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.

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 catch up on the recording of her recent Using Containers in Nextflow session.

Strengthening Australia’s Nextflow community through local and global collaboration

The Australian satellite site of the 2026 nf-core Hackathon has just taken place at the BioCommons node at Sydney Informatics Hub, the University of Sydney. The hands-on event brought together members of Australia’s  Nextflow and nf-core community to contribute to nf-core projects, while strengthening connections locally and across the global community.

Twelve participants from University of NSW, University of Sydney, and University of Melbourne came together to collaborate in person on cutting-edge nf-core projects, with support from two Nextflow Ambassadors on BioCommons’ team, Dr Georgie Samaha and Dr Ziad Al Bkhetan.

As one of 29 global hackathon sites, the Australian team contributed to the international nf-core effort through asynchronous collaboration. Given our geography, the team was among the first to kick off the work, closing each day by connecting with the APAC teams working from sites in Aotearoa New Zealand and South Korea.

Attendees at the satellite site at the Sydney Informatics Hub, University of Sydney

The group made meaningful contributions to several nf-core projects, working to: close open issues and make a release for the nf-core ProteinFold pipeline; develop a new ConfigBuilder tool in the nf-core tools suite that helps users build Nextflow configuration files; and edit Nextflow for HPC training materials to support implementation by others with new documentation for trainers.

It was wonderful to see the progress made by the productive participants over three days together, and the outcomes reflect the depth of expertise and collaborative spirit of the Australian community. We are grateful to all participants for the energy and enthusiasm they brought. Thanks also to the Seqera team and the nf-core community for their support for the Australian satellite site of the hackathon, and especially for sponsoring our delicious lunch together on the final day!

Want to learn how to run and customise nf-core workflows? The Unlocking nf-core: customising workflows for your research workshop is taking applications now, and registrations are also open for our upcoming webinar Using Containers in Nextflow.

Taking Nextflow to the next level: HPC Workshop applications now open

Life sciences research increasingly depends on analysing large and complex datasets. Tools like the workflow management system, Nextflow, can make this process reproducible, scalable, and efficient. But for many researchers, getting started with Nextflow can feel like a daunting leap.

Earlier this year the Nextflow for Life Sciences workshop introduced the fundamental principles of Nextflow pipeline development and guided newcomers to build reproducible and scalable scientific workflows with Nextflow, creating a multi-sample Nextflow workflow for RNAseq data preparation as an example. Led by trainers from the Australian BioCommons team at SIH, University of Sydney and supported by the National Bioinformatics Training Cooperative, 90 learners gathered at satellite sites in Sydney, Melbourne, Brisbane, Adelaide, Canberra and Perth, giving researchers the chance to connect locally with peers while benefitting from the national-level training.

Participants praised the balance of theory and practice, and nearly 90% of attendees rated the content as “very good” or “excellent”. A key highlight was the use of research-relevant datasets that empower scientists to apply their new skills directly to their work. As one participant reflected, “I got lots of knowledge on how to build my own Nextflow pipeline. The RNAseq example was fantastic - so many workshops use ‘Hello World’ examples that are impossible to scale up.”

We are excited to announce that applications are now open for our follow up workshop Nextflow on HPC to be held in November. This hands-on workshop will will provide participants with the practical skills to configure, optimise, and troubleshoot Nextflow pipelines for efficient and scalable execution on High-Performance Computing (HPC) systems.

Participants can expect to learn how to identify the differences between traditional HPC job submission and workflow execution via Nextflow, and how to best configure and execute scalable Nextflow workflows on HPC systems. Managing software environments using tools like singularity, and adapt these to fit within different HPC ecosystem constraints will be covered, along with tips on troubleshooting Nextflow workflows on HPC systems.

To make the most of this workshop you’ll need to have experience running simple Nextflow pipelines, and be looking to scale up your workflows to an HPC environment. You will be supported with access to national Tier 1 computing resources at Pawsey and NCI, so you must be associated with an Australian organisation.

These Nextflow workshops are part of Australian BioCommons’ mission to make advanced bioinformatics tools more accessible to researchers across the country. By combining national expertise with local support, this training is helping build capacity and strengthen the life sciences community.

Find out more about the workshop and submit your application: Nextflow on HPC.

Applications close 3 November 2025.

Multi-model 3D visualisation enhances Nextflow pipeline for protein structure prediction

Predicted protein structures for LmrP visualised using the proteinfold pipeline

Advances in AI are taking protein structure predictions to a whole new level, accelerating research and enabling deeper analysis of protein structure and function. The nf-core community is embracing these developments by building the Nextflow proteinfold pipeline that integrates models such as Alphafold2, Colabfold and Esmfold and simplifies their use on a variety of computing infrastructures. 

BioCommons’ Dr Ziad Al Bkhetan, Product Manager - Bioinformatics Platforms and Australian Nextflow Ambassador, identified an opportunity to optimise the existing nf-core proteinfold pipeline for Australian researchers using the Australian Nextflow Seqera Service. Ziad initiated this effort by reaching out to the original developers from the Center for Genomic Regulation (CRG) in Spain with an offer to reconfigure the pipeline and add new features. This sparked an international collaborative effort that connected researchers and experts from Australian BioCommons, the CRG, the Sydney Informatics Hub (SIH) at the University of Sydney and the Structural Biology Facility (SBF) at UNSW, at several hackathons and summits to enhance the pipeline. The enhanced, community-driven pipeline is now available to all through nf-core’s curated set of open‑source analysis pipelines. 

The pipeline borrows a useful reporting and visualisation feature already implemented in Galaxy Australia. Front-end developer for BioCommons, Minh Vu, augmented the pipeline to implement this feature which allows the parallel execution of multiple models and generation of reports that visualise the resulting structures simplifying comparison and benchmarking of the outputs. Several state-of-the-art tools such as AlphaFold2, ColabFold, ESMFold are included in the pipeline with additional models including RoseTTAFold-All-Atom, HelixFold3, Boltz, RosettaFold2NA and AlphaFold3 to be added soon.

The ability to run different models through the pipeline without writing new code removes the impediment of command line or complicated compute infrastructure. Reflecting on the project in the Nextflow Podcast, Phil Ewels, Product Manager for Open Source at Seqera, said:

 “With almost no setup and no real prior experience, you can run these state of the art models and compare them all in a dynamic visual report. That’s pretty amazing.”

While it is designed to integrate with Seqera Platform, there’s no requirement to use it that way. Running the Nextflow pipeline on the command line gives the exact same reports. The code is freely available for others to use or improve via the nf-core repository of pipelines.

Ziad’s presentation about the collaboration and these new features was spotlighted as a highlight of the recent Nextflow Summit in Seqera’s Nextflow Podcast. Bioinformatics Engineer at Seqera, Dr Florian Wünnemann acknowledges there is great value in improving shared resources:

 “I think it really represents the best of the Nextflow community: they are developing tools and not just keeping it for themselves, but directly giving them back to the larger community.”

Rob Syme, Scientific Support Lead at Seqera Labs, believes the work speaks to the Nextflow and Seqera ethos of giving scientists and researchers the tools they need to build other tools.

“I love this project: it was an amazing outcome that required no input from Seqera or Nextflow. Yes, Seqera Platform could absolutely build an alignment viewer into the platform, but it wouldn’t be as good as if researchers themselves develop it. It wouldn’t be as good as the one that Ziad and the team have developed because research moves so incredibly quickly.” 

The collaboration within the international nf-core community has been a rewarding experience for all involved parties, and CRG has forged a new working relationship with BioCommons to continue development and maintenance of the pipeline. CRG’s Dr Cedric Notredame said of the experience:

“The collaboration with BioCommons has been so valuable. It has showcased the effectiveness of nf-core as a collaborative tool. Thanks to this framework, all of our teams were able to simultaneously contribute to the pipeline with minimal technical coordination. The pipeline is now one of the most complete go-to resources, covering the needs of a wide community of biologists interested in structural aspects of genomics.”

The improvements made to the visualisation code during the project will also be fed back into the Galaxy codebase. BioCommons’ close connections with research communities means that the national Structural Biology Computing community is now testing and finessing the pipeline, and supporting the creation of user documentation.

Sharing what’s been learnt through a publication about the nf-core/proteinfold pipeline is on the horizon, and a pilot Australian ProteinFold Service is under development.

Nextflow workshop combines benefits of hands-on training and community building

BioCommons’ Nextflow for the life sciences workshop heralds a return of our dispersed model of training that combines the benefits of in person and online events to enable access to experts and foster local connections that are essential for continued learning. First pioneered in 2019, this model has been successful in ensuring scalable and more equitable delivery of short-course bioinformatics training across Australia and has been adapted internationally.

Nextflow for life sciences workshop participants will join in person satellite sites at host universities and research institutes across Australia where they will connect with peers and be supported by experienced local facilitators as they put their new Nextflow skills into action. Each of these sites will connect online with Nextflow experts and lead trainers Fred Jaya and Dr Michael Geaghan at the University of Sydney’s, Sydney Informatics Hub who will introduce key concepts and demonstrate how to use fundamental Nextflow elements to develop, execute, and debug a scalable multi-step life science workflow.

Find out more and apply for the workshop. Applications close 27 June 2025.

This workshop is made possible by an exceptional network of facilitators and trainers from the national Bioinformatics Training Cooperative.

WorkflowHub: a registry for computational workflows

A new paper in Nature Scientific Data describes a public and inclusive registry dedicated specifically to the sharing of computational workflows: WorkflowHub.

Australian BioCommons’ Research Community Engagement Lead (Proteins / Metabolites / Workflows), Dr Johan Gustafsson, is the lead author of a stellar group of international experts. They have worked hard on their shared passion for a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR).

The WorkflowHub registry is designed to allow any scientist, regardless of expertise level, to contribute and share computational workflows. It indexes workflows from any scientific domain, in any format, in any workflow language, regardless of whether it uses a workflow management system and supports users to increase the FAIRness of their workflows.

By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

The paper describes how WorkflowHub’s structure, design, standards, community engagement, and continued evolution support:

1) collaboration, sharing and credit for workflow developers, projects, and consortia;

2) integration with added-value services, platforms, and capabilities that support the workflow life cycle (i.e. creation, version control, execution, maintenance, reuse and citation); and

3) wizards and inbuilt features that ease the process of sharing workflows alongside the constellation of associated digital artefacts that give a workflow its scientific context.

Read the paper in full Gustafsson, O.J.R., Wilkinson, S.R., Bacall, F. et al. WorkflowHub: a registry for computational workflows. Sci Data 12, 837 (2025). https://doi.org/10.1038/s41597-025-04786-3

Join our co-working session on 24 June to try out WorkflowHub for yourself.

New seminar series ignites curiosity and builds practical AI skills in the life sciences

AI is reshaping life sciences by enabling researchers to analyse complex datasets, automate workflows, and gain deeper insights into biological processes. Australian BioCommons is supporting the community to adopt these technologies through a series of training events that explore what’s possible and build skills in using AI effectively.

We’ve invited a diverse range of your peers from across academia and industry to share their experiences of using AI in the life sciences. Between June and September you’ll hear how AI is being used to push boundaries, solve problems, and reimagine the way we do science. From multi-omics analysis to drug discovery, structural biology and the ethics of AI in science, they will explore diverse applications across the life sciences, focusing on the stories, insights, and experiences behind the research.

Register for the webinars

In August, our online workshop Machine learning in the life sciences will provide a hands-on opportunity to compare and contrast commonly used algorithms for constructing predictive models, explore some of their trade-offs and identify types of scenarios in which they can be applied.

In case you missed it, Australian BioCommons’ AI Technical Lead, Dr Benjamin Goudey, recently broke down AI concepts, clarified key terminology, and showcased real-world examples in this recorded webinar: Deciphering AI for the Life Sciences. 

AI is a fast evolving field so rest assured that further events are in the pipeline. 

Browse all upcoming training and events 

Australia's inaugural nf-core Hackathon Outpost boosts local Nextflow capability

The first-ever Australian satellite site of the international nf-core Hackathon has just taken place in Sydney. Seventeen participants from across the country came together to collaborate on cutting-edge Nextflow projects. This marked a significant step in strengthening Australia’s Nextflow and nf-core community, fostering new collaborations between researchers, bioinformaticians, and Nextflow enthusiasts.

International registrations for the 2025 nf-core Hackathon almost reached 1000, with about half opting to join remotely and the remainder spread across 44 sites globally. The organisers were thrilled to finally have an Australian site. Thanks to our time zone, we were among the first to kick off each day of asynchronous work, along with colleagues across the ditch in Aotearoa New Zealand. 

Australian BioCommons arranged for key participants including multiple Nextflow Ambassadors from multiple cities to join our local hosts, Sydney Informatics Hub at the University of Sydney. Participants represented Pawsey Supercomputing Research Centre, National Computational Infrastructure, Peter MacCallum Cancer Centre, QCIF, Queensland University of Technology, Sydney Informatics Hub, University of NSW, and Australian BioCommons. 

The group spent three days at Moore College, a fantastic venue with an open workspace and an expansive terrace with city views - providing an ideal setting for focused work, brainstorming, and cross-team collaboration. While the hackathon was all about accelerating nf-core developments, it was also a valuable chance for collaboration outside of participants’ regular networks. Seqera sponsored our working lunches, but the Newtown cafe and restaurant scene ensured participants stayed well-fueled throughout the whole hackathon!

Over the course of three productive days the group divided up to tackle key projects in Nextflow development, including:

• Working towards a new release of the nf-core ProteinFold pipeline; 

• Developing a Nextflow for HPC training for Australia’s national supercomputers, NCI’s Gadi HPC and Pawsey’s Setonix HPC;

• A nf-test working group to write and apply unit tests to existing institutional pipelines.

As well as progressing some locally important projects, the gathering was a great opportunity to discuss Nextflow training collaborations and how we can work together to ensure more Australians can access the Nextflow skills and resources they need. Keep an eye on our training events listings to see the outcome of these new national relationships.

We are so grateful to the Seqera team and the nf-core community for their enthusiasm and efforts to welcome the Australian satellite site of the hackathon. And massive thanks to the participants who contributed their time and energy to make this event both productive and fun! With the success of this first Australian outpost, we’re already looking forward to next year’s nf-core Hackathon. 

Australian palaeoenvironments and biodiversity to be reconstructed through metagenomic analysis of sedimentary ancient DNA by national collaboration with Indigenous partners

Dr Vilma Pérez uses environmental DNA techniques to understand when and how environments have changed and responded to disturbances

A fascinating new project now has access to the specific computational resources required to build high resolution records of Australia’s changing ecosystems over the past millennium. The research will reconstruct Australian palaeoenvironments and biodiversity using metagenomic analysis of sedimentary ancient DNA collected from mainland Australia and the Torres Strait Islands as part of codesigned projects involving leading Australian researchers and Indigenous partner organisations. Streamlined bioinformatics analysis pipelines will be essential to process the large volume of samples expected to come in from this collaboration.

Sedimentary ancient DNA (sedaDNA) analysis is a transformative tool for studying past biodiversity and its responses to environmental, climatic, and human-induced change. The project aims to build capacity for the growth of sedaDNA research in Australia by automating bioinformatic analyses into a single Nextflow pipeline that can easily produce a robust and reproducible taxonomic profile of both modern and ancient target species found in sediment samples. BioCommons was keen to support the research with access to both ABLeS and our Australian Nextflow Seqera Service. 

This project is part of the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures (CIEHF) which seeks to create a lasting impact by integrating Indigenous and Western knowledge frameworks to model environmental, cultural, and historical change in Australia over the past millennium and into the near future. 

Dr Vilma Pérez is an environmental microbial ecologist at the Australian Centre for Ancient DNA, The University of Adelaide, who can now access the national computational infrastructure she needs for her research after being onboarded to BioCommons’ ABLeS and Seqera services. Vilma's expertise in using environmental DNA techniques to understand when and how environments have changed and responded to disturbances will be put to good use in CIEHF’s novel genetics research program.

Led by CIEHF Chief Investigator Assoc Prof Ray Tobler from the Evolution of Cultural Diversity Initiative at the Australian National University, the research program will use high-resolution landscape genomic analyses of selected Australian native flora and fauna, as well as ancient DNA recovered from archaeological sediments (sedaDNA).

This work will help reconstruct past Australian ecosystems to understand how biodiversity, from microbes to plants and animals, has changed over time, and how it has responded to environmental shifts, including Indigenous Australian landscape management practices that have helped care for Country for thousands of years.

Gaining access to the right computing infrastructure is one thing, but appropriate computing and data management mechanisms are needed to ensure that Indigenous genomic data resources are ethically managed to the benefit of Indigenous Australians. Mutual partners, Bioplatforms Australia, were able to connect CIEHF with colleagues at the National Computational Infrastructure (NCI) who are working with the National Centre for Indigenous Genomics (NCIG) to host their sensitive sequencing data. Given Indigenous genetics research requires unique ethical approaches, NCIG is leading the way in building a genome resource for the research community under Indigenous Governance and will no doubt have many insights to share. 

As part of our ongoing support for CIEHF, Dr Ziad Al Bkhetan, Product Manager - Bioinformatics Platforms at BioCommons, and Dr Kelly Scarlett, Manager - Partnerships and Engagement at Bioplatforms Australia will participate in an upcoming sedaDNA workshop hosted by CIEHF researchers at the University of Adelaide.

This workshop sits within the Genomics research stream which is part of a suite of nine chosen to ensure a holistic, interdisciplinary approach. Find out more about how CIEHF’s research streams are addressing unique environmental, cultural, and historical complexities of Australia through an integrated approach, leveraging both Indigenous knowledge systems and researcher’s fields of expertise.