Australian researchers can now rapidly analyse their SARS-CoV-2 data using published tools and workflows by using a new dedicated Galaxy COVID-19 compute node hosted at Pawsey Supercomputing Centre. The ability of Galaxy Australia and Pawsey to jointly deliver this enabling data analytics platform has been made possible as part of the COVID-19 Accelerated Access Initiative in which Australia’s national HPC facilities responded quickly to the pandemic with streamlined, prioritised and expedited access to computation and data resources. NCI Australia and the Pawsey Supercomputing Centre have now announced that the Galaxy COVID-19 compute node would be hosted on Pawsey’s newly deployed Nimbus Cloud, guaranteeing tailored resources for urgent public health research.
Read MoreMembers of our team recently advanced the Australian BioCommons Software and Containers project by participating in two strategic meetings at Pawsey Supercomputing Centre in Perth. The March events drew together partners who are contributing to the national roll out of a common bioinformatics software containerisation and meta-data standard, and a common implementation standard of the open-source container-orchestration system Kubernetes for use by Australian life scientists.
Read MoreResearchers from universities in Germany, Belgium, Australia and the USA, have used publicly available novel coronavirus (COVID-19) genome data and published their analyses using Galaxy, an open source research platform.
The joint paper, written by the international Galaxy team, demonstrates how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way. In the wake of the COVID-19 pandemic, the researchers showed how Galaxy could facilitate the exchange of data and reproducible workflows between authorities, institutes and laboratories dealing with the virus. The international Galaxy platform, through the provision of highly accessible, globally shared data and analytics platforms, has the potential to transform the way biomedical research is performed. By offering access to data and an open and reproducible analytics environment, the Galaxy platform ensures that progress is no longer limited by access to samples and data.
Read MoreThe recent public health emergency arising from the COVID-19 outbreak has demonstrated the necessity for a rapid, collaborative and international response. The development of fast and effective countermeasures relies on the global research community’s ability to share data and perform fast and reproducible analyses.
A joint paper by Galaxy teams from Australia, Europe and the United States demonstrated how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way. The study “No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics” re-analysed all COVID-19 genomic data available in the public domain using Galaxy platforms and open software tools. The publication highlighted the inadequate accessibility of raw data associated with COVID-19 research, and described how the work completed on Galaxy opened up the possibility for any researcher worldwide to perform their own analyses with the data, analysis pipelines and public computational infrastructure freely available.
Read MoreThe development of personalised treatments that target rare paediatric cancer subtypes can be enhanced through global collaboration. Comparing an Australian patient's tumour to a larger group of other tumours allows insights that lead to better outcomes. But geography and rules to protect personal data in different jurisdictions can make the sharing and comparing of essential data difficult or even impossible.
In an effort to fix this, the Australian BioCommons is part of an international collaboration that came together in Sydney this month. Members of the partnership between the Australian BioCommons, BioPlatforms Australia, ARDC, Children’s Cancer Institute, D3b and Seven Bridges have been working to provide an integrated bioinformatics research platform with compute, storage, and file metadata tagging all in one place.
Read MoreA new investment from the Australian Research Data Commons (ARDC) will enable significant expansion of the Australian BioCommons ‘Bring Your Own Data (BYOD)’ Platform.
Earlier this year, discipline-focussed research-orientated platforms were invited to apply for investment to support better connections between data-related resources, industry and researchers. The Australian BioCommons submitted an application involving eight partner organisations: Bioplatforms Australia, Australian Access Federation, AARNet, National Computational Infrastructure, University of Sydney, University of Melbourne, QCIF and Pawsey Supercomputing Centre. The proposal, BioCommons Bring Your Own Data (BYOD) Expansion Project, detailed how this group would work together to build on the foundational work already being coordinated through the BioCommons.
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