analyses in paediatric respiratory research, including epigenomics, transcriptomics, and metagenomics. This support has facilitated studies ranging from characterising the human respiratory virome to understanding early-life epigenetic programming of the airway, as well as building sustainable bioinformatics capacity through Nextflow and nf-core training.”

Australian BioCommons encourages ABLeS project teams to share publications, software, datasets and other outcomes arising from their allocations so they can be showcased across the community. These examples represent only a small sample of the diverse research communities currently supported through ABLeS. As the BioCommons’ Product Manager, Bioinformatics Platforms, Dr Ziad Al Bkhetan has been thrilled to see the ABLeS service grow: 

The publications that are rolling in clearly demonstrate the uplift that happens when ABLeS connects researchers directly to the computational resources they need. Now in its fifth year, ABLeS continues to expand, enabling more projects to take full advantage of the excellent research infrastructure available to Australian researchers. 

Learn how ABLeS can support your research

See who else is using ABLeS

ABLeS is co-funded by Bioplatforms Australia, National Computational Infrastructure and Pawsey Supercomputing Research Centre