Galaxy Australia’s 10 millionth job relied on popular locally-developed tool

At any one time, there is a wide array of research being done using Galaxy Australia. When the ten millionth job was submitted to the service recently, it illuminated the importance of good bioinformatics software. The particular job was one of a bunch that analysed various pathogen samples for known antibiotic resistance genes.

Over the last 7 years, more than 40,000 users representing researchers, students, trainers and trainees have demonstrated the platform's versatility across a wide range of fields. This milestone job investigating antimicrobial resistance employed the ABRicate tool, authored by Australian bioinformatician Torsten Seemann. Further investigation showed that 490,507 jobs run on Galaxy Australia also used ABRicate in their workflows!

The University of Melbourne’s A/Prof Torsten Seemann is the Lead Bioinformatician at the Centre for Pathogen Genomics and the Director of Bioinformatics at Doherty Applied Microbial Genomics. As a world-renowned bioinformatician he has developed cutting edge analysis approaches to enhance the use of genomic data. Torsten has authored many popular software tools for the analysis of bacterial sequence data, particularly in the fields of public health and clinical microbiology. He is also a strong advocate for open-source software and open science.

He created ABRicate for the mass screening of assemblies for antimicrobial resistance and virulence genes. Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available antimicrobial resistance databases.

The name ‘ABRicate’ was chosen as the first 3 letters are a common acronym for ‘Anti-Biotic Resistance.’ The word also has the form of an English verb, which suggests the tool is actually taking action against the problem of antibiotic resistance, and it is uniqueit unique enough to be easily searchable. 

The tool is widely available to anyone who needs it, and can be found in many repositories. It is one of over 10,000 tools available in the Galaxy Toolshed. There is a tutorial available on the Galaxy Training Network which supports the use of this tool: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition. 

Torsten was recently awarded The Chan Zuckerberg Initiative’s Essential Open Source Software for Science grant for the development of another tool, Snippy. This open-source software tool was written to rapidly identify genetic differences between bacterial genome sequences, and work is underway to allow Snippy to support the latest genome sequencing technologies and viral and fungal pathogens too. 

In recognition of the ongoing important contributions that Torsten makes, an award was established in his name. The annual ABABCS ‘Torsten Seemann Outstanding Bioinformatics Software Developer Award’ (previously sponsored by the ARDC) recognises an outstanding EMCR bioinformatic software developer from the Australian community with a view to promoting further efforts to develop and share bioinformatics methodologies.

Are your essential tools available on Galaxy Australia? Request an installation by the Galaxy Australia team if there’s a tool you think should be made available for everyone to use. 

Nominate your favourite tool’s author for the Torsten Seemann Outstanding Bioinformatics Software Developer Award. 

Partners meet to start building the digital infrastructure needed for human genomics research though GUARDIANS

A diverse group came together, including special guest Dr Melissa Konopko from ELIXIR who is standing here with BioCommons’ Prof Bernie Pope.

Australian researchers are set to make significant strides in discovering, accessing, and analysing human genomics data. The first in-person meeting of a significant new collaboration brought together partners who are committed to implementing the Australian BioCommons’ GUARDIANS program.

The meeting in Sydney represented the start of two years of implementation work as part of the GUARDIANS mission to empower Australian researchers to easily and securely discover, access, analyse and use human genomics data across national infrastructure, using the latest tools and resources.

The project brings Australian BioCommons together with Australian Access Federation, Children's Cancer Institute / ZERO, Garvan Institute of Medical Research, National Computational Infrastructure (NCI), QIMR Berghofer Institute of Medical Research, University of Melbourne, and University of Sydney. The project builds on years of foundational work in the Human Genomes Platform Project which also included a funded program and contracted schedules of work with partners. 

This first GUARDIANS meeting helped to build a sense of shared purpose as the group established effective ways of working together across their diverse organisations. Explorations into the policies, processes, and technologies that will be required during the project were driven by the open exchange of ideas, and collaborative discussions on solutions to potential challenges.

Scientific Product Manager at ELIXIR, Dr Melissa Konopko, travelled from the UK to share her insights into the Genomic Data Infrastructure (GDI). There were many parallels to learn from this project which is enabling access to genomic and related phenotypic and clinical data across Europe through establishing a federated, sustainable and secure infrastructure to access the data. 

Explore how GUARDIANS is accelerating human genomics and related omics research in Australia through the development of world-class digital infrastructure.

Contact us if you’d like to learn more.

Productive connections in the global Nextflow community forged by co-working

A group of Nextflow enthusiasts will come together in Sydney to take part in the global nf-core hackathon in March. By hosting the first Australian satellite site, we hope to unlock new opportunities for both national and international collaboration.

The global nf-core community curates a set of open‑source analysis pipelines built using Nextflow and they connect regularly through in person and online events. For the first time, the international hackathon’s network of live sites is extending to Australia, with the Australian outpost of the 2025 nf-core hackathon facilitating participation during our waking hours across 24-26 Mar 2025. The group will work on a variety of projects including development of training materials and nf-core workflows alongside our five local Nextflow Ambassadors and their international colleagues.

BioCommons’ Product Manager, Bioinformatics Platforms, Dr Ziad Al Bkhetan is a Nextflow Ambassador who has experienced the value of forging strong relationships in the global Nexflow community. In his work leading the Australian Nextflow Seqera Service, Ziad identified that Proteinfold, an existing nf-core pipeline for Protein 3D Structure prediction, had great potential for Australian researchers. 

Ziad identified several ways to improve Proteinfold and connected with the original developers at the Centre for Genomic Regulation (CRG) in Spain, to reconfigure the workflow, add new features, and contribute the updates back to nf-core. Ziad’s demonstration of the new tool at the last Nextflow Summit created excitement in the Nextflow community. Seqera, the team behind Nexflow, was delighted that their community-driven approach is resulting in new tools being developed by people at the research interface. CRG was pleased to see that their contribution to the community facilitated a new working relationship between their Spanish biomedical research institute and Australian BioCommons. Ziad and the team from CRG will continue to work on their workflow at the nf-core hackathon, and welcome contributions from any other community members. 

We’re looking forward to connecting with the Seqera team and international peers at the nf-core hackathon to develop workflows and training materials  asynchronously. There is a growing list of projects being proposed and we can expect that the range will expand as teams around the world get to work.

Finding the right collaborator can fast track a project like nothing else, and specialist fields of research almost guarantee your perfect match will be on the other side of the world. We’ve already seen how strategic events can bring global developer communities together to forge valuable new relationships in the Nextflow community, and hope to catalyse more of these opportunities. 

Let us know if you are interested in joining the nf-core hackathon: Australian Outpost.

Addressing DNA sequencing data submission challenges at global scale: your invitation to learn from the experts

Data submission to international repositories is an essential task for researchers, but it can often come with challenges. A range of special events for Australian researchers will focus on streamlining the data submission processes for various data types, addressing common challenges, and providing best-practice guidance on interacting with the European Nucleotide Archive (ENA).

BioCommons is partnering with specialists from the ENA and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) to deliver a series of hands-on workshops and online community discussions to help Australian researchers share their valuable data. The ENA is committed to maximising the impact of the ENA platform, sequencing technology and data, and will travel to Australia to support local researchers' data submission and discuss our particular needs.

The two-week program in late March and early April will feature seven targeted workshops covering submission and retrieval workflows for specific data types (raw reads, assembled and annotated genomes, metagenome assembled genomes (MAGs) and environmental DNA (eDNA)). Three interactive online community discussions around the same themes round out the program and offer the opportunity for Australian researchers to share their experiences, challenges and potential solutions directly with international specialists from the ENA.  

ENA is a globally recognised open platform for the management, sharing, integration, archiving and dissemination of nucleotide sequence data. This comprehensive resource preserves the world’s public-domain output of sequence data and is an essential tool for many researchers, but sometimes people can struggle with using it. Given that submission of omics data and associated contextual metadata to global data repositories is considered best practice and is mandated by science publishers, we want to enable researchers to facilitate the long-term preservation, findability and reusability of their data.

This is a unique opportunity to gain invaluable insights and practical skills from leading experts in omics data management and submission. Whether you're a seasoned researcher or just starting out, these workshops and discussions will empower you to confidently navigate the complexities of data sharing. 

'Roundtable' Community Discussions: Challenges and solutions

01 - 03 Apr, 10:00-12:00 AEDT

Join our online 'Roundtable' Community Discussions with members of the ENA team. 

Each session will focus on a different theme: Genomics - genome annotations and assemblies, and pangenomes; MAGs - submitting MAGs at scale, and how to submit MAG data when there are gaps in the NCBI species taxonomy; and eDNA - recent changes enabling eDNA sequences to be more findable through submission to ENA. Register here for roundtables.

Hands-on Training workshops: Data submission and retrieval

25 Mar - 03 Apr, 13:00-16:00 AEDT 

Learn directly from the ENA team in a range of practical online training workshops to explain genome assembly and annotation, MAG and eDNA data submission and retrieval.

Our community consultations teased out some of the challenges faced by Australian-based researchers in the data submission process, and BioCommons published a set of recommendations to address them. One ambition of a range of ongoing activities around interfacing with international omics data repositories is to facilitate improvements by connecting the right people. 

The European Nucleotide Archive (ENA) is a Global Core Biodata Resource, an ELIXIR Core Data Resource and is hosted by EMBL-EBI. It is one of the three nodes of the International Nucleotide Sequence Database Collaboration (INSDC). 

INSDC is actively seeking additional members to enhance Global Participation.

Pawsey enables more flexible and scalable DNA analysis

This story about researchers accessing high performance computing via the Australian BioCommons Leadership Share (ABLeS) was first published by the Pawsey Supercomputing Research Centre.

Dr Hasindu Gamaarachchi and Bonson Wong, the researchers behind Slorado, the new open source software for nanopore sequencing basecalling on AMD GPUs. Credits UNSW Sydney

Researchers from UNSW Sydney and the Garvan Institute of Medical Research have developed Slorado, the first open-source software/library solution for nanopore sequencing basecalling on AMD Graphic Processing Units (GPUs). Using Setonix, Australia’s most powerful supercomputer at the Pawsey Supercomputing Research Centre, this development enables researchers worldwide to process nanopore sequencing data on any mainstream GPU hardware for the first time, expanding computational options for the global bioinformatics community.

Oxford Nanopore Technologies (ONT) sequencers generate time-series raw signals that need to be converted into DNA bases through a process called basecalling. While ONT’s Dorado software supports NVIDIA GPUs for this process, AMD GPUs are currently not supported.

Led by Dr Hasindu Gamaarachchi and PhD candidate Bonson Wong, the team has created a streamlined version of the industry-standard Dorado basecaller that removes previous hardware limitations while maintaining and in some cases increasing performance. This innovation allows researchers to utilise AMD GPUs, including those in Pawsey’s Setonix, Australia’s fastest and most energy-efficient research supercomputer, reducing processing times and wait periods for critical genomic research.

Pawsey CEO Mark Stickells underscored the impact of this development:
“Dr Gamaarachchi’s work highlights our mission to accelerate scientific discovery. Fast, efficient bioinformatics is key to addressing challenges in medicine and biotechnology, from genomic analysis to drug discovery and personalised medicine. By enabling nanopore sequencing on Setonix’s AMD GPUs, we are breaking down computational barriers and empowering researchers with world-class tools,” Mark said.

“This collaboration demonstrates how state-of-the-art infrastructure can transform research workflows and broaden access to advanced computational tools.” He continued.

Dr Gamaarachchi and Bonson Wong shared their vision for Slorado:
”Our goal was to expand computational options for the bioinformatics community. By enabling basecalling on AMD GPUs and making the software fully open-source, we are empowering researchers to process their data more efficiently using both AMD and NVIDIA hardware.”

Slorado supports up to eight GPUs simultaneously on the same node, delivering unprecedented processing capabilities when combined with systems like Setonix. Researchers can now achieve faster results without enduring lengthy queue times, accelerating the pace of critical genomic discoveries.

The team access to Setonix has been supported via the Australian BioCommons Leadership Share (ABLeS).

To know more about Slorado, register for an online event on 18 Mar 2025:

Accelerating Nanopore Analysis: Introducing the new Open Source Slorado.

Interstate students converge in Melbourne to enhance their bioinformatics

AMSI BioInfoSummer offers a valuable opportunity each year to explore current bioinformatics research and developments. For the most recent conference, BioCommons helped make the experience more accessible to 18 students from around Australia by sponsoring travel grants.

Organised by the Australian Mathematical Sciences Institute, the conference was hosted by the ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems (MACSYS) and Melbourne Integrative Genomics (MIG) at the University of Melbourne.

As part of AMSI BioInfoSummer 2024’s well-rounded program, the ‘Emerging technologies’ theme included a ‘Hello Nextflow!’ workshop, presented by Australian BioCommons and our Sydney Informatics Hub Node at the University of Sydney.

Learn more about the outstanding recipients of our travel grant.

New bioinformatics pipeline for the identification and detection of viral genomes from Oxford Nanopore sequencing

An example output plot generated by the pipeline

Pathogenic viruses and viroids infecting plants can result in significant economic and ecological losses. In recent years, advances in Oxford Nanopore Technologies (ONT) have enabled real-time sequencing of long sequences through portable sequencers and thus offered a new avenue for plant virus diagnostics and research. A team from Queensland University of Technology (QUT) led by Assoc Prof Roberto Barrero and the Queensland Cyber Infrastructure Foundation (QCIF), have developed a new bioinformatics pipeline that facilitates the detection of viruses and viroids from both amplicon and metagenomic ONT data using different analytical strategies.

The pipeline called ONTViSc (ONT-based viral screening) can: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly map reads to a known reference. The pipeline is written in Nextflow, ensuring that it is reproducible, scalable, and can be run on a diverse set of compute infrastructures. It was written by Dr Maely Gauthier and tested by Dr Magda Antczak. 

The workflow was developed in consultation with both researchers and diagnosticians at the Australian Government’s Department of Agriculture, Fisheries and Forestry (DAFF) to understand how it would best cater to their needs based on their current and projected internal usage of ONT, as they transition some of their processes to the new technology. The pipeline has been validated with edge samples and helped resolve the complete genome of novel plant viruses.

The ONTViSc pipeline is now available for anyone to deploy or adapt through QUT’s GitHub repository, and the how-to guide is available within the Australian BioCommons How-to Hub. 

Magda utilised the Australian Nextflow Seqera Service to develop, optimise and run the ONTViSc pipeline, and spoke about the benefits of this fully subsidised service in December at the Australian Bioinformatics and Computational Biology Society (ABACBS) National Seminar Series.

The completion of this pipeline development has led to an independent nation-wide project aimed at transforming biosecurity diagnostics by making standardised bioinformatics workflows and interactive reports accessible to all DAFF biosecurity sites. The project, DNA to Decisions: Concise communication of genomics data for easier decision making is supported by a partnership between Australian BioCommons (as part of Workflow Commons), QCIF, QUT and DAFF.

Boosting genomic medicine in Sri Lanka

A group of Sri Lankan medical doctors, research lab workers and university students have just completed a hands-on bioinformatics training program using Galaxy to learn about genomics. Galaxy Australia team member, Dr Nuwan Goonasekera, joined an international panel of experts to deliver the workshop Bioinformatics for Genomic Medicine.

The US Embassy in Sri Lanka and Genelabs Medical offered the three week course to empower Sri Lankan genomics researchers to independently process and analyse DNA and RNA sequencing data. Participants gained the skills needed to identify clinically actionable mutations, helping to guide treatment plans based on patient data.

Dr Shurjo Sen from the NIH National Human Genome Research Institute (NHGRI) Office of Genomics Data Science requested Nuwan teach the 28 participants to use Galaxy in collaboration with the University of Colombo. The Galaxy Australia service underpinned the training while trainees were learning how to use Galaxy for sequence analysis and Nuwan made good use of Galaxy Australia’s Training Infrastructure as a Service (TIaaS). They also accessed the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) to learn cloud computing and variant interpretation techniques. Use of this cloud-based genomic data sharing and analysis platform, along with Galaxy, will empower these Sri Lankan genomics researchers to access and analyse large genomic datasets in a collective and collaborative way.

Researchers come together to tackle the bioinformatics of fungal genomics

Bioplatforms Australia brought together members of the Functional Fungi and Plant Pathogen Omics National Initiatives for a hands-on fungi bioinformatics workshop. Recognising that high throughput sequencing is the new normal for fungi research, hosts Prof Benjamin Schwessinger (Australian National University) and Dr Alistair McTaggart (Psymbiotika Lab) guided 38 researchers through theory sessions, hands-on practice, and real examples of applying bioinformatics to fungal research. Attendees were of diverse backgrounds  in commercial enterprise, academia, government research and citizen science.

Each theory session was followed by a hands-on demonstration using Galaxy Australia. For example, Dr Mareike Möller (ANU) led a theory session on fungal genome assembly covering key concepts such as why long reads are essential for assembling complete genomes, and why genome assembly is like tackling the world’s hardest jigsaw puzzle. This was followed by Dr Anna Syme’s demonstration of genome assembly on Galaxy Australia. Anna wrote six dedicated workflows for fungi, which are now publicly available for any Australian to reuse or adapt on Galaxy Australia. To access them, head to Public Workflows and filter by tag ‘fungi’. If you’re just getting started with workflows, watch Anna’s Top Tips for using Galaxy workflows.

Benjamin and Alistair ensured the workshop was directly relevant to real-world fungal and plant pathogen research. All demonstrations used fungi data shared by Alistair, plus Dr Tara Garrad and Dr Kelly Hill from the South Australian Research and Development Institute, which remains available in the Bioplatforms Australia Data Portal.

Workshop participants felt that the mix of hands-on and theory sessions was ideal; demystifying the technology and bringing clarity to the broad array of options available in Galaxy Australia. Workshop materials and metadata are available in the Australian BioCommons Training Materials Zenodo repository.

Helping the bioinformatics community harness the computing resources they need

Exploring GPUs with Sarah at the ABACBS Conference workshop

The challenges researchers face when accessing high performance computing was addressed at a recent workshop led by a national group of experts. More than 40 researchers and bioinformaticians explored strategies for the adoption, usage, and optimisation of Graphics Processing Units (GPUs) at ABACBS 2024 in December.

The workshop was co-ordinated by Dr Andrew Lonsdale (Peter MacCallum Cancer Centre), Dr Sarah Beecroft (Pawsey Supercomputing Research Centre) and Dr Johan Gustafsson (Australian BioCommons). It featured a wide range of speakers covering practical insights on resource availability, portable code that runs efficiently on multiple GPU platforms (NVIDIA, AMD, and Intel), and real-world use cases.

The availability of GPUs in the Australia context was introduced by Andrew Lonsdale (Peter Mac), and Georgie Samaha (BioCommons) offered practical guidance on accessing GPUs via national resources and access schemes. Sarah Beecroft (Pawsey) provided a concise introduction to high performance computing principles including GPU access, to ensure everyone shared similar foundational knowledge. George Bouras (University of Adelaide) then demonstrated how to integrate machine learning frameworks like PyTorch with the Slurm scheduler, while Edward Yang (WEHI) presented best practices for writing interoperable, maintainable GPU code.

Highlighting real-world applications, Keiran Rowell, Nathan Glades, and Josh Caley (UNSW Structural Biology Facility) showcased how GPUs are empowering researchers to handle large, complex structural biology datasets, and Wytamma Wirth (University of Melbourne) illustrated the power of online GPU resources to accelerate in Bayesian phylogenetics analyses.

Feedback showed that attendees appreciated the variety of speakers and the balance of technical depth with practical applicability. They particularly highlighted the workshop’s interactive approach, which included live polling and ample Q&A sessions.

Half of the attendees reported they were already using GPUs, and the other half planned to adopt them soon. Two-thirds were keen to integrate existing GPU-enabled bioinformatics tools, while one-third aimed to develop new GPU-accelerated algorithms, underscoring the community’s readiness to embrace GPUs both as a means of immediately accelerating current workflows, and as a basis for innovative tool development.

This workshop aimed to support researchers with the knowledge, skills, and resources they need to unlock the full potential of GPU computing, and participants reported that they were keen to go on to investigate GPU applications beyond AI/ML, gain deeper insights into GPU architectures, and participate in more hands-on training sessions.

Attending the ABACBS Conference is a great way to connect and strengthen the GPU-enabled bioinformatics community in Australia, and Australian BioCommons sponsors and attends the conference each year to hear from researchers and bioinformaticians and to share responses to their research infrastructure priorities. Stay tuned for more information about ABACBS 2025 in Adelaide!