Into the great genome: new tracker for Australia’s genomic biodiversity

This press release is republished with permission from CSIRO. Read the original here.

Tracking our progress on genomes across Australian species for research, monitoring, conservation and protection.

A world-first tool is tracking Australia’s progress in sequencing the full genomes – or genetic blueprints – of the country’s 250,000-plus known and catalogued species.

Launched today, Genome Tracker reveals that only two per cent of Australia’s known and catalogued species have had their genome sequenced at least once.

The online dashboard is part of the Australian Reference Genome Atlas (ARGA), a platform delivered through the Atlas of Living Australia, Bioplatforms Australia, Australian BioCommons and the Australian Research Data Commons.

Regent Honeyeater (Anthochaera phrygia). Image credit: Joel Poyitt (CC-BYNC)

CSIRO’s Dr Kathryn Hall, ARGA project lead, said Genome Tracker is a step change in how genomic data coverage can be tracked, assessed and prioritised.

“Whole genome sequencing for plants and animals provides insights for ecology, conservation biology, agriculture and biosecurity,” Dr Hall said.

“It lets us peer back through evolutionary time to understand how species have adapted to the unique landscapes of Australia.

“Genome Tracker clearly shows which parts of the family tree of life have strong representation and which are under-sequenced or entirely missing.

“It helps researchers map existing genomic coverage and highlights under-represented areas for research."

The ultimate goal is to have genomes published for a wide cross-section of Australian biodiversity.

“Genomes help us understand the adaptive traits of species – how they’ve uniquely adapted to their environment and how they’re evolving,” Dr Hall said.

“The higher branches in the taxonomic tree of life represent older genomic divergence.”

Genome Tracker tells us that these ancient branches currently have just 32 per cent genomic coverage. Improving their representation will deepen our understanding of how species have diversified and evolved over time.

“These are exciting times for biology. Genomes give us roadmaps to trace how life came to be as it is today – and how we can work with that knowledge to protect it for generations to come,” Dr Hall said.

“We can look at what drove changes in organisms, and this could help predict how species might adapt in the future.

“As ecosystems change, this data spotlights populations for monitoring, conservation and protection.”

Taxonomic descriptors, species occurrence records, and ecotype layering allow researchers to use ARGA to filter and search the indexed genomics data, and to track every species in Australia.

Genome Tracker and ARGA use existing research infrastructure capabilities of the Atlas of Living Australia (ALA), Australia’s national biodiversity data infrastructure which is hosted by CSIRO, the national science agency.

Fast facts:

• Tasmanian Devil (Sarcophilus harrisii): Australia’s first published genome. Released in 2011, it was critical for research into Devil Facial Tumour Disease, conservation, and as a model for cancer resistance studies.

• Tammar Wallaby (Notamacropus eugenii): The first kangaroo genome, fully published in 2012 after three years of work. It revealed the genes for encoding special antimicrobial proteins in its milk and around 1,500 smell-related genes.

• Regent Honeyeater (Anthochaera phrygia): The first honeyeater genome was published in 2019. It showed only a 9 per cent loss of genetic diversity despite low population numbers, highlighting the need to preserve remaining genetic diversity and prevent inbreeding.

• Numbat (Myrmecobius fasciatus): Published in 2022, the genome showed they have reduced bitter and sweet taste receptors, but enhanced umami receptors, as an adaptation to their specialised termite diet.

• Orange-bellied Parrot (Neophema chrysogaster): Genome published in 2025, the first for a critically endangered parrot. It will help strengthen captive breeding programs. The first parrot genome was only published in 2024.

• Southern Corroboree Frog (Pseudophryne corroboree): Published in 2025, this genome is three times the size of the human genome. The genome will help researchers understand which genes affect resistance or susceptibility to the chytrid disease. Ultimately, the conservation goal is to breed frogs’ resistance to the chytrid fungus for release back into the wild.

 Explore Genome Tracker

The Australian Reference Genome Atlas (ARGA) is enabled by funding from the National Collaborative Research Infrastructure Strategy and delivered by the Atlas of Living Australia (ALA), Bioplatforms Australia, Australian BioCommons and Australian Research Data Commons (ARDC) (https://doi.org/10.47486/DC011).

ARGA and ALA are hosted by CSIRO, Australia’s national science agency, as key Australian biodiversity data infrastructure. ARGA integrates data sourced from a number of international repositories, including NCBI GenBank, EMBL-ENA and Bioplatforms Australia.

Global collaboration across life science data infrastructures boosted by Australian BioCommons, Bioplatforms Australia and EMBL

A new Memorandum of Understanding (MoU) between Australian BioCommons, Bioplatforms Australia and the European Molecular Biology Laboratory (EMBL) recognises the scientific benefits of collaboration between researchers from different countries, and the importance of Australian and European cooperation in science and technology.

Key areas of collaboration described in the MoU that will take place over the next 5 years include: 

• scientific collaboration (with a particular focus on AI, Data, Services, Infrastructure, and Omics);

• access to shared services and infrastructure; 

• development and delivery of training opportunities (especially for early-career researchers), scientific visits, joint meetings, conferences, and workshops; and 

• possible collaboration on joint funding opportunities.

The collaboration will build on an existing multi-decade history of engagement between the parties across several established strengths including the delivery of training programs, staff exchanges, international knowledge sharing, and joint collaborative activities to establish and advance life sciences bioinformatics infrastructure. The parties have complementary natures, scientific strengths, and missions, particularly in bioinformatics and data provision. All three are committed to the mutual benefits of international partnerships to foster scientific knowledge, skills, and innovation. 

Bioplatforms Australia supports life science research by investing in infrastructure and expertise in genomics, proteomics, metabolomics, and bioinformatics. Australian BioCommons, supported by Bioplatforms Australia, provides national bioinformatics infrastructure. EMBL is a leading intergovernmental organisation in molecular biology, with its European Bioinformatics Institute (EMBL-EBI) serving as a world-leading source of public biological data. 

Read Bioplatforms Australia’s announcement here

Read EMBL’s announcement here

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.

Stop the rot! Plant Bacteriologist’s genome assembly becomes Galaxy Australia’s 11 millionth job

Image courtesy of Dr Toni Chapman

An enthusiastic new user recently submitted the lucky 11 millionth data analysis job to the Galaxy Australia platform. Plant Bacteriologist Dr Toni Chapman has begun regularly using the service for her genome assemblies of bacteria important to agricultural plant biosecurity and production.

As a Senior Research Scientist in Agriculture and Biosecurity at the NSW Department of Primary Industries and Regional Development (DPIRD), Toni’s work spans both diagnostics and research. Using NovaSeq and HiFi sequencing technologies, she assembles bacterial genomes to help growers diagnose the cause of disease symptoms in their plants or to identify bacteria present in suspect samples collected by biosecurity officers.

In the past, Toni needed to rely heavily on bioinformaticians for assistance with genome assembly of the bacteria she works with. Now after attending a training workshop and signing up for access to the fully-subsidised Galaxy Australia service, she independently completes more of the analysis steps and is able to identify the bacterial pathogens herself.

“Over time I have been learning to code and to use various programs for genome assembly, but only returning to it on a casual basis makes it very hard to maintain the necessary skills in the bioinformatics space. Being able to design workflows in Galaxy Australia that I can come back to at any time makes assembling genomes easy, even if there has been weeks or months between visits.”

Toni contributes to the Plant Pathogen ‘Omics Initiative, which is generating molecular reference data for plant pathogens in Australia. Established by Bioplatforms Australia to support research in plant protection and enhance biosecurity surveillance efforts, the national plant pathogen community is collaborating to create high quality data that can be shared with all researchers via the Data Portal. Toni was one of a large group that came together with members of the Functional Fungi and Plant Pathogen ‘Omics National Initiatives for a hands-on bioinformatics workshop, learning how to use Galaxy and the programs needed for genome assembly using their own real-world scenarios.

As part of her contribution to the Initiative, Toni is conducting genome assembly on Pseudomonas species that cause disease in plants, to update the taxonomy of collection isolates and gain a more accurate view of which pathogens are in Australia. In another project, she is sequencing the bacterial pathogens that cause soft rot disease in plants. The incidence of soft rot is increasing, and so is the range of bacteria that can cause the disease. The newly assembled genomes of these bacteria are updating existing culture collection identities and helping to understand the diversity of bacteria that cause soft rot infections in Australia.

If you’d like to find out more about her work, see Dr Toni Chapman’s publications.

If you are interested in hearing about the different types of research that Galaxy Australia gets used for, watch this recorded webinar: No code, no problem - data analysis for biologists with Galaxy Australia.

Smooth migration for BioCommons’ Apollo service: AARNet and Globus support critical data transfer

This AARNet news story is republished with permission

As part of planned infrastructure changes at the Pawsey Supercomputing Research Centre’s Nimbus cloud, Australian BioCommons began preparing to move key components of its Australian Apollo Service to new infrastructure. A central part of that transition involved securely transferring over 15 terabytes of user data — ensuring research continuity for life science teams around the country.

To support the process, BioCommons turned to AARNet and Globus for a robust, high-performance solution.

Powering digital biology

Australian BioCommons is a national research infrastructure initiative accelerating life sciences research by providing digital platforms and services for data-intensive biology. One of its flagship offerings is the Australian Apollo Service — a hosted virtual environment that enables researchers to launch, manage and run complex bioinformatics workflows on demand.

The Pawsey Supercomputing Research Centre, a Tier 1 government-funded national facility, hosted the Apollo service from 2020, providing access to genome curation and visualisation software to hundreds of researchers across Australia.

As the underlying cloud infrastructure at Pawsey (Nimbus) was being phased out and Apollo’s environments could be redeployed elsewhere, the associated user data, including datasets vital for current and future analysis, needed to be transferred efficiently and with minimal disruption to services.

Finding the right approach for large-scale transfers

Initial attempts to move the data using traditional tools quickly highlighted performance limitations. Transferring even a single terabyte took multiple days, and with the additional goal of preserving metadata using tarball archives, BioCommons needed a more scalable and dependable approach.

To meet these needs, the team explored using Globus, a research-grade data transfer service designed for large-scale scientific workflows. Critically, Globus operates over the AARNet research and education network, which provides the high-speed connectivity required for rapid, reliable transfers across sites.

“What stood out with Globus was how straightforward it was to get going,” said Justin Lee, Platform Developer and System Administrator at Australian BioCommons. “The documentation AARNet provided made it easy to deploy, and once set up, it just worked. We didn’t need to manage every detail as it handled the complexity for us.”

Setting up endpoints and running the transfer

AARNet provided setup guides and workshop resources to assist with deployment. Working from these materials, Justin was able to spin up the required Globus endpoints in less than a day — one at Pawsey, where Apollo had been running, and the other at the new AARNet-hosted Nectar Research Cloud node, where Apollo would be hosted going forward.

After a successful test transfer, the full migration began the week ahead of the Easter holiday period. With Globus managing the transfer, the system automatically handled retries, integrity checks, and restarts.

By the time teams returned after Easter, the entire 15 TB of data had been moved, smoothly, securely, and without interruption.

Supporting research continuity through reliable infrastructure

For researchers using the Australian Apollo Service, no changes were needed to how they interacted with their environments. Once the transition was complete, data access resumed smoothly and workflows continued as before.

“From our perspective, it was great to see how quickly the BioCommons team could get up and running with Globus using the self-service resources,” said Greg D'Arcy, Digital Research Product Manager at AARNet. “It shows how institutions can take ownership of complex transfers without needing deep expertise, especially when time is limited.”

“It all worked as expected,” added Justin. “Having reliable tools and a clear setup process made the whole migration straightforward.”

Building resilience for life sciences research

This successful migration showcases the value of collaborative partnerships and purpose-built infrastructure in enabling modern, data-driven research. By leveraging Globus and the AARNet research network, BioCommons ensured that life science researchers could continue their work without missing a beat, even during a significant infrastructure shift.

The Australian Apollo Service forms part of the national Australian BioCommons infrastructure. BioCommons partners with QCIF to manage the Australian Apollo Service, which is underpinned by computational resources provided by AARNet’s ARDC Nectar Research Cloud node. These efforts are supported by funding from Bioplatforms Australia and the Queensland Government RICF. Bioplatforms is enabled by NCRIS.

An Australian community for computational structural biology

The active new community is receiving support from a range of partners and advocates, including L-R Johan Gustafsson (BioCommons), Steven Manos (BioCommons), Kate Michie (UNSW) and Andrew Gilbert (Bioplatforms Australia)

The explosion of possibilities presented by deep learning approaches in structural biology research has created many new opportunities and challenges. A passionate group of structural biologists has formed the Australian Structural Biology Computing Community, to approach this new era as part of a community that shares computational knowledge, methods, and resources. 

This community-driven approach brings together a diverse group of people, with initial contributions forming around leads from the Structural Biology Facility at UNSW, and an academic panel of experts from Monash University, Walter and Eliza Hall Institute of Medical Research (WEHI), University of Western Australia (UWA), Australian National University (ANU), Bio21 Institute of Molecular Science and Biotechnology (Bio21), University of Melbourne, La Trobe University, University of Queensland (UQ) - IMB, University of Sydney, Griffith University, Swinburne University of Technology, CSIRO, and the University of Adelaide. Anyone involved in structural biology in Australia is invited to join and there are lots of different ways to get involved.

The Community for Structural Biology Computing in Australia webpage is a useful new resource for all users of computing for structural biology research in Australia. The page is constantly evolving and expanding, and it currently focuses on the use of deep learning methods in Structural Biology. It includes practical guides on topics like “Best practices for presenting and sharing AlphaFold models in a paper” as well as news items and announcements for relevant courses and meetings. 

Australian BioCommons supports the community by hosting quarterly online meetings that aim to tease out how computational structural biologists’ challenges might be addressed with community-scale responses and national research infrastructure solutions. If you join the mailing list via the community webpage, you will receive updates and invitations to community meetings and the discussions in Slack.

BioCommons began providing broad, fully subsidised, access to structural prediction in 2022 by making AlphaFold2 available within its Galaxy Australia service. The Australian AlphaFold2 Service provides both an easy-to-use interface and dedicated GPUs to Australian researchers. When BioCommons hosted the international 2023 Galaxy Community Conference, the keynote speech by Chief Scientist of the Structural Biology Factility at UNSW, Kate Michie, generated much excitement around forming an Australian community of practice for computational structural biology as an avenue for collectively addressing the challenges presented by deep learning in structural biology. 

BioCommons has supported key research stakeholders to refine the new community’s purpose, began running quarterly community meetings, and helped to establish the shared community spaces like the Australian Structural Biology Computing website and GitHub. As well as facilitating consultations with infrastructure partners and the broader computational infrastructure community, a group of national panel of experts has been identified. 

This community collaborates with their peers to:

• Collectively create and maintain community forums and centralised collaboration platforms to support collaboration and knowledge sharing (i.e. methods and documentation);

• Foster collaboration between structural biologists, computer scientists, and data scientists, thereby creating interdisciplinary teams to help tackle complex challenges, validate results and ensure robust applications of deep learning methods;

• Lead the review, prioritisation, testing, optimisation, and sharing of deep learning codes, software and approaches that are of broad relevance and interest to the Australian research community;

• Develop quality assessment tools to help evaluate the quality of calculated structures, and help guide researchers towards reliable predictions; and,

• Address the ethical implications of AI-driven structural predictions, as well as discuss transparency, bias and interpretability to ensure responsible use of these technologies.

The Australian Structural Biology Community is poised to tackle a set of pilot activities aimed at fast tracking a national response to the challenges facing computational approaches in structural biology. A much anticipated future output is an infrastructure roadmap document that will formalise and describe the high level requirements of the community. This collaborative effort between the new Australian Structural Biology Community, Australian BioCommons, and BioCommons infrastructure partners will support the Australian Structural Biology community as new needs arise relating to bioinformatics tools, software, infrastructure or training.

Keep in touch by subscribing for updates at the Community for Structural Biology Computing in Australia webpage. 

Join a Metagenome Assembled Genomes hackathon

The Optimising Metagenome Assembled Genomes building workflows hackathon is taking place in October and we want to know if you’d like to join!

Multiple ELIXIR nodes and the international Galaxy community are coming together in Europe to participate, and BioCommons is planning to offer a complementary event in Australia.

What is this?

Hackathons involve collaborative group work with people outside your normal network, solving problems around a shared topic of interest within a limited period of time. The aims of the event are:

• Enhancing FAIR MAGs building Workflows

• Developing user-friendly training materials

• Advancing workflow evaluation methods (using CAMI infrastructure & real data)

• Building intelligent computational resource estimation tools

The event takes place 6-9 Oct 2025. It will run in person in Freiburg, Germany and online.  If there is enough interest, BioCommons will organise an in-person event in Australia to overlap with the European event.

What’s in it for me?

• Collaborative group work: You'll work with people outside your usual network.

• Expert connections: You'll connect with a national and international group of experts and enthusiasts.

• Workflow enhancement: You'll contribute to enhancing MAG workflows.

• Training material development: You'll participate in developing related training materials.

• Skill development: While specific skills are not required, you can enhance your knowledge of microbiome data analysis or MAGs.

• International participation: Opportunity to participate in an international hackathon with colleagues in Europe.

Who can join in?

It is open to anyone who wants to build MAGs or anyone with a general interest in MAGs, microbiome analysis and the associated training to run MAG workflows. To join in the hackathon, some knowledge of microbiome data analysis or MAGs is preferred. There is no cost to join.

How would this work?

Australian BioCommons regularly run satellite events that facilitate participation in global hackathons. If there is interest, we would ideally work together in person in Australia. Given European business hours coincide with Australian evenings, we would connect with the European hackathon team during some overlapping hours in the afternoon and work asynchronously for the other hours.

Are you interested in joining in?

If you think that you might be interested to join in this hackathon event, please get in touch with Tiff Nelson by 20th June 2025.

Repurposed hardware boosts national capacity and powers innovation

This story is co-published with QCIF Ltd

After successfully completing a previous project, QCIF Ltd made available high-performance hardware to the Australian BioCommons, giving the hardware a second life in enabling research and uplifting national capacity for the benefit of the scientific community. 

Well suited for running AlphaFold 2 jobs, the five General-Purpose Graphics Processing Units (GPGPUs) are now being used to enhance the national compute network behind the Galaxy Australia service.

The impact of this repurposing goes beyond infrastructure improvements. It has significantly expanded Galaxy Australia's capacity to support research and innovation by enabling the use of other GPU-enabled tools that offer major benefits to the scientific community. GPU processing can provide massive improvements in computational efficiency, decreasing processing times to less than 5% of conventional equivalents.

Dr Cameron Hyde, a bioinformatician at QCIF who supports the development of national software platforms like Australian BioCommons' Galaxy and Apollo services, co-authored the original AlphaFold 2 wrapper that enabled the tool to run within Galaxy Australia, ensuring both a friendly user-interface as well as instant access to the GPU clusters required to power the tool. He shared his enthusiasm for the new possibilities unlocked by the repurposed hardware which was originally part of an investment made in 2021 by the Australian Research Data Commons (ARDC) to support national platform projects and now directly enhances the bioinformatics services he helps deliver to Australian researchers. “Now that we have five GPU nodes of our own, we have room to experiment and explore new GPU-enabled tools. This gives us room to innovate beyond AlphaFold and accelerate scientific discovery in other research domains.”

For example, Galaxy Australia’s lead Bioinformatician Michael Thang has been using the hardware to explore running Nanopore’s “Dorado” on Galaxy Australia. Dorado is a high-performance basecaller for Oxford Nanopore Technology sequencing data. This innovation would enable researchers to conduct their entire analysis, from raw sequencing data through to assembled genome, all within the Galaxy Australia service.

Collaboration driving innovation

Developed by Google DeepMind, AlphaFold is an AI system that predicts a protein’s 3D structure from its amino acid sequence with accuracy comparable to experimental methods. In 2020, Australian BioCommons identified an opportunity to democratise access to this powerful tool by making AlphaFold 2 available through Galaxy Australia. This gave Australian researchers much greater accessibility to AlphaFold 2, allowing life scientists to easily visualise proteins in a manner inaccessible to all but dedicated structural biology researchers. This advance has supported research into protein-protein interactions, activation and inhibition mechanisms, and drug design.

By 2025, use of AlphaFold 2 has surged, evolving from an analytical tool for individual proteins into a routine screening tool for studying protein-protein interactions. To support this shift, Dr Hyde collaborated closely with Australian Structural Biology Computing Community to develop extensions to the AlphaFold Galaxy tool, including new output formats, input parameters, and an option to re-use intermediate files for improved efficiency.

Supported by the Australian BioCommons, AARNnet, QCIF Ltd, and The University of Melbourne, the optimised system now provides fully subsidised access for all Australian researchers via the Australian Alphafold Service. We extend our sincere thanks to the Australian Research Data Commons (ARDC) for providing the hardware to QCIF Ltd and enabling its reuse by Australian BioCommons.

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.

Microbiology Lab empowers microbial data analysis with integrated tools, workflows and compute

Galaxy Australia’s Microbiology Lab is now providing researchers with rapid access to popular tools, workflows and compute for analysis and visualisation of microbiomes and omics data from microbial isolates.

Development of this curated view of Galaxy Australia was driven by the international microbial research community who identified the most commonly used tools in the field through meticulous research, surveys and community consultations.

The Lab integrates more than 220 tools and 65 workflows with step-by-step tutorials and structured learning paths for a suite of different analyses. Microbiology Lab pairs perfectly with the computing power of Galaxy Australia, which is underpinned by computational resources provided by AARNet, ARDC Nectar Research Cloud, the University of Melbourne, QCIF, Pawsey Supercomputing Research Centre, National Computational Infrastructure, and Microsoft Azure. From raw data, to differential analysis, visualisation and assembly, Microbiology Lab makes it easy to get started with reproducible analysis of microbial data.

Galaxy Australia’s Microbiology Lab is the latest release in a series of Labs supporting research domains. It represents an important step forward in Australian BioCommons activities to support Australian microbial research. The Microbiome Analysis Infrastructure Roadmap for Australia identified a need to implement a shared platform that eases access to preferred tools and workflows for analysis of microbial data with sufficient computational power. This fully-subsidised resource is expected to improve efficiency for researchers.

If you are an Australian researcher with an interest in microbial isolates and microbiomes, be sure to take a tour of the Galaxy Australia Microbiology Lab and try it out now!