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.

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.

Phylogenetics collaboration takes researchers back to basics with new training

Charles Darwin's first sketch of an evolutionary tree. Source: Wikimedia commons

A new online tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

Using real-life data, and tools available in Galaxy and SplitsTree, the tutorial demonstrates the principles behind a variety of methods used to estimate phylogenetic trees from aligned sequence data or distance data. With a conversational style Michael discusses why phylogenetics is important, unpicks phylogenetics terminology from the roots to the tips and explains concepts such as multiple sequence alignment, how alignments are used to build trees, and phylogenetic networks.

Having the materials readily available online is already bringing benefits to Michael’s teaching at the University of Tasmania.

“Having the materials online with exercises in Galaxy is just fantastic for my university teaching. It means that students don’t have to take notes and frees them up to engage more deeply in class. Once they understand the concepts they can easily try out basic phylogenetic analyses and see how the tools work without needing to know how to code. ” - Professor Michael Charleston, University of Tasmania

Michael first created the concept of a workshop that explained the principles behind building phylogenetic trees in 2019 when experts from around Australia came together to consult on his materials ahead of a national workshop. Rather than providing an introduction to the topic, mathematician Michael’s deeper explanations of the underlying theories for people already creating phylogenetic trees found a unique niche. After amassing 24,000 views on the BioCommons YouTube channel, the need for an updated standalone tutorial was obvious. 

Michael worked closely with the BioCommons training team over the last year and a half to develop this tutorial by tailoring and refreshing the materials and activities for the self-contained and easy to use Galaxy platform. This activity is part of the BioCommons’ commitment to making our training materials FAIR.

Try out the Phylogenetics: back to basics tutorial in the Galaxy Training Network.

Or if you prefer live training, join us for a workshop based on the tutorial in July.

Training with real-world genetic data to advance Australia’s urgent conservation goals

Katarina (right) working closely with Mikaeylah (left).

A diverse group of researchers converged at The University of Melbourne this month to work through their unique bioinformatics challenges under the guidance of The University of Auckland’s Dr Katarina Stuart. The genetic outlier analysis workshop invited participants to bring along their own datasets to analyse over two days. Working with real-world data offered attendees the opportunity to apply new techniques in their field, learn how methods may need to be tweaked, and importantly progress their research.

Mikaeylah Davidson, a PhD Candidate in the Faculty of Science’s One Health Research Group at The University of Melbourne, relished the opportunity to bring her own data: 

Being able to engage with the data I'm actively working on was incredibly beneficial, as it provided me with the chance to seek assistance in troubleshooting issues I am currently encountering, as well as gaining insight into recurring challenges and how to address them effectively. This hands-on approach was incredibly helpful.

Mikaeylah’s research explores the potential of selective breeding as a tool to combat wildlife disease. While selective breeding has been used extensively for genetic improvement in domesticated animals, its application in conservation remains largely unexplored. Mikaeylah’s PhD is focused on the Southern Corroboree frog, which is critically endangered due to the introduction and spread of the deadly amphibian chytrid fungus. 

Aiming to leverage the existing conservation breeding program based within the zoos, she hopes to identify phenotypic and genetic traits associated with resistance to the chytrid fungus. If successful, this could pave the way for the implementation of a selective breeding program aimed at reducing detrimental alleles and amplifying beneficial ones within the population. Ultimately, the goal is to breed Southern Corroboree frogs that have a heightened tolerance to the fungus, enabling their survival in the wild despite the presence of chytrid.

The highly practical workshop stepped through the use of command line programs, while providing the opportunity to ask questions of their use, functions and applicability. Multiple genetic outlier analysis methods were explored while learning how and when different methods should be used. The pros and cons of different methods helped explain which are best suited to different data types. This type of information can be very difficult to find without experience, or many hours of working though various software and protocols, according to Elliott Schmidt, a PhD Candidate from James Cook University: 

I believe that this workshop has saved me many hours of troubleshooting my genetic outlier analysis. Coming away from the workshop with example scripts composed using my own data has given me confidence that my approach to analysing my data is appropriate and efficient, and can now be completed independently.

Elliott flew down from Townsville to progress his research into how evolutionary perspectives can be incorporated in conservation of a coral reef fish. His PhD project explores how different populations of a coral reef damselfish, Acanthochromis polyacanthus, distributed across the Great Barrier Reef may respond differently to warming ocean temperatures. He’s tackling this question by investigating local adaptation, differences in developmental plasticity, and population genetics. By incorporating physiological experiments with population genetics Elliott hopes to identify potential differences in vulnerability to warming temperatures between different populations as well as provide explanations for these differences via genetic analysis.

Hearing about the challenges faced by researchers working with different datasets was a highlight, and many of the 11 participants reported valuing the opportunity to engage in discussions with peers. Working intensively with their expert trainer and each other’s data, their ability to query and interpret varied datasets was honed. Mikaeylah particularly enjoyed the highly interactive elements:

Working through our real data enabled me to further my understanding of my own, while also offering insights into the challenges others face with their datasets. I found the exchanges on results interpretation very helpful, and also interesting, as they allowed me to learn how to interpret diverse datasets and troubleshoot different issues which may arise.

This workshop was part of a series of events made available through a collaboration between the Genetics Society of AustralAsia (GSA) and Australian BioCommons. There was also an online genetic outlier analysis workshop held in February, and another in person workshop will be held this July in conjunction with the GSA2024 Conference in Sydney. The workshops were supported by GSA’s Workshop Support Program that aims to help share knowledge and/or exchange ideas across genetics.

More information on the next hands-on workshop: Genetic outlier analysis (Sydney).

From corals to the classroom: an interview with Dr Ashley Dungan

It can be a struggle to keep up with the latest bioinformatics tools. Researchers have diverse needs and limited time to shop around for new techniques to analyse their data, let alone troubleshoot a new platform. What better way is there to learn a new approach than from researchers actively using useful tools in their own work? BioCommons collaborates with experts to deliver training workshops that help researchers glean insights and practical tips directly from their peers.

Dr Ashley Dungan, Research Fellow at The University of Melbourne, worked with BioCommons to train researchers from 22 different Australian institutes and organisations to use the bioinformatics platform, Quantitative Insights Into Microbial Ecology 2 (QIIME 2). Ashley originally developed the workshop for a local audience, alongside Melbourne Bioinformatics staff Dr Gayle Philip and Dr Vicky Perreau. Given the success of this all women team, BioCommons was keen to assist them to bring the training to a national audience. You can read about the impact of that training in our related story.

We interviewed Ashley to find out more about her research and why she chose to work with the National Bioinformatics Training Cooperative to uplift the skills of fellow researchers. 

Ashley, can you tell us a little bit about your research?

I’m a Research Fellow in conservation microbial ecology. Broadly, I’m interested in the functions of bacteria in a range of systems with the end goal of manipulating those communities to achieve a better outcome for the host/system. To put this in the context of conservation, I’m interested in protecting our biodiversity and preventing the loss of species and ecosystems by providing animals with beneficial bacteria, or probiotics. So far, most of my research has been in coral-associated bacteria. 

What motivates you to provide training to other researchers?

I didn’t start off my scientific career as a microbiologist. When I joined my PhD program, the focus was on coral probiotics and I was daunted by the prospect of having to do any bioinformatics. I found that most training resources were written by experts in a language that was really only available to other experts. Where was the dummies guide? Other resources were hidden behind a paywall or required attendance somewhere in Europe or North America. The training I was able to attend wasn’t immediately useful to me, or I’d have to fully rewrite the code (which I wasn’t skilled enough to do). 

I was lucky that a fellow PhD student at the time (Dr Leon Hartman, who now works at the Walter and Eliza Hall Institute of Medical Research) walked me through everything and gave me lots of code. But the reality is that most students/scientists won’t have this type of resource. So I wanted to come up with a training solution that:

• Was written for biologists by biologists, avoiding computer science jargon wherever possible

• Was free

• Could be attended in-person, virtual, or do it yourself

• Where attendees could immediately run the code for their own use.

What’s the best part of training other researchers?

Data analysis isn’t easy but when you can see a community of like-minded people together, that’s powerful. There is nothing more satisfying than giving people the confidence to incorporate new techniques and ask new questions in their research. I’m proud of the team that put this together – it really wouldn’t have happened without Gayle and Vicky. And how cool is it that we are women doing microbiology and bioinformatics! The odds of that happening, even in 2024, in a bioinformatics workshop are still exceedingly low but we are committed to breaking down barriers for women in science.

How did you scale your training to a national audience?

Gayle and Vicky helped me create the QIIME 2 workshop that we ran locally for University of Melbourne participants. But we wanted to bring this training to all Australian researchers, and ensure that anyone could attend virtually. I worked closely with Dr Melissa Burke (Training and Communications Officer at BioCommons) to adapt the workshop to ensure it was fully accessible online. Melissa then coordinated a half-day workshop where we had 45 participants from 22 different institutes/organisations around the country join us, including 60% who identified as female or non-binary. Working with Melissa and the National Bioinformatics Training Cooperative was a fantastic experience and I highly recommend that others interested in providing bioinformatics training get involved.

What’s next for you?

I’ve now trained Laura Geissler (my PhD student) to run the QIIME 2 workshops and she will take over the sessions hosted by Melbourne Bioinformatics. Looking ahead, all my fellowship applications now include creating a new workshop alongside doing primary research. First up, I’d like to create workshops focused on whole genome assemblies and metagenomics.

You can learn more about the BioCommons national training program on our website, or read how Ashley’s QIIME2 training led to an Australian first in respiratory disease research.

New online tutorials embed genomics into conservation management decisions

Photo credits: Left Kate Quigley, centre Nick Bradsworth, right Carolyn Hogg.

A new online course is available that promises to increase the use of genetic data in Australian conservation management actions. Developed by the Threatened Species Initiative (TSI) and the University of Sydney in collaboration with some of Australia’s leading conservation geneticists, the tutorials have been made freely available to everyone via the Australian BioCommons YouTube Channel.

Genetics and genomics are powerful tools for understanding global biodiversity, with a wide range of applications for policy, ecology, translocations, evolutionary biology and more. The Conservation Genomics for Threatened Species Management course was developed by TSI, which brings a network of researchers into direct contact with conservation agencies and policy makers, enabling research outcomes to directly influence on the ground conservation decisions. As one of Bioplatforms Australia’s key Framework Initiatives, TSI reached out to BioCommons for support to edit and host their community’s content.  Prof Carolyn Hogg, Senior Research Manager, Australasian Wildlife Genomics Group at the University of Sydney, and Science Lead and Chair of TSI, brought together a panel of field experts to explain how cutting-edge genomics technologies, genetic tools and advanced computational biology can assist and guide conservation management strategies.

The inaugural @ThreatenedSpGen workshop on using genetics for conservation management was a hit! A great group of people from all over, really engaged in upskilling their genetic literacy. #ictc23 @ellemclennan @persoonia @BioplatformsAus @Sydney_Science @Science_DBCA pic.twitter.com/zumixBBW1p

— Prof Carolyn Hogg (@HoggCarolyn) November 12, 2023

The ten modules can be viewed independently, and the course materials have already been used at a workshop during the 2023 International Conservation Translocation Conference. The suite of videos will be added to over time, but so far feature speakers from the University of Sydney, Monash University, University of Adelaide, Australian National University, Minderoo Foundation, Arthur Rylah Institute for Environmental Research, Research Centre for Ecosystem Resilience at the Botanic Gardens Sydney, Taronga Conservation Society Australia, NSW Government Savings our Species program, and the Government of Western Australia Department of Environment and Conservation. 

You can learn more from Carolyn about how TSI is bridging the gap between genomicists, bioinformaticians, conservation experts and decision makers to help save Australian species by visiting the refreshed TSI website. Or watch her BioCommons webinar ‘Conservation genomics in the Age of Extinction’, to learn more about using cutting-edge genomics technology and advanced computational biology to assist in conservation management for species recovery.

View the Conservation Genomics for Threatened Species Management playlist

Students investigate beetle genetic variation using new Apollo training instance

Teaching genetics is easier and more effective now that a powerful online tool is being made available to Australian researchers and trainers. Students can use a tailored training instance of the web-browser accessible system, Apollo, for real-time collaborative curation and editing of genome annotations.

This new feature of the Australian Apollo Service allows trainers to focus on teaching genome annotation curation, without being burdened by installation and maintenance of Apollo. All the hosting and system administration of customised Apollo instances is taken care of for service users. Life scientists and research consortia based in Australia can apply for an instance that is ready-made for training, and is up to date with the latest release of the software. 

Molecular evolution and population genetics researcher, Assoc Prof Charles Robin signed on to the Australian BioCommons’ Apollo service through a recommendation from a colleague at Melbourne Bioinformatics. After facilitating some Australian BioCommons online workshops, Charles now uses an Apollo training instance when teaching genetics to third year undergraduates at the University of Melbourne. Each student is provided with their own login where they can visualise DNA sequences, perform annotations and explore without overwriting each others’ work. Charles finds Apollo ideal for teaching:

“It’s great that the transcriptome maps really well to the genome. By playing within Apollo, students get to see the AC / GT rule and how this can be reinforced by the transcript. Things like alternate splicing are also easily visualised.”

Two adult beetles, one with a CRISPR deletion in the gene called cardinal that is involved in eye colour. The genetic modifications were performed in Charles’ lab.

The class answers research questions like ‘which of the genes in this region includes this particular mutation?’ or ‘how do you find the candidate gene in this region?’ using real world data from a beetle with a gene mutation. Charles deliberately chooses genomes that are ‘untidy’:

“You want a non-model genome to identify gaps and changes. Students can have an expectation that all annotations on a genome are true, and using Apollo allows them to see that this is not the case.”

Charles rates the reliability of the software as a key factor in why he uses Apollo for teaching genetics:

“So much software gets left without regular updates and from year to year you realise that it isn’t maintained or updated. So we look for things that are stable - this is the reason we call on the Australian Apollo Service.”

Using Apollo to curate genome annotations

The Australian Apollo Service performs all system administration, build and deployment of the instance on behalf of users, with support provided through a help desk, user documentation and training events. The deployment of a full technology stack, long term hosting of data, maintenance updates and security are all covered, providing customised, local instances of the Apollo software for individual genome projects or training. 

Australian BioCommons are working with Apollo project principal investigator Prof Ian Holmes to understand researchers’ needs within Apollo, with an aim to provide improved annotation and visualisation features for genome annotation research.

Launch Apollo to learn more

Australian BioCommons delivers collaborative distributed infrastructure to enable life science research. BioCommons partner QCIF is offering the Apollo Portal service, and it is underpinned by computational resources provided by the Pawsey Supercomputing Research Centre. These efforts are supported by funding from Bioplatforms Australia (BPA) and Australian Research Data Commons (ARDC). BPA and ARDC are enabled by NCRIS.

BioCommons supports the creation of specialist training with Genomics for Australian Plants

Australian BioCommons partners broadly in our efforts to drive coordinated solutions to life science researchers’ problems. We connect the appropriate large organisations, small facilities, collaborative initiatives and individual experts to solve community-scale challenges. This means we’re well placed to hear about new resources and help to bring training opportunities to fruition. 

Genomics for Australian Plants (GAP) is developing genomics resources to enhance our understanding of the evolution and conservation of the unique Australian flora. Established in 2018, the Australian State and National Herbaria and Botanic Gardens came together with Bioplatforms Australia to form the GAP initiative that has flourished as an active national consortium of researchers and expert working groups.

One of GAP’s goals is to build capacity in the management and application of genomic data and to provide tools to enable genomic data to be used to identify and classify biodiversity at a range of scales. Bringing together staff from Royal Botanic Gardens Victoria, CSIRO’s Centre for Australian National Biodiversity Research (Canberra) and Australian Tropical Herbarium (Cairns), Bioplatforms Australia and Australian BioCommons, GAP’s phylogenomics-bioinformatics working group has combined newly developed and existing scripts into an integrated workflow for the assembly of target capture data. 

Keen to share these resources with researchers who can use them, the group has been working with BioCommons to offer a series of events to train others in using these novel pipelines. Theoretical webinars and hands-on training workshops will be delivered virtually in conjunction with the upcoming Australasian Systematic Botany Society Conference.

BioCommons offered advice on how to train others in what we’ve built: what was possible to run live, which computational environment would work best and the practicalities of leading a group through hands-on learning exercises. With their support we’ve been able to focus on our strengths like making sure the pipelines, data and technical information are spot on.

- Lalita Simpson, Research Community Project Manager,
Genomics for Australian Plants - Phylogenomics Project.

Introductory overviews of the challenges of conflict within target capture datasets and strategies to employ during analysis will be delivered as short public webinars:

• Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation (20 May)

• Detection of and phasing of hybrid accessions in a target capture dataset (10 June)

For participants who would like to take the next step, a series of three interactive in-depth workshops will be delivered as part of the ASBS conference. The analysing target capture datasets workshops are suited to researchers analysing target capture datasets and will provide hands-on training in the use of workflows covering the processing of raw sequence reads, as well as strategies for resolving paralogy and hybridisation. 

• GAP phylogenomics bioinformatic pipeline – Part 1: Assembly of raw reads using HybPiper (6 July)

• GAP phylogenomics bioinformatic pipeline – Part 2: Yang and Smith paralogy resolution (7 July)

• HybPhaser – Detection and phasing of hybrid accessions in a target capture dataset (8 July)

Further information and registration details are available on the ASBS2021 conference website.