GUARDIANS partners gather in Brisbane to align on national human omics infrastructure

Partners collaborating on the future of Australia’s human omics research data ecosystem gathered in Brisbane this month for their second in-person meeting. This effort is driven by the GUARDIANS program that is delivering digital research infrastructure for human omics data nationally.

Building a complex national ecosystem for this data demands more than just the technical tools, it needs active collaboration and a genuine community of practice. Coming together to review the foundational achievements of Year 1 of the program and strategically align activities for Year 2, the meeting fostered an environment of open communication, mutual learning, and collective problem-solving across the two days.

The first day  of the program focused on partner presentations, with teams highlighting their progress and challenges. These covered data commons deployments, data access control frameworks, and platform integration, and the presentations concluded with an engaging retrospective discussion.

A/Prof Natalie Taylor, UNSW, speaking on ‘Implementation to Impact’

Partners and GUARDIANS team members at QIMR Berghofer

A highlight of the day was the keynote presentation on ‘Implementation to Impact’ from A/Prof Natalie Taylor, UNSW, speaking to systematic approaches to bridge the gap between research evidence and clinical practice. She challenged the attendees to design infrastructure not just for technical functions, but for real-world adoption to deliver real health outcomes. 

The second day focused on practical applications, featuring a series of workshops to showcase the progress and frameworks across the project. An integrated data access and release management workflow was demonstrated by the Collaborative Centre for Genomic Cancer Medicine, the Garvan Institute of Medical Research showcased their Elsa, CTRL and REMS tools, and QIMR Berghofer gave a highly practical review of consent and the data access request process.

The session from the GUARDIANS’s Ethical, Legal, and Social Implications (ELSI) team navigated through the complexities of cross-border omics data governance. This was complemented by the ‘Threat Modelling’ workshop run by the BioCommons Cybersecurity Specialist. Finally, GUARDIANS Project Managers led a workshop to identify concrete opportunities for inter-organisational interoperability in Year 2, ensuring future efforts are integrated rather than siloed.

The strategic discussions and practical demonstrations in Brisbane showed that progress is being made towards a national human omics research data ecosystem. 

“Reflecting on Year 1, the significant outcomes include technical tools and infrastructure, and also the genuine community of practice and collaborative environment we’ve built,” said Prof Bernie Pope, A/Director (Human Genome Informatics) at BioCommons and Lead for the GUARDIANS project.

“This foundation will be crucial as we tackle increasingly complex challenges in delivering this national data ecosystem. ” 

Read more about the GUARDIANS program

ELSI presentation on ‘Omics Data Beyond Borders - Law, Ethics and Governance’

GUARDIANS team and partners discussing collaboration opportunities

---

The GUARDIANS program is accelerating human omics research in Australia through the development of world-class digital infrastructure. The program is led by Australian BioCommons with contributions from partner organisations including the Australian Access Federation, Children’s Cancer Institute Australia, Garvan Institute of Medical Research, National Computational Infrastructure, QIMR Berghofer Medical Research Institute, The University of Melbourne, and The University of Sydney. GUARDIANS forms part of Australian BioCommons’ Human Genome Informatics Initiative and receives National Collaborative Research Infrastructure Strategy (NCRIS) support through Bioplatforms Australia.

Building a trusted ecosystem to accelerate research: the Australian Cardiovascular disease Data Commons

A new paper describing the progress and vision of the Australian Cardiovascular disease Data Commons (ACDC) project has been published in Nature Reviews Cardiology. This national-scale project is designed to accelerate the fight against Australia’s single biggest killer through creating a comprehensive, secure, scalable and internationally integrated data infrastructure, offering cardiovascular researchers around the world the opportunity to uncover the hidden drivers of disease risk and progression, as well as patient recovery and survivorship.

Authors Corey Giles and Peter J. Meikle from the Baker Heart and Diabetes Institute (Baker Institute) describe how the ACDC project will provide researchers with secure access to pooled data from approximately 400,000 individuals across 18 clinical and population cohorts within Australia.

These cohorts contain a wealth of diverse information, including rich omics phenotyping, genotyping data, longitudinal cardiovascular outcomes, and comprehensive imaging data.

The path to a comprehensive, secure, scalable, and internationally integrated data infrastructure connected to global best practice analysis platforms includes many complex phases. Led by the Baker Institute, contributions from a diverse group of participants are co-ordinated by BioCommons. Baker Heart and Diabetes Institute, ACvA, University of Sydney, 23Strands, CSL Limited, BioCommons, data custodians and other partners are working together on infrastructure establishment, cohort onboarding and harmonisation, testing, validation, use case exploration, user experience, documentation, training, governance and intellectual property arrangements. BioCommons leads the implementation of the critical digital infrastructure underpinning ACDC as part of the Australian BioCommons Human Genome Informatics activity.

The highly collaborative project receives advice and oversight from a multi-disciplinary Scientific Advisory Committee made up of clinicians, researchers, digital infrastructure experts, and consumer representatives. The group has representatives from BioCommons, Baker Heart and Diabetes Institute, University of Sydney, University of Tasmania, Busselton Health Study, RENCI, NHLBI, University of Chicago, Broad Institute, HeartBeat Victoria, as well as a large number of data custodians. They are responsible for shaping the scientific objectives of the platform and providing feedback to the Project Management Committee to ensure that the development and implementation of the ACDC platform aligns with those objectives.

The ACDC project is synchronising the efforts and experiences of a large and diverse group of experts who together can advance the early detection of disease processes and the discovery of new disease-modifying pathways that contribute to cardiovascular disease development.

Read the paper Building the Australian Cardiovascular disease Data Commons.

Learn more about how BioCommons is implementing the ACDC infrastructure.

The ACDC project is led by the Baker Heart and Diabetes Institute and funded by Bioplatforms Australia and the Medical Research Future Fund (MRFF 2022 National Critical Research Infrastructure Grant: Building an Australian Cardiovascular disease Data Commons). Additional contributions are being made by the Baker Heart and Diabetes Institute, ACvA, University of Sydney, 23Strands, CSL Limited, Australian BioCommons, data custodians and other partners.

Partners meet to start building the digital infrastructure needed for human genomics research though GUARDIANS

A diverse group came together, including special guest Dr Melissa Konopko from ELIXIR who is standing here with BioCommons’ Prof Bernie Pope.

Australian researchers are set to make significant strides in discovering, accessing, and analysing human genomics data. The first in-person meeting of a significant new collaboration brought together partners who are committed to implementing the Australian BioCommons’ GUARDIANS program.

The meeting in Sydney represented the start of two years of implementation work as part of the GUARDIANS mission to empower Australian researchers to easily and securely discover, access, analyse and use human genomics data across national infrastructure, using the latest tools and resources.

The project brings Australian BioCommons together with Australian Access Federation, Children's Cancer Institute / ZERO, Garvan Institute of Medical Research, National Computational Infrastructure (NCI), QIMR Berghofer Institute of Medical Research, University of Melbourne, and University of Sydney. The project builds on years of foundational work in the Human Genomes Platform Project which also included a funded program and contracted schedules of work with partners. 

This first GUARDIANS meeting helped to build a sense of shared purpose as the group established effective ways of working together across their diverse organisations. Explorations into the policies, processes, and technologies that will be required during the project were driven by the open exchange of ideas, and collaborative discussions on solutions to potential challenges.

Scientific Product Manager at ELIXIR, Dr Melissa Konopko, travelled from the UK to share her insights into the Genomic Data Infrastructure (GDI). There were many parallels to learn from this project which is enabling access to genomic and related phenotypic and clinical data across Europe through establishing a federated, sustainable and secure infrastructure to access the data. 

Explore how GUARDIANS is accelerating human genomics and related omics research in Australia through the development of world-class digital infrastructure.

Contact us if you’d like to learn more.

Creative collisions: Bio Day a hit at Supercomputing Asia 2024

This month's Supercomputing Asia (SCA) conference featured a dedicated ‘Bio Day’ which focused on the intersection of biology and computing. Life scientists were enthusiastically invited to interact with the Asia Pacific high performance computing (HPC) community at the Sydney event. The conference organisers offered special access to almost 40 researchers and research infrastructure providers who were keen to participate in the biology-focused sessions. This extra support to add the unique voice of life scientists to the HPC forum was generously provided through Bioplatforms Australia's platinum sponsorship of the event.

Bio Day commenced with Prof Alex Brown, Director - National Centre for Indigenous Genomics, delivering a keynote presentation ‘Towards a National Indigenous genomics Ecosystem within Australia.’ As Professor of Indigenous Genomics at the Telethon Kids Institute and The Australian National University, Alex is an internationally leading Aboriginal clinician/researcher who has worked his entire career in Aboriginal health in the provision of public health services, infectious diseases and chronic disease care, health care policy and research.

Later, sessions titled ‘Building the Foundation: Genomic Data Infrastructure for Precision Medicine and Beyond’ showcased several key pieces of research infrastructure that Australian BioCommons has developed to support life scientists including:

• The Australian BioCommons Leadership Share (ABLeS)

• The Australian Alphafold Service

• The newly funded GUARDIANS project

• A pilot program bringing Seqera Platform to Australian researchers

Some of BioCommons’ significant national partners such as the Australian Amphibian and Reptile Genomics Initiative (AusARG) and international collaborators ELIXIR were also showcased on Bio Day. Additionally, Dr Kate Michie’s (UNSW) talk revealed the ‘Transformative Impact of Deep Learning on Accelerating Molecular Research: A Focus on AlphaFold2 and its Implementation Challenges.’ The Skills and Training Track on the same day also featured our training guru, Dr Melissa Burke, presenting our unique Training Cooperative model.

Sessions held on Bio Day illuminated the unique challenges that bioinformatics research brings to HPC, including:

• Episodic and extended access is required for compute resources

• Compute use is reliant on experimental outcomes, and difficult to predict in advance

• Software is diverse, rapidly evolving, and in many cases not optimised for HPC

• Researchers may have limited experience working in HPC environments

The light shone on these unique challenges stimulated some uncommon conversations at SCA, which aim to improve life science researchers' access to appropriate and scalable bioinformatics methods and compute resources. Dr Johan Gustafsson, Bioinformatics Engagement Officer at BioCommons said:

The conference was a unique opportunity to bring two worlds together - researchers working hard in their particular field of biology don’t normally attend HPC conferences, and vice versa. So it was great to see them starting to speak the same language!

Uwe Winter, BioCloud DevOps Engineer at BioCommons attended a workshop on the recently launched Trillion Parameter Consortium (TPC), a group formed to address the challenges of building large-scale artificial intelligence (AI) systems and advancing trustworthy and reliable AI for scientific research.

Discussions at the TPC workshop brought up a lot of exciting ideas on utilising AI in a fully automated research environment. I was inspired to hear TPC’s future plans and can’t wait to apply them to BioCommons infrastructure for the benefit of Australian researchers!

Overall, Bio Day at SCA was a fantastic chance to continue important conversations around the specialised support and infrastructure that life scientists need. BioCommons extends our thanks to Bioplatforms Australia for their sponsorship and to the conference organisers for running a successful event.