Every year, the Pawsey Supercomputing Centre provides access to a range of supercomputing services to the Australian research community and international collaborators. We call this the Pawsey Uptake Projects, which provides researchers with access to dedicated Pawsey staff time for researchers in a collaboration to help maximize the research impact of the Pawsey Supercomputing Centre resources.
A supercomputing showcase
This Pawsey Friday showcased three researchers who took advantage of the Pawsey Uptake Projects opportunities as well as various training initiatives at the Pawsey Supercomputing Centre. Over fifty attendees gathered via Zoom to hear the researcher presentations, learn how to access Pawsey systems and get in touch with our expert staff.
Mahsa Mousavi – A workflow for analysis of environmental DNA (eDNA) data
As part of her role in the Curtin TrEnD Lab, Mahsa develops bioinformatic pipelines for analysis of environmental DNA data which is one of the major research focuses in TrEnD lab. Environmental DNA coupled with metabarcoding is revolutionising the way biodiversity can be monitored across a variety of environment. However, the large number of tools deployed in downstream bioinformatic analyses often place a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility.
With training from Pawsey on using containers and Nextflow, Mahsa has been enabled to configure her workflows to be reproducible, scalable and efficient when using supercomputing resources, which have enabled her work to faster parallelise, resume easily and be portable.
Paul Hancock – Porting workflows to a HPC environment
Paul is a Research Fellow at Curtin University and Murchison Widefield Array (MWA). His main research interests include: explosive transient events and radio variability, space situational awareness with the MWA, and software that supports and enables astronomy research. Paul’s uptake project focused on porting a workflow that had been developed on a desktop system to one that could work in an HPC environment.
After an intensive training session at Pawsey, Paul’s group was able to use Nextflow and Singularity containers to create v2.0 of Robbie which can now be deployed on Pawsey systems. Additional support from Pawsey meant that the scope of their research projects could be massively expanded as they are now able to process orders of magnitude more data than before.
Monica Kehoe – Incorporating supercomputing resources into diagnostic workflows
Dr. Monica Kehoe is a Plant Virologist and Molecular Plant Pathologist working for the Western Australian Department of Primary Industries and Regional Development (WA DPIRD) in the diagnostic and laboratory services section. Her current work focuses mainly on the development, validation and use of molecular methods for plant disease diagnostics across a broad range of broadacre and horticultural crops.
Monica’s ultimate goal is to incorporate supercomputing resources into the diagnostic workflow. Towards this aim, the 2018 uptake project successfully ported a workflow to Pawsey that reduced the time to a complete virus genome from weeks, to just hours. This pipeline was built specifically for Illumina sequencing data, and Monica is now working on porting the analysis of Nanopore sequencing data for diagnostics to Pawsey as well to help improve the turnaround time to result for these analyses.
Did you miss this Pawsey Friday? It is now available on Pawsey’s YouTube channel to watch.
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