Contributing to open and accessible training with 500+ bioinformatics resources

Did you know that an international community has been coordinating the creation of freely accessible educational data analysis training resources for over a decade? This sustained stewardship from the Galaxy community has resulted in a collection of over 500 tutorials covering 35 topics that have been written, reviewed and maintained by people committed to open and accessible training.

What do these training resources cover?

Galaxy Training is a collection of tutorials developed and maintained by the worldwide Galaxy community. There have been 511 contributors, including the Hall of Fame: Australian BioCommons team who have contributed to 37 tutorials in support of life sciences computation. The library of tutorials available in Galaxy Training cover a wide range of scientific fields including genomics, climate science, ecology, statistics, machine learning and more. The resources combine videos, slides and worked examples that are accessible to everyone to use in their own time. The Galaxy community also hosts a massive online training event online each year to provide a further layer of support to learners. 

Different categories of training resources available

The group of BioCommons contributors work at Melbourne Bioinformatics, the University of Queensland, and QCIF Digital Research, supporting researchers through training and improvements to the Galaxy data analysis platform. The Galaxy Australia service is made available for Australian life science researchers to more easily perform their data analysis. The web-accessible platform offers fully-subsidised accessible, reproducible, and transparent computational biological research. The Galaxy Australia service contains over 2,000 bioinformatics tools (for genome assembly, annotation, epigenetics, metabolomics, metagenomics, proteomics, statistics, transcriptomics, variant analysis and visualisation) and over 220 reference datasets (e.g. publicly available genome builds).

There are now over 650,000 registered Galaxy users internationally, and the Galaxy Community is always encouraging new users to get more involved. There are lots of different ways to contribute to the Galaxy Training Network (GTN), from reporting suggesting tune-up opportunities as you step through the tutorials, all the way to creating new content you think would be useful to others. Contributions can be driven by an individual sharing a specific thing they developed in the hope that it can help someone else with a similar niche interest, or involve a large effort to coordinate big changes that will benefit a very large group of people. The integration of the Galaxy Training Network with WorkflowHub was made possible thanks to a collaborative effort between Australian BioCommons and the Galaxy Training Network and WorkflowHub teams. All Galaxy Training workflows are now registered with WorkflowHub, with workflows contained in every new tutorial automatically pushed to WorkflowHub.

Where can I access Galaxy Training resources?

Investigate the Galaxy Training workflows: Galaxy Training on WorkflowHub. 

View a webinar introduction to using Galaxy Australia for different biological applications: No code, no problem: data analysis for biologists using Galaxy Australia - Dr Tiff Nelson and Dr Tristan Reynolds

Register for the free and online Galaxy Training Academy 2026

Galaxy Australia’s 14 millionth job was a win for sustainable crop production

The 14 millionth data analysis job was recently submitted to the Galaxy Australia platform, marking another major milestone for this national service. University of Queensland Senior Research Fellow, Dr Donald Gardiner, uses the platform to understand how pathogens cause disease in plants. His work highlights how essential access to the right research infrastructure is in sustaining Australia’s agricultural and biodiverse future.

How does Galaxy Australia support sustainable agriculture?

As part of the Queensland Alliance for Agriculture and Food Innovation, Donald works in a diverse group that includes molecular biologists, plant pathologists and biotechnologists to solve plant disease problems. Their work has been central to the ARC Hub for Sustainable Crop Protection, looking at innovative ways to protect Australian agriculture.

Dr Donald Gardiner

Donald’s work using Galaxy Australia spans several research projects, focusing on pathogens threatening the nursery and garden, forestry, agriculture and horticulture industries, as well as natural ecosystems. He is investigating the impact of Myrtle rust on the Mytaceae family of plants, including eucalypts and tea tree. The threat that pathogen Fusarium oxysporum poses to Australia’s banana industry, and risks to ginger and cereal crops are all better understood by Donald’s use of Galaxy Australia’s tools for genome assembly, annotation, RNA-seq and phylogenomics analysis.

How do molecular biologists use Galaxy Australia for bioinformatics?

For researchers like Donald whose lab work is complemented by key steps involving bioinformatics, the platform serves as a ‘truly enabling’ resource.

‘Galaxy allows me to skip much of the backend set up work for getting pieces of software to run. As someone who is not solely undertaking bioinformatic work, the need to have relatively simple ways to run programs is really important as I can’t dedicate massive amounts of time to bioinformatics.’

The service provides a comprehensive suite of software tools that are ready to use, allowing life science researchers to focus on the biological impact of their work rather than how to perform the analysis themselves, or relying on external bioinformatics expertise.

Find out more about Dr Donald Gardiner’s research

Learn about the different types of research that Galaxy Australia gets used for: No code, no problem - data analysis for biologists with Galaxy Australia (webinar)

Streamlined Science: Single sign-on with BioCommons Access

In a significant step towards integrating the tools and data that Australian life science researchers need, a new approach to accessing services across the Australian BioCommons ecosystem is coming. Launching in late March 2026, BioCommons Access will simplify access to multiple analysis and data services using a single sign-on. The availability of curated bundles of tools and data, and connections between services will streamline the research workflow.

BioCommons’ priorities are directed by the needs of life scientists, so services are always shaped by their research-driven stories. Rather than chasing new features down exciting tech rabbitholes, we nurture communities to hear researchers’ insights into how new services or better access to existing research infrastructures could transform their work.

We’ve heard that researchers feel like they are forced to become the ‘network switch’ between the many isolated services they need to run increasingly complex workflows. Rather than managing multiple accounts, and manually jumping between different platforms, our BioCommons BioCloud team is building a linked ecosystem with a single sign-on that allows access to and transition between analysis and data services, including simple data transfer and increased visibility of available resources. Galaxy Australia and the Bioplatforms Australia Data Portal will be the first two services connected and available through BioCommons Access, with additional services to follow.

Australian BioCommons Access will enable:

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

• Streamlined use of Galaxy Australia and the Bioplatforms Australia Data Portal using one login

• A central portal to manage your user profile across services

• Connection to curated bundles of tools and data 

• Fast one-click transfer of data between services (coming in May 2026).

The data and analysis needs of the Threatened Species Initiative (TSI) shaped the first service “Bundle” that is available as an add-on to BioCommons Access. When new members join this national consortium, they can sign up just once to start analysing the TSI data in the Bioplatforms Data Portal using Galaxy Australia. By adding the TSI Bundle to their registration, researchers are approved to access both embargoed and sensitive data as well as specialised and directly relevant analytics resources that are curated and managed by the TSI and Galaxy Australia. 

BioCommons Access will be available from March 26th 2026, replacing the requirement for individual logins to Galaxy Australia and the Bioplatforms Data Portal. Existing users will be supported to migrate to the new system.

Future developments in BioCommons Access include the addition of institutional logins via the Australian Access Federation (AAF), new bundles to support national research communities, and additional integrated services.

The BioCommons Access service is the result of a deep collaboration between Galaxy Australia, the Bioplatforms Australia Data Portal, and the BioCloud team. BioCloud is the BioCommons division responsible for designing and operating the foundational and integration platforms that power molecular life sciences research in Australia.

Bringing together software engineers, cloud infrastructure specialists, and user experience experts based at the University of Melbourne and the University of Sydney, the BioCloud team builds secure, scalable platforms that enable researchers to work seamlessly across national capabilities. Expertise in digital identity and access management to deliver BioCommons Access was strengthened through a strategic partnership with BizData.

Visit the BioCommons Access page for more details

Help shape the future of AI in life sciences research and training

Artificial intelligence (AI) and machine learning (ML) are rapidly changing the way we work in life sciences. To ensure our community is well supported, Australian BioCommons is gathering input to map exactly how these technologies are being applied, particularly regarding molecular data analysis.

By sharing the current tools, processes, bottlenecks and skill gaps you experience, you will help prioritise national investments in digital infrastructure and directly shape our upcoming training programs.

How can you help shape the 2026 priorities?

We are looking for researchers and support staff at all levels of experience, from those who have never used AI to those who rely on it every day. Your perspective is valued regardless of your technical background.

There are two ways you can contribute:

• Add your voice to the survey: Contribute to our national data collection to help identify trends and gaps across the Australian research ecosystem.

  Take the National AI Survey

• Join a focus group to contribute to our training programs: Share your specific challenges and ideas in a 60-minute interactive Zoom discussion. Register your interest by Friday 13 March 2026.

  Submit your expression of interest

What happens next with your feedback?

We value your time and insights and we want to share what we learn along the way. In April, we will present a summary of our findings back with the community in a dedicated webinar. We will take a look at the initial training plan, giving you a sneak peek into the workshops and resources we’ll be launching later this year.

Register for the webinar

Accelerating deep learning in Australian structural biology research

Enabled by rapid advances in deep learning methods for protein structure prediction, computational structural biology is driving major innovations in life sciences research. However, making effective use of these technologies requires cutting-edge software, highly specialised hardware, and interdisciplinary expertise.

To tackle these challenges, a passionate group of researchers officially formed the Australian Structural Biology Computing (ASBC) community in early 2025. Supported by BioCommons, this community-led initiative set out to share computational knowledge, methods and resources. Less than a year later, we can already see the value they bring to the Australian research sector.

How has the ASBC community grown?

Since its formation, the community has been moving quickly to address the needs identified in the Australian Structural Biology Deep-Learning Infrastructure Roadmap. The roadmap has already demonstrated its value to the sector, having been viewed over 1,100 times and downloaded over 900 times, in addition to being used in funding applications and publications. 

To further connect researchers, BioCommons assisted in the development of a new Community Platform website that is now live, serving as a virtual hub for all users in Australia, with new resources and opportunities for contributions being added to the platform over time.

What training and resources are now available?

Capacity building has been a key focus for the ASBC community, and they have been integral to several key activities in 2025:

• The community was instrumental in providing expertise for the ‘Leveraging deep learning to design custom protein-binding proteins’ webinar series, coordinated by BioCommons and featuring five individual guest speakers across the program of events

• The facilitation of a 2025 ABACBS workshop ‘Leveraging peak Australian compute to enable workflows for predictive structural biology at scale’ to help researchers run protein prediction workflows on Australia’s peak high-performance computing (HPC) systems. 

• Collaborating with EMBL-EBI to develop the self-paced ‘Foundations in Structural Biology’ module (available now) for a global audience.

Get involved

• Learn more and join the ASBC community

• Investigate ways to engage with the community and its resources: https://www.biocommons.org.au/structural-biology

Roundtable convenes new community to chart Australia’s research infrastructure roadmap for AI in life sciences

A roundtable to discuss the opportunities and implications of the use of AI in the life sciences was recently convened by Australian BioCommons and Bioplatforms Australia. It brought together almost 30 experts from diverse groups across Australia to share insights, experiences, and perspectives on AI in biosciences. 

While helping to inform the strategic direction of Bioplatforms and BioCommons in this rapidly evolving area, the event also provided a valuable chance for researchers to hear from the Interim Director of EMBL European Bioinformatics Institute, Dr Johanna McEntyre, about how Europe is approaching our shared challenges. Given the Memorandum of Understanding between Australian BioCommons, Bioplatforms Australia and the European Molecular Biology Laboratory (EMBL), it was a wonderful opportunity to reflect on the value of international collaboration in this space while Jo was visiting Australia.

(L-R) Jeff Christiansen, Johanna McEntyre and Benjamin Goudey

While research infrastructure was the focus, a varied group of people who use, develop or support AI in Australian life science research participated in presentations, panel discussions and interactive exercises. People from universities, research institutes, computation service providers and other NCRIS facilities shared how they are using and building AI, and learned about needs, gaps, and constraints to their work. 

The roundtable was a step towards finding strategic partners who can help to map the current landscape, identify gaps and define investment priorities. As our AI in Molecular Life Sciences community coalesces, we can expect to gain a deep understanding of the challenges facing Australian life scientists using and developing AI tools and models, and benefit from having a diverse partner network acting as a collective watchtower for trends and opportunities that can define the new shape of life sciences computing. 

If you have insights into how AI will impact research methods and future discoveries, please consider contributing to the development of a BioCommons Infrastructure Roadmap for AI in the Life Sciences by engaging with this newly formed group.

• Sign up to join a new community of people who will work together to identify and document the infrastructure challenges and investment priorities for Australian life sciences

• Other opportunities to help shape the future of AI in life sciences research and training in Australia

Introducing Spatial Sampler, the ‘cheat sheet’ to answering biological questions

A new tool is available to help researchers quickly answer important questions about their spatial omics data. This new resource, called Spatial Sampler, collates example R scripts for a variety of comparative analyses to fast track analysis.

QCIF Digital Research Senior Bioinformatician, Dr Sarah Williams, developed the resource for her own use, and upon realising its potential value to others she went on to share the collection of examples via the BioCommons’ Workflow Commons project.

What is Spatial Sampler?

Spatial Sampler is a collection of ‘How-To’ guides framed around testing specific biological questions. 

Each How-To includes:

• An example workflow using a real dataset, which explains why each step is necessary

• What input data is needed

• What the output looks like

• A code snippet that can be copy-pasted

Who needs Spatial Sampler?

Spatial Sampler is a collection of complete, step-by-step workflows using real data that run comparative tests between different experimental conditions. The worked examples act as a ‘cheat sheet’ for spatial omics analysis. Most existing tutorials stop at the quality control and clustering stages, and a need for testing between groups is what inspired Sarah to develop Spatial Sampler: 

When I started working with spatial data, I could find tutorials for how to load, QC and annotate my datasets. But I struggled to find complete workflows for testing experimental questions. I wanted a collection of examples using real data - so that’s what Spatial Sampler aims to provide. I had inspiration from amazing existing resources such as The R Graph Gallery. I’m now looking forward to others using Spatial Sampler and contributing more tools and resources that the community can use.”

Different elements of Spatial sampler will help different people:

• Newcomers to spatial omics can apply worked examples to their own datasets

• Busy bioinformaticians can use code snippets to run specific tests without rewriting code

• Trainers can readily adapt open source instructions for their own training.

What is spatial omics?

Spatial omics combines the power of single-cell transcriptomics with spatial localisation, allowing researchers to measure gene expression and morphology while retaining the individual locations of transcripts within their native tissue environment. By inheriting analytical strengths from both single-cell technologies and microscopy, it enables the testing of complex new hypotheses about expression patterns and cellular interactions that are lost in data from a single modality.

This exciting new field is now moving from a niche to a fully-fledged production analysis technique, and given the rapid growth in utilisation, analysis methods are constantly being invented as new applications are discovered. Now that it is possible to generate high-quality data at scale, the downstream analysis options have expanded accordingly to help answer specific biological questions. 

An example of this is in quantifying changes in the tumour microenvironment, such as changes in cell type composition between tumour subtypes, changes in immune cell migration between groups, or expression changes in different cells by experimental group or tissue region.  

Spatial Sampler was initially developed by Sarah to analyse data from the Griffith Central Facility Genomics for A/Prof Nic West and Dr Amanda Cox (Griffith University) relating to their research projects in the mucosal immunology and cancer immunology spaces.

Sarah’s role at QCIF Digital Research is co-funded by Australian BioCommons.

Explore Spatial Sampler

Register now for the workshop that will provide a practical introduction to comparative analysis of spatial omics data using Spatial Sampler

Meet the team: Kylie Davies, Senior Business Analyst

Describe your role at Australian BioCommons

My role with Australian BioCommons has been to work as a business analyst for the GUARDIANS project - a multi-organisational project aimed at uplifting Australia's Genomic research capabilities and opportunities through the creation of national infrastructure that brings down barriers to the secure sharing of human genomic data. The better and quicker this access can be, the better and broader the opportunities to solve complex and challenging human diseases.

How can Business Analysts improve infrastructure and/or scientific research?

The role of the Business Analyst (BA) is always multifaceted. At the start of a project the BA focuses heavily on unpacking the project work packages with the input of subject matter experts, and translating these into detailed use cases and requirements. Even in Agile units this work is critical. The BA sits between the technical development team and the Project Management (PM) team; and between the future users and the project team (both technical and PM).

“Your role is to get into the weeds enough to unpick the key deliverables and major challenges, while managing the expectations of stakeholders to help the team achieve delivery of a technical product that is fit for purpose and delivers the key requirements.”

A good BA will have experience and some understanding of technical matters, User Experience considerations and project scope. They should be a good listener and good at eliciting information in a relaxed way. We are just one part of the team, but we make a vital contribution in ensuring the planned infrastructure is delivered in such a way that it meets the real needs of users, with all parties being clear about the key deliverables from a business value perspective. Even research infrastructure has a measured business value. If this is delivered, not only does it serve scientific researchers better, but it means the business case for future improvements (and further project funding) easier to make.

Tell us about the impact of your role

I think for some of the project teams across the GUARDIANS project and its predecessor project, on which I also worked, they had not worked through requirements with a Business Analyst before. They found that the process clarified the details of their plans and freed them up to get cracking on development work without circular discussions and going down too many rabbit holes mid-development.

In the research world, it is necessary to allow for enquiry and discussion. It's different from commercial environments in that we need to allow flexibility for exploration. I needed to learn that when I first worked with researchers starting in 2021. There is a necessary tension between maintaining freedom to explore and avoiding paralysis by analysis.

I think probably one impact I had as the BA was to convene forums and exercises for that exploration to really flourish, but then encourage decisions to be made at a certain point through the documentation of requirements. The feedback I have received indicated that the project teams felt that they were clearer about their goals and felt heard, and yet unified, in their development plans as a result of the work we did together. Then as the products were rolled out, they could demonstrate to wider audiences not only what they had developed, but how each element served use cases.

I should add I have learned a lot too in my role from other BAs. There are a couple of other BAs working on GUARDIANS and it's been a pleasure and learning experience particularly to see them work with stakeholders. We also have a highly experienced BA inhouse at BioCommons in the form of Farah Zaib Khan and I am in awe of Farah's work. We have caught up a few times to share techniques.

What’s next?

I am retiring soon. I am happy to be retiring although it's come a little earlier than I had originally planned, due to my own cancer diagnosis mid 2023. I continue to be well but it is a progressive form of disease so the medical interventions are becoming more frequent, but still not too terrible.

I am living proof of the benefits of medical research. The prognosis for the type of cancer I have was extremely poor a decade ago, but I have been able to access three new cancer drugs delivered to us very recently by clinical research. The drug I am on now was TGA approved in 2025! This has delivered tangible and hugely valuable benefits for me. I have been able to work and enjoy a good quality of life. I undertook a wonderful adventure holiday in 2025. Thank you to Australia's research community for this.

2026 will see me nesting more at home. I have a large garden and grow some produce and I am aiming to ramp that up as soon as I finish work. I have adult children who are some of my favourite humans and plan to catch up with them and friends a bit more. And fish and boat with my husband who is retiring at the same time.

I will continue to be involved in two voluntary consumer representative groups for cancer treatment centres, and I hope to follow the progress of GUARDIANS and BioCommons as a remote observer.

Australian BioCommons and Southern eDNA Society partner to deploy national infrastructure

Australian BioCommons and the Southern eDNA Society (SeDNAS) have signed a Memorandum of Understanding (MoU) to acknowledge, and work towards, the shared infrastructure challenges faced by life science researchers performing eDNA analysis. By collaborating with the community to document the current research landscape, this partnership aims to deploy national-scale bioinformatics infrastructure that supports life science researchers across Australia and New Zealand.

What is eDNA and why is this needed?

Environmental DNA (eDNA) involves the capture of nucleic acids from an environment, such as water, soil or air, to identify the organism in that environment without needing to visually observe them.

Southern eDNA Society logo

This method allows researchers to cost-effectively monitor biodiversity, track invasive pests, and detect rare species over large areas with minimal disturbance to the organisms (such as animals or bacteria) being identified. However, the rapid adoption of these methods across academia, government, and industry has created a pressing need to better coordinate the digital infrastructure and data resources required to support this growing community. eDNA analysis generates massive amounts of data that requires comparison to curated reference databases, such as GOLD (Genomes OnLine Database) and SILVA. As such, practitioners are facing challenges regarding the availability and coordination of the necessary digital infrastructure.

The partnership between SeDNAS and Australian BioCommons

To leverage combined expertise and resources, this partnership brings together the SeDNAS community of experts and practitioners with the bioinformatics infrastructure experience of  Australian BioCommons. The collaboration recognises that science benefits from researchers working together, and that shared national infrastructure can help alleviate the identified challenge.

Next steps: building the roadmap

Key activities to support the eDNA community include:

• Community consultation engagement activities, such as surveys and community meetings, to collect the specific bioinformatics infrastructure requirements of life science researchers

• Strategic planning to develop targeted, community-endorsed infrastructure roadmaps that describe the national bioinformatics research infrastructure needed to support the field

• Capacity building by raising awareness of existing infrastructure and collaborating on priorities such as training, upskilling, and data resource development.

Get involved

Visit the Southern eDNA Society (SeDNAS) website

Empowering wet-lab postgraduate students with computational and communication skills

Australian BioCommons team members have helped to equip the next generation of researchers with the skills and confidence to work at the cutting edge of data-driven science.

As part of EMBL Australia’s 10th annual PhD course, consisting of over 60 high-achieving PhD students in the early part of their research careers, Dr Benjamin Goudey and Dr Giorgia Mori joined other experts at South Australian immunoGENomics Cancer Institute (SAiGENCI) to deliver sessions across the two-week program.

The topics ranged from emerging life sciences technologies to Artificial Intelligence (AI) foundations and scientific modelling, and also included science communication and ethics. The goal of BioCommons’ involvement was to help bridge the gap between the wet-lab results and dry-lab computational skills that make up modern scientific research.

Dr Giorgia Mori’s training expertise had the room buzzing as students worked in small groups to identify the most effective data visualisation methods to explore how to tell a compelling story with their data.

BioCommons’ AI Technical Lead, Dr Benjamin Goudey, delivered a dynamic crash course regarding these topics, giving a clear, high-level understanding of when and why AI/ML can be an appropriate tool in the life sciences.

As noted in EMBL Australia’s event report, Madison Hindes from Adelaide University came away with a new appreciation for dry-lab science:

“I definitely thought science happened in a lab until coming here and now I can appreciate there is much more to it than that.”

Read EMBL Australia’s summary of the event

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Winners of the ‘visualising data’ session (L-R): Zuriel, Martina, Maddie, Levi, Suet Li

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Dr Giorgia Mori instructing PhD students on visualisation considerations

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Dr Benjamin Goudey leading the session on AI and ML tools

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Attendees of the session