Progress on national plan for Containers and K8s

Members 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.

Kubernetes (K8s) is an open-source system for automating deployment, scaling, and management of containerized applications. It groups containers that make up an application into logical units for easy management and discovery. Kubernetes is currently used by many individual research groups in Australia, but there is no currently no communication, coordination or local support for the service.

Two days of strategic discussions took place during the Australian BioCommons Software and Containers Workshop and the ARDC-funded National Kubernetes Core Services Planning Meeting. The workshop reviewed the ongoing progress of a large collaborative project led by the Australian BioCommons to identify the use cases for a coherent environment around containers and to coordinate the essential elements required to build the interoperable national infrastructure. The Planning Meeting discussed the implementation of a national eResearch program for supporting container orchestration and the use of Kubernetes.

A large group representing significant stakeholders including Pawsey, Australian BioCommons, ARDC, NCI, AARNet, ELIXIR Europe (remote attendance), CSIRO, Monash University, Melbourne University, Intersect, University of NSW, University of Tasmania/ TPAC, University of Queensland/ RCC, QCIF and University of Sydney worked together to define their next steps in the national Kubernetes plan.

These strategic meetings followed on from ten days of hands-on training by HPCNow! to upskill the Pawsey operations and end-user support teams in the Kubernetes system. Read more about Pawsey’s growing expertise in container orchestration solutions here.

We’ll keep you updated on how this coordinated effort will provide new bioinformatics solutions for Australian research community.

Rapid, collaborative and transparent analysis of novel coronavirus on Galaxy Australia

Published in partnership with ARDC

Researchers 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.

The Australian Research Data Commons (ARDC) and Bioplatforms Australia have partnered with Australian BioCommons to ensure that Galaxy Australia maintains tools, workflows and reference datasets for the Australian research community. The ARDC investments have seen the Genomics Virtual Laboratory and Galaxy Australia become essential services for training and analysis in data-intensive biomedical research. The total investment in grants and compute allocations to all Genomics Virtual Laboratory and Galaxy related projects since 2012 was approximately $6.43M, of which $5.18M was in project grants and an estimated $1.25M in underpinning compute and data storage resourcing. This support was augmented by national coinvestment of $6.69M ($4.23M project co-investment plus (estimated) $2.46M compute provisioning) from the University of Melbourne, Queensland Cyber Infrastructure Foundation, Research Computing Centre (UQ), Bioplatforms Australia.

Through coinvestment from the ARDC’s Platforms Programs over the next three years, work is underway to broaden Galaxy Australia’s capabilities by increasing the communities that can use the platform and the types of analyses the platform can perform. The most recent "BioCommons BYOD [Bring Your Own Data] Expansion Project" Platforms grant of $2.21M will bolster the contributions of Australian BioCommons, University of Melbourne, Bioplatforms Australia, Australia’s Academic and Research Network, Australian Access Federation, National Computational Infrastructure, Pawsey Supercomputing Center, Queensland Cyber Infrastructure Foundation, Melbourne Bioinformatics, and Sydney Informatics Hub.

Associate Professor Andrew Lonie, Director of Australian BioCommons, says digital technologies are proving transformational for researchers in the life sciences domain:

“The enhanced Galaxy Australia platform will position Australia at the forefront of bioinformatics infrastructure and substantially improve Australian researcher’s access to bioinformatics.”

ARDC’s Director of Platforms and Engagement, Dr Andrew Treloar says the breadth of ARDC investment in research platforms ensures Australia's world class research system continues to improve productivity, create jobs, lift economic growth and support a healthy environment:

“It’s fantastic to be investing in research-orientated platforms and services that integrate and provide access to a range of resources to researchers and industry. This is a great opportunity to collaborate with our partners and universities at the cutting-edge of research to provide Australian researchers with competitive advantage through data.”

During an outbreak like the COVID-19, the development and implementation of effective infection control and prevention measures relies on the global research community’s ability to share data in a timely manner and perform fast and reproducible analyses. Platforms like Galaxy Australia can enable and accelerate this process. Read more about Galaxy Australia’s role in the recent COVID-19 study below and visit the ARDC website to find out how the ARDC is supporting an expansion of the Galaxy Australia project.