Simplifying data movement for faster analysis: the new link between the Bioplatforms Data Portal and Galaxy Australia

Moving data is a key part of the research workflow, and can become a bottleneck if there’s significant separation between steps. Researchers are increasingly using multiple services and have to take on the role of the ‘network switch,’ moving their data back and forth to complete isolated functions.

A new data movement feature streamlines the connection between data and analysis, with a fast one-click transfer of data from Bioplatforms Data Portal for immediate analysis using the fully-subsidised Galaxy Australia service. By selecting your data and clicking 'Send to Galaxy', the previously manual process happens automatically and invisibly in the background - appearing in your Galaxy history ready for analysis.

The Bioplatforms Data Portal hosts over 400TB of valuable reference molecular life sciences data covering agriculture, biomedicine, the environment and industry. The data is generated by national collaborative projects using integrated ‘omics infrastructure to generate high-impact data and knowledge resources to support some of Australia’s biggest scientific challenges. The need to move data into an analysis environment like Galaxy Australia has now become very simple.

Biologist and bioinformatician, Dr Amy Tims, performs data QC, genome assembly, and data curation for the Australian Fish Genomics Initiative established by Bioplatforms Australia and Minderoo Foundation. Consisting of genomics, genetics and transcriptomics data from 56 partner projects representing fish species from all major Australian habitats, access to this huge volume of high-quality data is valuable for research into freshwater, estuarine and marine environments. Amy stated:

‘Being able to move data straight over to Galaxy from the Data Portal without having to copy-paste lots of URLs or download files first saves a lot of time and effort. The new connection makes it super-easy to grab your data and start analysing without any fiddly intermediate steps’

This integration was made possible by the introduction of the single-sign on system, BioCommons Access. Aiming to become a universal "key" to securely find, analyse, and move biological data, 3131 existing users of the Galaxy Australia and Bioplatforms Data Portal services were smoothly migrated across to the new system, and 3993 brand new accounts have signed up since March 2026.

What are the key benefits of BioCommons Access?

• Single sign-on access to multiple analysis and data services

• Streamlined use of Galaxy Australia and the Bioplatforms Australia Data Portal - other services coming soon!

• A central portal to manage your user profile across services

• Connection to curated bundles of tools and data 

Read more about how National supercomputing and expertise to enable the Australian Fish Genomics Initiative

Sign up for BioCommons Access

Read the FAQs on how to use the new data movement feature

Unlocking multi-omics data to transform cardiovascular precision medicine

The Australian Cardiovascular disease Data Commons (ACDC) is launching as a cloud-based research platform built to accelerate the discovery of new risk markers for heart attack and stroke. The ACDC aims to build a secure, scalable, internationally integrated data infrastructure connected to best practice analysis platforms to enable the identification of novel insights, therapeutic targets and predictive biomarkers for coronary artery disease. Ultimately, the platform will facilitate a translational pipeline to ensure the deployment and evaluation of these predictors within clinical practice.

Why is a national data commons needed for cardiovascular disease

There is a current, known clinical gap, with up to 27% of heart attack patients having none of the well-known risk factors when they initially present to a GP. These can include high blood pressure, cholesterol, diabetes or smoking, and many people with coronary artery disease go on to have a second, life-threatening event despite optimal treatment. The ACDC aims to tackle this gap by securely pooling multi-omics data, longitudinal outcomes, and imaging from approximately 400,000 individuals across 18 Australian cohorts.

Prof Peter J. Meikle (Project Lead, Baker Heart and Diabetes Institute) highlights the urgency behind the project:

‘We need to understand what's really driving disease in these patients who are flying under the radar. This data commons will speed up how quickly new health technologies reach patients, and we expect it will generate a new precision medicine ecosystem in Australia.’

Led by the Baker Institute, contributions from a diverse group of participants are co-ordinated by BioCommons. The Baker Institute, the Australian Cardiovascular Alliance (ACvA), the 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 the ACDC as part of the Australian BioCommons Human Genome Informatics activity.

Find out more at the online launch webinar

If you would like to learn more, you are invited to join a live webinar on 30 September 2026, 12 - 1 pm AEST. The session, featuring Prof Peter J. Meikle and Dr Tingting Wang (Baker Institute), and Prof Bernie Pope (Australian BioCommons), will explore how ACDC connects researchers to high-throughput data and global analysis environments. 

Key topics include:  

• Development of the data commons: an overview of the cloud infrastructure, data harmonisation processes, and federated standards built on the Gen3 platform 

• Research value of the platform: how secure access to pooled multi-omics, genomic, and imaging cohorts enables researchers to discover new risk markers and test Polygenic Risk Scores.  

• Future clinical applications: how the ACDC will streamline translational pipelines to bring new diagnostic tools into clinical practice. 

Register for the webinar

Shaping the next phase of Australian human omics infrastructure

GUARDIANS program leads and project delivery partners from across Australia gathered this month for the third GUARDIANS partner meeting. Held in Melbourne, the two-day event provided a forum to showcase achievements, discuss challenges, and plan for the future of secure, responsible genomic data infrastructure in Australia.

As this Australian BioCommons program enters its third year, the focus of the community is shifting from building the technical foundations to delivering sustainable, impactful and scalable solutions. Reflecting on the progress made so far, Prof Bernie Pope, A/Director, Human Genome Informatics at Australian BioCommons and Lead for the GUARDIANS project, noted:

‘We have reached a major program milestone - Phase I successfully demonstrates that Australia now has the production-ready digital research infrastructure, services, and expertise necessary to support human omics research at scale. We look forward to continuing our work in Phase II of the program, delivering national impact and lasting value for the broader research community.’

How do we build data systems for the future?

The meeting featured a comprehensive schedule of partner presentations, collaborative problem-solving sessions, and insightful keynotes that framed the program’s real-world applications.

The opening talk was a powerful joint presentation titled ‘Building Data Systems for Indigenous Precision Healthcare’ that explored how ethical, culturally informed data governance is driving equitable health outcomes. Delivered by Adam Heterick, Bioinformatician at Black Ochre Labs, The Kids Research Institute Australia and the National Centre for Indigenous Genomics (NCIG), Australian National University, and A/Prof Jimmy Breen, Chief Data Scientist of the Indigenous Genomics research group at The Kids Research Institute Australia in Adelaide, the presentation highlighted the key message of being ‘Open as possible, closed as necessary’ and the need for relationship building.

On the second day, Dr Matilda Haas, Director at Genomics Australia, spoke on strategic priorities for integrating genomics into healthcare, which sparked valuable discussions around data governance, infrastructure, and future touchpoints with the Precision Health Initiative. By mapping out these intersections, the partners explored how to ensure the frameworks and solutions currently being built will effectively support downstream clinical applications. 

What lessons are important for the GUARDIANS Program in Phase II?

Discussions over the two days converged on two important themes:

1. Governance, trust and responsible data use need to be embedded from the beginning

   Governance needs to be considered throughout the data lifecycle, alongside technical design, access, security and community engagement. Building trust early and establishing clear, practical governance enables collaboration rather than creating barriers to it.

2. Interoperability and collaboration are key to getting greater value from what we have built

   The importance of shared standards, common approaches, connected services and the ability for different environments to work together. The value of the infrastructure increases dramatically when services are connected and capabilities can be reused across projects rather than developed independently.

A new GUARDIANS website has been launched that shows how all of the strategic partners and activities are coming together to shape a new Australia's human omics ecosystem. It offers a comprehensive view on individual project updates, pilot services, and collaborative achievements from across the entire network.

Explore the GUARDIANS website

Join the Australian Outpost of BioHackathon Europe 2026

Are you interested in joining this year’s BioHackathon Europe, but can’t face the long haul flights? You should join the Australian Outpost team who will gather to work locally, while checking in regularly with our international colleagues.

This is a unique opportunity to participate in a significant global event and network with your international peers while working intensively on practical bioinformatics challenges. We will cover your costs when you come to Melbourne for the duration of ELIXIR’s BioHackathon: 9 - 13 Nov 2026. Participation will work mostly within our business hours, plus catch up live in the early evening with the teams in Barcelona. We always make it fun, and you’ll get to know others from around Australia while you learn new skills.

We’ve narrowed down the projects we’re interested in, and want to hear what you want the Australian Outpost of the BioHackathon to work on: 

• Project 31: Nextflow to Galaxy Workflow Portability and FAIRness via Modular LLM Agent Skills

• Project 30: BiCoReCa (Biodiversity Community Resource Catalogue): Towards Centralized Curation and Integration

• Project 16: MiCoKnowGraph: Designing a Microbiome Collaborative Knowledge Graph linking complex, multi-domain data

• Project 10: Enabling workflows and EDAM annotations to display in community website deployments

BioHackathon aims to:

• Advance the development of an open source infrastructure for data integration to accelerate scientific innovation

• Engage technical people in the bioinformatics community to work together on topics of common interest

• Strengthen interactions, establish and reinforce collaborations through hands-on programming activities.

Please contact us if you are interested in joining the Australian Outpost of the BioHackathon Europe, and tell us which project/s you would like to participate in, and why. You can read last year’s story and a previous participant's blog post on why attending is so valuable for inspiration. Once we get a feel for who is interested, we will select a team of people and organise our meetup. There’s no need to register for a place on the BioHackathon Europe website - they have reserved places for the Australian Outpost.

Express your interest by emailing comms@biocommons.org.au by 25 Sep 2026

Ready-to-teach Nextflow training material now available

Behind every successful workshop is more than a good training content. Instructors need tested exercises, suitable data and software, and a delivery plan they can trust.

Following the successful delivery of last year’s Nextflow for the Life Sciences workshop, the Sydney Informatics Hub and Australian BioCommons developed a reusable instructor package to support trainers in delivering introductory Nextflow workshops with less preparation.

The package builds on the workshop’s openly available training content and brings together structured teaching materials, detailed instructor guidance, and the software, data and files needed for delivery. It reduces duplication of effort and gives trainers a tested starting point for planning and delivering their own workshops. Trainers can use the materials as provided or adapt them for different audiences, learning objectives and workshop formats.

The package material has already been used by Peter MacCallum Cancer Centre, WEHI and Melbourne Bioinformatics to deliver an ‘Introduction to Nextflow’ workshop in July 2026. Reflecting on the preparation involved, the workshop organiser Richard Lupat said: 

The 2025 Nextflow for the Life Sciences hybrid workshop brought together participants across multiple locations and provided the starting point for the reusable training materials available today.

“This is the least preparation required for a workshop that I have ever needed to run!”

Work is underway to explore preconfigured virtual training environments as an extra support for future workshop delivery. Further information about opportunities to test these environments will be shared as the work progresses.

The team is also working towards packaging materials from the workshops ‘Nextflow on HPC’ and ‘Customising nf-core pipelines’ in the same way, with the longer-term aim of building a reusable collection of Nextflow training resources for the Australian training community.

Interested in delivering your own introductory Nextflow workshop, adapting the materials for your community, or learning more about future opportunities to test the virtual training environments? The Australian BioCommons training team can help: training@biocommons.org.au. 

Explore the package

Invitation to present your structural biology research

The Australian Structural Biology Computing Community (ASBC) is a group for anyone who uses computing for structural biology research in Australia. They have a newsletter you can subscribe to, a website full of resources, and they meet online at quarterly meetings.

Their community talk series invites speakers from across the international structural biology community to present their work. Meetings in 2026 have featured:

• Biswa Prasanna Mishra (Ve lab - Griffith University) - 11th March

• Cameron Gilchrist (Steinegger lab - Korea Basic Science Institute Ochang-center) - 20th May

• Roland Dunbrack (Dunbrack lab - Fox Chase Cancer Center) - 29th July

• Tom Goddard (ChimeraX - UCSF) - 16th September

To wrap up the year, there is an invitation to Australian EMCR researchers in structural biology computing to share their work at a special edition of the ASBC community meeting on 4 Nov 2026. Whether you're in the middle of a project, have completed a project, or published a paper, you are invited to give a 15 minute talk. 

Example projects could use methods related to structure prediction, structure search, protein design, functional annotation, molecular dynamics, CryoEM or other related areas. It is a great opportunity for EMCRs to promote their work with the national community and network with potential collaborators. Four talks will be selected via an informal and friendly application process. 

Please send your talk title and a ~250 word abstract to asbc@unsw.edu.au by 31 Aug 2026 to be considered. 

BioShell opens a new gateway to national compute for life science researchers

A new ready-to-use virtual environment offers researchers immediate access to a curated set of bioinformatics tools and datasets. BioShell provides a command line interface that is preconfigured for bioinformatics and uses national computer resources, at no cost to researchers.

By removing the usual ‘setup friction’, BioShell allows researchers to focus on their science, rather than troubleshooting environment configuration or software installations. BioShell offers access to a safe space to experiment on the command line with more power than available on a laptop, avoiding the steep learning curve, complex allocation requests, or specialised architecture required to use high performance computing (HPC) services. 

How does BioShell support life science research?

The rapid increase in the volume of available research data in the life sciences necessitates increasingly complex tools to perform effective analysis. BioShell supports researchers with a safe, pre-loaded, secure environment for working in the command-line environment, without the risk of breaking shared infrastructure. 

BioShell’s key capabilities include:

• Pre-installed workflow engines: ready-to-use software including Singularity, Nextflow, Jupyter Notebook, and RStudio

• Built-in support via Shelley: an intuitive command-line agent that allows novice users to search, and run containers from containerised bioinformatics tools with one command

• Full administrative control in a safe sandbox: researchers can run workflows and test pipelines with full privileges in an isolated environment.

How did BioShell evolve?

The development of this service, originally called BioImage, is evidence of sustained, national collaboration across Australian research infrastructures. Initially developed on Pawsey Supercomputing Research Centre’s Nimbus Cloud as part of a BioCommons project in 2023, it was further refined by the Sydney Informatics Hub (SIH) at the University of Sydney with regular usage for Australian BioCommons training workshops. Given how useful BioShell proved internally, the SIH team worked with the Australian Research Data Commons (ARDC) Nectar Research Cloud and National Computational Infrastructure (NCI) to ensure the BioShell environment works well with national compute resources.

Start using BioShell now

Researchers across any university or institute can access BioShell to spin up consistent virtual environments on demand. A new application for access to BioShell offers short-term access to national compute resources without the requirement for a full allocation request. For researchers with existing allocations, BioShell is also available via the image catalogue on the ARDC Nectar Research Cloud. 

Find out more and request BioShell access

Australian BioCommons partners with the Sydney Informatics Hub, the University of Sydney to manage BioShell, which is underpinned by computational resources provided by the Australian Research Data Commons (ARDC) and National Computational Infrastructure (NCI), building upon original development by the Pawsey Supercomputing Research Centre. This work is enabled by NCRIS via funding from Bioplatforms Australia.

Preview of BioShell’s command line interface, a Jupyter notebook, and RStudio instance.

Scaling bioinformatics and compute access for Australian molecular science research

Seqera has released a new case study featuring Australian BioCommons: Australian BioCommons Standardizes Bioinformatics and Scales Compute Access Nationwide with Seqera. It showcases how BioCommons enables the research community to analyse molecular and biological data at scale through the Australian Nextflow Seqera Service. By leveraging Nextflow and the Seqera Platform, and combining the right bioinformatics expertise and computational infrastructure, the service is driving real-world impact.

“We scaled national access to compute infrastructure. As a result, we now support more than 340 users from more than 40 different Australian organisations.”

— Ziad Al-Bkhetan, Product Manager, Bioinformatics Platforms, Australian BioCommons

The team at Australian BioCommons provides bioinformatics expertise, researcher support, and technical consultations to help researchers effectively utilise bioinformatics software and computational infrastructure for their work. This has standardised bioinformatics analysis nationwide, scaled compute access and capacity beyond institutional limits, and reduced costs by eliminating duplicated infrastructure and set up burdens for individual research groups.

“Seqera Platform has helped us a lot. We've been able to invite our researchers to jump in and see if the platform meets their needs. With the support of the BioCommons, we've had 15 researchers across 7 of our different research groups try it out. It's made launching pipelines easy for researchers who are not familiar with linux systems and command line.

— Julie Iskander, WEHI's Research Computing Platform Engineering team

The success of the Australian Nextflow Seqera Service has earned the team an invitation to present at the upcoming Nextflow Summit. They hope to share the journey of building this nationwide service, highlighting the collaborative effort required to coordinate multiple partners and the transformative impact delivered to researchers. The presentation, “Nextflow Across Australian BioCommons: From Community Training to National Research Infrastructure”, will cover how over the past few years BioCommons has taken a leading role in accelerating Nextflow adoption. Coordinated national activities have spanned live training, reusable training resources, community engagement, and establishing national-scale services for several general-purpose and specialised applications, such as molecular biology and biosecurity. Importantly, it will also describe how these complementary investments have supported the growth of a sustainable national Nextflow ecosystem and the importance of building  community capability alongside production research infrastructure.

Explore the Australian Nextflow Seqera Service or read the full case study at Seqera.io.

Australian BioCommons operates the Australian Nextflow Seqera Service in collaboration with Pawsey Supercomputing Research Centre, National Computational Infrastructure (NCI), and Seqera. The Service was established as an output of the Australian BioCommons Bring Your Own Data Expansion Project and is hosted on Amazon Web Services (AWS). These efforts are enabled by NCRIS via funding from Bioplatforms Australia.

Deep learning meets genome annotation: rapid gene prediction tool now available

The deep learning-based genome annotation tool, Tiberius, is now available in Galaxy Australia. After being wrapped and extensively tested, it is freely available for everyone’s use in the Genome Lab. 

Tiberius offers gene structure prediction from genomic sequences alone (ab initio). With accuracy that matches tools using extrinsic data, it provides end-to-end prediction of protein-coding genes. Tiberius can be installed and run by individuals, and also parallelised on HPC systems. But now that the wrapper is available in the Galaxy toolshed, it can easily be used by Australian researchers in the Galaxy Australia platform (or installed on any other international Galaxy instance). Tiberius has been trained on organisms in Bacillariophyta, Chlorophyta, Fungi, Insecta, Mammalia, Mesangiospermae, and Vertebrata, and all of those models are available on Galaxy.

During an internship with the Australian Tree of Life Bioinformatics team, University of Queensland PhD candidate, Jane Tung, did much of the initial work to get Tiberius up and running. She benchmarked the performance of three traditional and two machine learning-based eukaryotic genome annotation pipelines using datasets spanning fungi, plants, insects, fish, lizards, amphibians, birds and mammals. Tiberius completed the annotation in a fraction of the time and used fewer resources compared to the traditional pipelines, without a negative effect on quality metrics. Jane will be discussing these findings further in November via the webinar Benchmarking the latest annotation pipelines on Australian reference genomes.

The performance of Tiberius without RNAseq data made this tool the perfect candidate for rapid gene prediction on assemblies produced by the Genome Engine in the Australian BioCommon’s Australian Tree of Life (AToL) project. It has become an essential part of the Genome Engine that will enable rapid, automated assembly, annotation and publication of genomes.

While Tiberius was prioritised for inclusion because it’s an important part of the AToL project, individual researchers can also request the installation of new tools or datasets in Galaxy Australia. For researchers wanting to contribute to the international open source Galaxy community directly, there are supportive guidance videos for DIY tool wrapping. Proactive community members recently took up the challenge, and collaborated with BioCommons to make the first dedicated glycomics tool and workflow available on Galaxy.

Try out Tiberius in the Galaxy Australia Genome Lab

Register for the webinar Benchmarking the latest annotation pipelines on Australian reference genomes

Dr Sarah Beecroft recognised with national award for research enablement

Australian BioCommons is proud to announce that Dr Sarah Beecroft has been awarded the 2026 Early Career eResearch Excellence Prize by AeRO. The prize recognises Sarah’s excellence in research enablement, technical innovation, collaboration, and community leadership.

After many years of productive collaboration with Sarah, BioCommons now invests directly into Sarah’s role as Lifescience Applications Specialist at the Pawsey Supercomputing Research Centre. BioCommons co-funds this role with Pawsey in recognition that her work to support bioinformatics users through workflow development and optimisation, training, and advocacy is so integral to the success of life science research in Australia.

Sarah’s participation has been key to the delivery of many significant research outcomes, including the recent extraordinary addition of 17 million protein predictions to an international open access database by an Australian researcher, made possible by Sarah’s porting of workflows to enable usage of Setonix's AMD GPUs at Pawsey. 

It is wonderful to see that Sarah’s outstanding contributions to the eResearch community have been recognised with one of the AeRO awards. Congratulations Sarah, and keep up the good work! 

Sarah regularly shares her expertise via BioCommons training events. You can join her Getting started with GPUs for bioinformatics webinar live in September or catch up on the recording of her recent Using Containers in Nextflow session.