Cancer researchers level up their high performance computing

Researchers investigating cancer evolution and treatment resistance have successfully leveraged the Australian BioCommons Leadership Share (ABLeS) program to expand their high-performance computing (HPC) capabilities.

A group within the Computational Biology Program at Peter MacCallum Cancer Centre, led by Dr Anna Trigos, were offered guidance and access to national HPC resources through ABLeS. The Trigos Lab was supported to begin utilising the Pawsey Supercomputing Research Centre which significantly enhanced the lab's computational prowess.

The ABLeS experience helped the researchers to gain proficiency working portably across multiple large HPC environments, including a better understanding of the differences between their on-premise HPC and Pawsey’s Setonix, different scratch storage limitations, the portability and reproducibly benefits of setting up and utilising containers and Conda on HPC, as well as improving data management skills.

Members of the Trigos Lab Research group

The work served as a crucial feasibility study, providing insights that paved the way for the Trigos Lab to formally integrate external HPC resources into their research workflows. It also provided a vital head start for success in the competitive National Computational Merit Allocation Scheme.

Anna explained, “My team could demonstrate they could set up, test, benchmark, and optimise Nextflow pipelines critical for ongoing data processing. This experience put us in the right position to submit our first application for national compute, which was successful.”

Sharing her experiences with other ABLeS participants at the recent ABLeS User Meeting, Anna was happy to report the success of her Honours student David Le, whose analysis and simulation of 3D spatial cancer tissue data benefited greatly from the increased computational power.

The Trigos Lab focuses on understanding treatment resistance and response through the lens of both cancer evolution and ecosystems. While their primary focus is on multiple myeloma and prostate cancer, they also apply their methods to other cancers. They utilise omics data, including genomics, transcriptomics, epigenomics, and single-cell data, as well as patient imaging. Their methodology incorporates bioinformatics, computational biology, engineering, statistics, deep learning, and now HPC.

Learn more about Anna Trigos’ Multi-omic Evolution and Ecosystems Lab

Learn more about the Australian BioCommons Leadership Share (ABLeS)

DAWN of a new era for international wheat research

The enduring management of valuable genomics data can be a challenge as time goes on. The Diversity Among Wheat geNomes (DAWN) resource continues to yield valuable insights into the diversity among wheat genomes years after its initial creation, and is hosted on the Australian Apollo Service to ensure sustained and stable access for the international wheat research community.

DAWN supports the exploration of the genetics of wheat strains by providing an accessible way to visualise and compare the Trictium aestivum (bread wheat) genomes and associated data, such as protein-coding regions (exome capture data) and gene expression (RNA-seq data) to further understand genetic diversity. Researchers importantly now have the capability of collaboratively annotating wheat genomes and editing their models using the Apollo software. 

The original developer of DAWN, Dr Nathan Watson-Haigh, supported the capability expansion from static visualisations to collaborative annotations and is pleased to see researchers making excellent use of the resource. Rudi Appels, Professor (Honorary), University of Melbourne, Research Fellow, AgriBio, Latrobe University, is leveraging both the Australian Apollo Service and DAWN to continually identify and update variable regions in the wheat genome.

Rudi has witnessed rapid advances over his years involved in the research of the large and complex wheat genome, overcoming challenges in sequencing, assembly and analysis. He reflects that new tools offer new opportunities for increased engagement amongst researchers, which in turn supports better research outputs.

“For the analysis of the large datasets that underpin wheat genomes, the Apollo software has provided the much needed support for biology-oriented researchers such as myself. The Apollo software speaks in a visual language that enables biologists to communicate with their bioinformatics colleagues at a level normally reserved for computational and bioinformatics experts. Real-time sharing is now feasible too, which allows communal activity during teaching or working with colleagues.”

The ability to collaboratively improve genome annotations using Apollo fast-tracks advances. Computer-generated gene models based on work from other organisms such as rice, barley and Arabidopsis can provide a first approximation of structure. Using Apollo, RNA transcript data can be easily integrated to edit missing sections of genes, correct naming of genes, amend intron-exon structure details, and investigate sections of the genome sequence not tackled by the automated methods.

Read more about DAWN, Rudi’s research, or Apollo, or apply for your own access to the fully-subsided Australian Apollo Service.

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.

Join the Australian Outpost of BioHackathon Europe 2025

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

This is a unique opportunity to participate in a significant global event and network with your international peers while working intensively on practical bioinformatics challenges. We will cover your costs when you come to Melbourne for the duration of ELIXIR’s BioHackathon: 3 Nov to 7 Nov 2025. Participation will work mostly within our business hours, plus catch up live in the early evening with the teams in Berlin. We always make it fun, and you’ll get to know others from around Australia while you learn new skills.

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

• Automatic workflow for benchmarking BUSCO genes for phylogenomics

• Streamlining FAIR Metadata for Biodiversity Genome Annotations

• Expanding the Benchmarking Landscape for Long-Read-Transcriptomics including Novel Datasets and Pipelines

• METRICS - Monitoring of Key Performance Indicators for ELIXIR Services

BioHackathon aims to:

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

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

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

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

Please submit your expression of interest to comms@biocommons.org.au by 5 Sep 2025.

Deep dive into international research infrastructure: insights from the ELIXIR All Hands Meeting in Greece

Dr Andrea Guzmán Mesa, ELIXIR International Relations Officer, meets with Conrad, Steven and Christina from BioCommons

Each year, BioCommons sends representatives to the ELIXIR All Hands Meeting, an event that brings together over 400 international peers. This attendance is a valuable outcome of the Collaboration Agreement between BioCommons and ELIXIR, which allows for the extension of knowledge-sharing opportunities.

ELIXIR is a life sciences infrastructure that shares many functional similarities and interests with BioCommons, but on a vast Europe-wide scale. It brings together a workforce from over 240 research institutes spread over 21 member countries. The opportunity to have deep discussions on research infrastructure topics and leverage the experience of this specialist workforce is shared around the BioCommons team each year.

This year Dr Christina Hall (Assoc Director - Training and Communications), Dr Steven Manos (Assoc Director - BioCloud) and Dr Conrad Leonard (Technical Lead, Human Genome Informatics) travelled to Thessaloniki, Greece, to participate. 

As the organiser of the Australian Outpost of the annual BioHackathon Europe, Christina was invited to lead a workshop on ‘Enriching the virtual biohackathon experience’, along with Eva Alloza from the Spanish National Bioinformatics Institute. The collaborative workshop sought to gather recommendations for practices to support virtual participation at hackathon-style events.

Invited speakers from the Health Data Research UK, Barcelona Supercomputing  Center (Spain), ELIXIR Germany, Center for Genomic Regulation (Spain), Chiba University (Japan), ELIXIR Hub, and Australian BioCommons, shared many examples of hacking events that welcome virtual participation. The outcomes will soon be shared as a ‘cheatsheet’ for project managers of the upcoming BioHackathon Europe to support better virtual experiences for participants including those joining from Australia.

Australian BioCommons was mentioned in many different contexts during various sessions of the three-day meeting. Christina presented BioCommons as an example of ELIXIR’s international impact and she also formed part of the training panel discussion ELIXIR training services: a roadmap towards 2028 and the EOSC context.

Steven’s key focus was the interaction between communities and platforms. He emphasised that "consulting with communities - groups with shared needs who converge around special interests - is invaluable because they sit in between research infrastructures and the rest of the world." An interesting observation shared at the meeting was that communities, while keenly aware of their domain's needs and standards, often don’t know what’s happening in other platforms and believe their challenges require unique platforms. This frequently contrasts with the views of platform developers, who tend to deliver generic solutions lacking the flexibility and extensibility that communities need.

The meeting's collaborative and positive atmosphere always fosters forward-thinking approaches to take back to our own circumstances. For instance, there were discussions about how the common tendency to break down problems and solve individual steps could be enhanced by a concerted effort to consolidate solutions into a cohesive package as a final step. Additionally, adopting common vocabulary, easier-to-understand language, and good documentation were acknowledged as crucial. Engaging more researcher champions to liaise with communities was also recognised as very important.

For Conrad, a dominant theme was data interoperability and federation, with multiple sessions highlighting streamlined data flow, service accessibility, and the importance of collaboration. Excellent examples of FAIR principles in practice were showcased across data, software, and training. Another significant focus was on the challenges associated with managing sensitive data. Updates on secure research data environments, legal frameworks, and trustworthy access and analysis were particularly informative. The evolving role of AI was a strong and broadly discussed theme.

Staying current in a broad range of research infrastructure topics is challenging, and directly supported by opportunities like participating in this annual ELIXIR meeting. It provided a valuable opportunity to connect with European peers, gain insights into a wide range of current activities, share our experiences, and engage in deep discussions on topics of mutual interest.

Read more about the meeting in ELIXIR’s news story.

Thousands join international Galaxy training events

The Galaxy platform is celebrating its 20th anniversary this year. This collaborative data analysis platform is widely used by scientists around the world, and underpins many computational biology services. Galaxy Australia is one of the core services BioCommons delivers, so naturally we provide lots of opportunities for researchers to engage with the team, community and tools.

The Galaxy Australia team recently supported the Singapore Biology League, who chose to incorporate Galaxy into their online collaborative biology contest for the first time. This massive event welcomed over 2000 pre-university students who formed teams to run 2054 tools on Galaxy Australia over 4 hours. It was a great opportunity to broaden participants’ exposure to biology and bioinformatics beyond the school curriculum.

The week-long Galaxy Training Academy attracted more than 3500 people from across the globe this year. Seventy three Australian researchers were amongst the international cohort joining from their homes and offices to work through tutorials, with support as they needed it. Live help was provided in our time zones by Galaxy Australia’s Dr Anna Syme, Dr Igor Makunin and Dr Tristan Reynolds, who fielded questions on a wide range of topics from fungal genomics to bat ecology! Participants brought their own specialities as they learned how to use the fully subsidised Galaxy Australia platform for proteomics, genome assembly, transcriptomics, single cell RNAseq, microbiome analysis, machine learning and more. 

In the lead up to the Galaxy Training Academy, BioCommons’ Dr Tiffanie Nelson and Galaxy Australia’s Dr Tristan Reynolds helped researchers understand what’s possible by presenting the webinar: No code, no problem: data analysis for biologists with Galaxy Australia. Examples included how Galaxy Australia is being used for biosecurity screening, foodborne pathogen detection and building reference genomes of the critically endangered swift parrot, as well as a tour of the practical features of Galaxy Australia that make sophisticated workflows like these accessible to all, regardless of their computational skills. 

Get started by exploring the tutorials available: Galaxy Training Network 
If you’re an existing Galaxy Australia user, improve your methods with our Top Tips videos

Key elements to unlocking deep learning for structural biology identified by the Australian research community

In an inspired demonstration of collaboration, the Australian Structural Biology Computing Community has come together to publish the Australian Structural Biology Deep-Learning Infrastructure Roadmap. Taking a holistic view, that includes the existing challenges, critical research bottlenecks, and looking forward to a potential national strategy, this new research infrastructure roadmap has been developed by the community, for the community. 

Enabled by advances in deep learning methods for protein structure prediction and de novo protein design, computational structural biology has rapidly emerged as a powerful technology driving innovation in both fundamental and translational science. The technology underpins breakthroughs in drug design, diagnostics, personalised medicine, and synthetic biology, though a limitation has been that effective use requires concentrated interdisciplinary expertise and access to specialised hardware.

To understand these challenges, the Australian Structural Biology Computing (ASBC) Community was formed and has come together to lead a national, collaborative approach. This community-driven initiative, partnered with Australian BioCommons, brings together a diverse group of experts from leading institutions around the country. Authors of the roadmap represent Structural Biology Facility, Mark Wainwright Analytical Centre at the University of New South Wales, Pawsey Supercomputing Research Centre, University of Queensland, Walter and Eliza Hall Institute of Medical Research (WEHI), the National Computational Infrastructure, Sydney Informatics Hub and the School of Medical Sciences at the University of Sydney, School of Biomedical Sciences at the University of Melbourne, and the Monash Biomedicine Discovery Institute at Monash University. 

The roadmap outlines key deliverables that will expedite the availability and accessibility of structural biology approaches to researchers nationwide: 

• A dedicated community space to foster collaboration and share best-practice recommendations for software deployments, benchmarking, validations and insights developed within the community. 

• Community training resources to on-board diverse stakeholders within the context of computational structural biology and strengthen the national impact of community expertise. For example, the Leveraging deep learning to design custom protein-binding proteins webinar series.

• National computational infrastructure built on increased hardware investment and a user platform to facilitate efficient, high-throughput utilisation of national computing resources and drive translational outcomes enabled by curated and validated computational structural biology technologies. 

• Alignment, integration and engagement with global best-practice efforts for computational structural biology infrastructure and research. 

A robust, sovereign capability in computational structural biology and protein design will position Australian universities, research institutes, and industry at the forefront of global innovation.

Read the Australian Structural Biology Deep-Learning Infrastructure Roadmap 

Join the Australian Structural Biology Computing Community 

Watch the Community’s webinar series Leveraging deep learning to design custom protein-binding proteins

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.