Reflections on the successes of a national genomics consortium
BY DR JOHAN GUSTAFSSON, AUSTRALIAN BIOCOMMONS
The Bioplatforms Australia Genomics for Australian Plants (GAP) Framework Initiative recently published a preprint of the capstone paper for the consortium. I have helped to support GAP for more than four years as part of Australian BioCommons, and so this publication has led me to reflect on the journey. Over this time, I saw a national community thrive and grow, collaborate broadly and deeply to resolve challenges in bioinformatics, and ultimately create novel research outputs.
Firstly, I feel fortunate that I was able to support and contribute to the GAP effort, as it is an ambitious program of work that has brought together a national community of researchers, bioinformaticians, project managers, facility staff, and infrastructure specialists from research institutes, herbaria, data production facilities, computational facilities, and universities across Australia, and included an on-going international collaboration with the Plant and Fungal Tree of Life (PAFToL) Initiative.
Secondly, while the community is itself an achievement, and will underpin future work in Australian plant genomics, I think it's also important to highlight and celebrate the genuine drive and energy that the GAP teams bring to pushing the boundaries in sample preparation and bioinformatics, to improving the metadata and data offerings that underpin plant genomics, and to making their foundational work accessible and understandable for a broader research audience.
A few key highlights specific to bioinformatics come to mind immediately:
Containerised Nextflow workflows (read the paper) that streamlined the reuse of the software set required for the GAP phylogenomics aspect
The detailed integration and validation of metadata that accompanies the thousands of GAP data entries that are progressively being added to the European Nucleotide Archive.
The successful convergence of GAP bioinformaticians on supercomputing resources at the National Computational Infrastructure, supported by the ABLeS program, and the step change in capability and throughput that resulted from this convergence.
It was both wonderful and humbling to see the first draft version of a phylogenomic tree for Australian flowering plants, the Australian Angiosperm Tree of Life (AAToL).
I can’t wait to see the future successes that GAP will make possible, and in particular the next stage of AAToL.