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.

World-leading Australian science: 17M protein structures added to the AlphaFold Database to accelerate the fight against antimicrobial resistance

Australian researcher, George Bouras, has recently contributed an extraordinary 17 million protein predictions to an international open access database. The availability of the large-scale dataset in the AlphaFold Protein Structure Database will have a transformative impact on the international fight to combat antimicrobial resistance. 

As the lead of the AllTheBacteria protein structure prediction project, the Adelaide University bioinformatician and current PhD student completed his world-leading work using resources made available through a BioCommons partnership with Pawsey Supercomputing Research Centre. George’s work became possible only when the right human and compute resources came together. Working closely with BioCommons, Pawsey’s Dr Sarah Beecroft containerised the ColabFold tool for use on Setonix's AMD GPUs. Once ColabFold was ported and stable, George could utilise the massive scale of Pawsey’s Setonix to create the 17 million structural predictions for bacterial proteins. 

Source image: AlphaFold prediction of a banna virus spike protein VP4 (AF-0000000365762994-v1). Design credit: Karen Arnott/ EMBL-EBI.

George was honoured to contribute to the AlphaFold Database, one of several high-value datasets for microbial and viral proteins selected from specialist communities. This integration of essential, high-quality datasets from users reinforces the AlphaFold Database’s role as an inclusive, and community-driven resource. The database provides open access to over 200 million protein structure predictions, and the developers,Google DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI), are wanting to expand their impact for specialist areas including pandemic preparedness, antimicrobial resistance, neglected tropical diseases and environmental sciences.  

“I hope that access to these novel bacterial protein structures derived from high-quality genome assemblies will lead to better understanding of the function of all bacterial proteins.” – George Bouras, lead of the AllTheBacteria

The availability of the ColabFold container for use on Setonix’s AMD GPUs also allowed George to generate more than 3 million phage and viral structures, which are now used for protein structure-informed bacteriophage genome annotation hundreds of thousands of times each day by researchers around the world. 

This example shows how close working relationships with both researchers and the Tier-1 HPC infrastructures enables BioCommons to precisely respond to community needs and accelerate Australian science at a scale. Making valuable tools accessible on national platforms is a focus of the BioCommons BioCLI project, and this work paves the way for the creation of a new national protein folding service further streamlining the use of Pawsey computing resources.

A publication about this work is currently under peer review, but in the meantime you can read the release from EBI.

GlyCombo: the first dedicated glycomics workflow on Galaxy

In a win for the international glycomics community, the first dedicated glycomics and carbohydrate software tool is available on the global Galaxy platform thanks to a group of Australian researchers. GlyCombo, a high-throughput tool for glycan (sugar polymers present in protein samples) identification is now providing glycomics researchers with a streamlined, reproducible way to process their complex mass spectrometry (MS) data within Galaxy Australia. The workflow that performs a conversion of raw files, GlyCombo search, and visualisation of results glycan and polysaccharide compositions from mass spectrometry files has been shared through the publication on the GlyCombo Galaxy workflow on WorkflowHub.

The availability of this tool and workflow is the result of collaboration between the Galaxy Australia team and Protea Glycosciences, an innovative Australian glycosciences company based in Wollongong.

Dr Chris Ashwood and Dr Maia Kelly, Protea Glycosciences

By wrapping their open-source GlyCombo tool for Galaxy, Protea Glycosciences has made state-of-the-art analytical techniques accessible to researchers worldwide with just a few clicks.

How GlyCombo simplifies glycomics analysis

Rapid identification of glycans present in MS samples is a cornerstone of glycomics research and is integral to robust glycomics analysis pipelines, yet glycomics research is often limited by a lack of throughput and reproducible data analysis to enable subsequent structural elucidation. Protea Glycosciences was established in 2023 to address this gap, bringing a structure-oriented approach.

While traditional web-based tools utilise point-and-click interactions, GlyCombo enables researchers to rapidly process large-scale, complex MS datasets with greater efficiency and reproducibility. Through text-based commands, glycomics researchers can automate the assignment of monosaccharide combinations, handle multiple adduct searches, and anticipate off-by-one errors, while simultaneously maintaining detailed records of their analytical workflows. 

The Galaxy GlyCombo workflow successfully monitored the glycomic consequences of biotransformation, detecting the drastic compositional shifts resulting from sialidase treatment directly within a fully reproducible, browser-based workflow.

Bringing the tool to Galaxy Australia

Protea Glycosciences have wrapped their open source tool for the platform, and the Galaxy Australia team have provided technical support to enable this easy access to the software. The integration of GlyCombo onto Galaxy Australia is a prime example of how national research infrastructure supports the Australian life sciences ecosystem, and how BioCommons and Galaxy Australia support industry-based Research and Development. Hundreds of researchers from Australian small-to-medium enterprises (SMEs) and startups use these subsidised services and the generous computational and working data storage quotas to accelerate their work.

“We built GlyCombo as an open-source tool to solve an analytical challenge, but software is only useful if people can run it. Galaxy makes complex workflows reproducible and accessible without local infrastructure or programming expertise. Partnering with Galaxy Australia was a direct path to putting rigorously tested glycomics workflows in front of researchers who need it and lowers the barrier to entry for the broader glycomics community.” - Dr Chris Ashwood, Director, Protea Glycosciences.

Learn more

• Check out the GlyCombo software tool on Galaxy Australia

• Access the Galaxy workflow on WorkflowHub

• Read the paper: GlyComboCLI enables command line-based FAIR workflows for glycan composition assignment in mass spectrometry data

Global collaboration advancing AI and biomedical data infrastructure

As part of a week-long international engagement program, BioCommons brought together research data infrastructure experts from the USA, Finland, New Zealand and across Australia. The Human Genome Informatics division at BioCommons hosted Prof Robert Grossman, University of Chicago, the founder and lead of the Gen3 platform, to strengthen the collaborative and technical capability required to build world-class human genomics and biomedical data infrastructure in Australia.

Participants engaged in a series of strategic discussions and technical demonstrations focused on solving the complex challenges of data commons development, federated data access, security and governance frameworks, and international interoperability initiatives. 

Reflecting on the growing importance of research data infrastructure, Prof Matthew Watt, Associate Dean Research at the University of Melbourne’s Faculty of Medicine, Dentistry and Health Sciences, noted that ‘well-designed data ecosystems are no longer optional - they are foundational infrastructure for modern biomedical discovery.’

Prof Robert Grossman presenting during his seminar at the University of Melbourne

A particular highlight of the week was a seminar, ‘In Praise of Midscale Language Models and AI Commons and Their Applications to Biology, Medicine and Healthcare’, which sparked significant interest in how secure infrastructure can support the next generation of AI-driven biomedical research.

The discussions highlighted the value of strong international collaboration in advancing secure, scalable, and interoperable approaches to genomics and health data sharing, while also strengthening relationships across the global research infrastructure community. Participants noted the high quality of strategic conversations, which not only strengthened relationships but also reaffirmed Australia’s position as a leader in deploying these sophisticated systems.

How is Gen3 utilised in Australian human genomics research?

The Gen3 platform provides a robust framework to receive, manage, and describe massive datasets, allowing them to be shared securely with authorised users. It is the technology behind numerous US National Institutes of Health (NIH) projects that house data from hundreds of thousands of samples.

BioCommons has successfully led the implementation of Gen3 platforms for several landmark national projects, demonstrating our capability to adapt global best practices for the Australian research landscape. These include:

• OMIX3: Led by the University of Melbourne, OMIX3 utilises mass spectrometry to enable the parallel collection of proteomics, metabolomics and lipidomics data, and is the first successful implementation of a Gen3 platform outside of the USA.

• Australian Cardiovascular disease Data Commons (ACDC): Led by the Baker Heart and Diabetes Institute, ACDC provides a secure, Gen3-powered infrastructure to pool data from 400,000 individuals across 18 clinical cohorts. 

• Biological Psychiatry Data Commons (BPsych-DC): Led by the Consortium for Preclinical Psychiatric Research, providing a national digital infrastructure to harmonise multi-omics data across cellular, animal and human psychiatric models, bridging the gap between discovery and clinical impact

Prof Bernard Pope, GUARDIANS Program Lead and A/Director (Human Genome Informatics) at BioCommons, reflected on the highlights of the week: 

‘Data commons are the backbone of collaborative genomic research. The ability to securely connect, govern, and analyse large-scale datasets is increasingly critical for translating research discoveries into meaningful health and clinical impact.’

‘The success of projects like OMIX3 and ACDC is built on years of shared expertise between our team and the architects of Gen3. By hosting international experts through the GUARDIANS program, we are ensuring that Australian researchers have access to the same secure, scalable technologies that power the world’s largest genomic projects.’

Take a closer look at the GUARDIANS Program: https://www.biocommons.org.au/guardians

Research communities can build their own digital labs with Australian innovation: Galaxy Labs Engine

The Galaxy Labs Engine has been described in a new paper, including how it supports the easy creation of tailored research environments. Several domain-specific portals have now been generated on Galaxy Australia that guide researchers through curated and globally synchronised bioinformatics analysis resources

The Galaxy Labs Engine (GLE) allows research communities to build and synchronise their own Galaxy Labs, which guide users through curated tools, workflows, and training resources. These bespoke interfaces are especially helpful for researchers who are new to the analytical methods or technologies specific to the domain. 

Galaxy Labs are an extension of the established feature of ‘Galaxy Flavours’, subdomains which offer curated content for specific research domains. However, these subdomains have been limited by having static deployments, being difficult to replicate across servers, and often provide inconsistent user interfaces. By separating the content from technical deployment, the engine allows research communities to build custom Labs that stay synchronised with global resources through GitHub.

Development of the GLE service was led by the Galaxy Australia team, originating from a project at the ‘Aussie Outpost’ of the ELIXIR BioHackathon Europe, hosted by Australian BioCommons in 2022. 

The GLE has been used on the Galaxy Australia server to build the Microbiology and Single cell Labs, with the eDNA Lab currently being built, joining the Genome and Proteomics Labs as part of the expanding list of pre-configured Labs available. The engine is already being employed abroad by Galaxy France for their Ecology Lab, and to encourage global collaboration all Lab content is hosted in the Galaxy Project’s Codex GitHub repository. 

Reflecting on how the team is always developing new ways to empower researchers, Galaxy Australia Product Owner Dr Gareth Price noted:

‘Our goal was to make constructing a Galaxy Lab an easy and accessible process for the whole community. Our team is already looking ahead as we finalise the deployment of an AI-assisted Lab builder, again reducing the technical barriers for researchers to start on their own Lab journey.’

You can read the paper in Gigascience

Explore the Galaxy Labs on the BioCommons website

Read Dr Gareth Price’s blog post on Galaxy News

Collaborating globally to develop a foundational structural biology training module

An international joint effort spanning the course of a year has produced a cutting-edge self-paced training resource in structural biology. The Foundations of protein structure module was developed by the Australian Structural Biology Computing (ASBC) community, the European Molecular Biology Laboratory European Bioinformatics Institute’s (EMBL-EBI) Protein Data Bank in Europe, and BioCommons, with the aim of providing accessible training for researchers who want to understand and use protein structures in their work.

‘Alignment, adoption and contribution to global best-practice efforts’ were aims of the Australian Structural Biology Deep-Learning Infrastructure Roadmap, developed in partnership between the ASBC and BioCommons in 2025. By co-designing this module with our partners at EMBL-EBI, we are excited to contribute to the resources they provide to an international audience of researchers.

What is the module and how does it benefit researchers?

Many researchers, undergraduates and clinicians want to use protein structures in their work, but don’t necessarily have the prerequisite knowledge to bridge the gap between theory and practice. This module onboards researchers to the domain, by providing an understanding of the fundamental concepts of protein structural biology, including protein composition, folding, architecture, dynamics, and interactions.

Protein structure elements (Image: EMBL-EBI Training)

For example learners gain insight into:

• The sequence-structure-function relationship

• Secondary, tertiary and quaternary structures, including alpha helixes and beta sheets, motifs, domains, and folds

• The dynamic and flexible nature of proteins and how this impacts biological function.

Who developed ‘Foundations of structural biology’?

The module was co-designed over twelve months by collaborators based across Australia and the United Kingdom. As the team was working across continents and vast time zones, they relied on a mix of asynchronous drafting and regular online meetings for coordination, planning, and discussion of the content.

The contributors were:

• From the ASBC and BioCommons: Dr Michael Healy (University of Queensland), Dr Kristina Gagalova (Curtin University), Dr Kate Michie (UNSW), Dr Thomas Litfin (UNSW and Australian BioCommons), and Dr Johan Gustafsson (Australian BioCommons)

• From EMBL-EBI: Dr Jennifer Fleming, Dr Paulyna Magaña, Dr Flaminia Zane (reviewer), and Dr Ajay Mishra (reviewer).

Beyond the module itself, this project has strengthened the connection between EMBL-EBI, the ASBC, and BioCommons, and will lead to further collaboration on a set of structural bioinformatics modules that will complement and extend existing EMBL-EBI training resources.

Foundations of protein structure has been released as an online tutorial by EMBL-EBI Training as part of their mission to deliver world-class training in data-driven life sciences.

Meet the Team: Mok, UX Designer

Describe your role at BioCommons

I’m a user experience (UX) Designer at BioCommons, which means that I help improve infrastructure and scientific research by being the friendly translator between complex systems and real humans. This type of role is new in the life sciences field, making it a lot of fun, as I sit at the intersection of science, data, and human-centred design, helping researchers, bioinformaticians, and software engineers make sense of the inherently complex biological tools and platforms they use everyday.  The goal is to make it look easy - even when it’s not!

It’s challenging work, because the problems are big and complex. You’re designing for expert users, emerging technologies, and systems that genuinely matter.

There’s a lot to learn, a lot to ask, and plenty of moments where curiosity and collaboration are essential. This makes the role deeply rewarding, as your work doesn’t just improve usability; it helps accelerate research, supports discovery, and amplifies the impact of national life-science infrastructure.

How can UX Designers improve infrastructure and/or scientific research?

Think of scientific infrastructure as a powerful machine: data platforms, tools, pipelines, and services that can do amazing things. A UX Designer ensures that people can actually use that power without needing a PhD in ‘figuring stuff out’. 

By taking complicated processes and reshaping them into smooth, logical journeys, we turn confusion into clarity. This saves researchers time and frustration - when tools are intuitive, scientists spend less time wrestling with interfaces and more time doing what they love: discovering, analysing, and innovating.

Good UX also makes infrastructure more accessible. It opens the door for students and early-career researchers to use advanced systems confidently, rather than those tools being limited to the experts that already know the ropes. By asking the right questions early and understanding user needs upfront, we help teams build the right thing the first time. This reduces rework and ensures that research workflows flow smoothly, helping insights travel from idea to impact more quickly.

What is the real-world impact of human-centred design at BioCommons?

At BioCommons, my impact is all about making powerful research infrastructure feel simple, friendly, and usable. I focus on turning complex scientific tools into clear experiences, helping researchers spend less time navigating systems and more time doing great science. 

By listening to users and smoothing out workflows, I help ensure that BioCommons tools are not just functional, but adopted and used to their full potential. In short: I make hard things easier, science faster, and national infrastructure more human.

What makes solving scientific problems so rewarding?

This is not your average UX gig, and that’s exactly the point. I get to work closely with scientists, engineers, product leads, and stakeholders who are passionate about what they do and who will happily stretch my thinking.

It is incredibly rewarding to work in a space where UX isn’t just ‘nice to have’, but genuinely transformative. There is a unique joy in those moments where a complex process suddenly becomes clear and usable.

In short: it’s a role for UX designers who like their work meaningful, their challenges meaty, and their wins shared with science itself!

View Mok’s profile on the BioCommons website