Supercomputing access powers paediatric research
Dr Patricia Agudelo-Romero presents a poster at the 2024 AAAI conference (supplied).
Demand for high performance supercomputing resources among life scientists is increasing thanks to consistent growth in both the scale and complexity of omics datasets and analyses. The Australian BioCommons Leadership Share (ABLeS) offers a specifically tailored mix of infrastructure and computational resources to support life sciences research, providing an alternative access mechanism to Tier 1 resources outside of onerous merit-based applications.
The Kids Research Institute Australia, formerly Telethon Kids Institute, is a great example of the support ABLeS provides to research groups. As a word-class paediatric research centre, The Kids is committed to improving children’s health across its 4 key research themes: Indigenous Health, Brain and Behaviour, Chronic and Severe Diseases, and Early Environment. Many of its programs require sophisticated computational biology tools and resources, including the P4 Respiratory Health for Kids team. The P4 team focuses on the significant healthcare burden of childhood respiratory diseases, with around 20% of Australian children developing recurrent respiratory disorders such as wheezing and asthma.
Dr Patricia Agudelo-Romero, Senior Research Fellow, leads the computational biology and bioinformatics arm of the Wal-yan Respiratory Research Centre within The Kids and is a key member of the P4 team. She uses ABLeS resources to conduct omics analyses including epigenetics, transcriptomics and metagenomics. Patricia and the P4 team recently presented two studies enabled by ABLeS - understanding the methylation landscape of in utero programming in relation to asthma risk factors (part of the AERIAL study), and exploring the complexity of the human respiratory virome. The methylation study was a featured poster at the 2024 American Academy of Allergy, Asthma & Immunology conference, while the lung virome work won best selected talk at the Microbiome Virtual International Forum in 2022, having uncovered a high diversity of bacteriophages in the airways, which may play an important role in modulating the lung ecosystem.
ABLeS enabled both our studies to process more than 2,300 FASTQ files from targeted high-throughput methylation sequencing and shotgun metagenomics experiments, using two methylation-related nextflow pipelines and one related to virus discovery. These large-scale and computationally demanding analyses would not be possible without cutting-edge resources like our access to the Pawsey Supercomputing Research Centre provided through ABLeS.
In alignment with the open-science principles of ABLeS, Patricia has made her nextflow pipelines publicly available through the nf-core community - namely the EVEREST for viral assembly and characterisation, and target-methylseq-qc which performs downstream analyses after running a standardised nf-core methylseq pipeline. The same nf-core pipeline is being applied in another project at The Kids Institute, where the Clinical Epigenetics team are analysing whether a mediterranean diet induces DNA methylation changes in pregnant women as part of the ORIGINS study. ABLeS is enabling the team to run the methyl-seq pipeline, including ensuring the pipeline can be run on the upcoming Australian Nextflow Seqera Service.
Could your research team benefit from what ABLeS offers? Watch Dr Ziad Al Bkhetan give an overview of the service.