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!

Australian researchers tells us about their bioinformatics training needs

Word cloud from responses to the prompt “I need to learn…”

Australian BioCommons and the National Bioinformatics Training Cooperative regularly surveys the life science community to find out what they need to learn, how they want to learn and if this is changing over time. The results of our 2023 survey are now available on Zenodo.

The survey shows that people want live training supported by self-paced materials. This was an exciting outcome for those of us in the training world as it’s a fantastic way to cement new skills and promote ongoing learning! 

As for the topics they need to learn, there is continued need for training on analysis of omics data, workflow management and a variety of tools, platforms and computational methods. Emerging topics from our 2021 survey (e.g. single cell RNAseq and Machine learning) remained popular in 2023. Spatial omics was revealed as an emerging training need reflecting the growing use of this method. The responses show that for trainees the focus is on what they need to achieve rather than how they need to achieve it highlighting the important role that subject matter experts and trainers have to play in shaping best practices. Australian BioCommons and our National Bioinformatics Training Cooperative are using these results to help us make sure that the training we offer is relevant.

We share the results of the survey in the spirit of openness and in the hope that it will spark conversations about the bioinformatics training needs of the life science community locally, nationally and internationally.

Keen to dig into the results? Read the report and download the data from Zenodo.

Success of BioCommons-ELIXIR partnership showcased on the international stage

A showcase of outcomes that are being realised through international collaboration between life science data infrastructures were recently discussed by the global research infrastructure community at an international gathering. 

The 2024 International Conference on Research Infrastructures (ICRI 2024) explored global trends, challenges, and opportunities in research infrastructure. The December meeting was held in Brisbane - the first time ICRI has been hosted in the Asia Pacific - and attracted policymakers, research institution leaders, facility operators, users and researchers. Around 420 people from 50 nations travelled to Australia, including delegates from 11 Southeast Asian and Pacific nations, for this year’s event. Another 500 people joined online from 39 nations. 

Significantly, the 2024 event was the first ICRI to focus on Indigenous knowledge and engagement. Organising the meeting was a joint effort between Australia’s national science agency (CSIRO), the European Commission, and the Australian Department of Education. 

With a Euro-Australian bioinformatics infrastructure collaboration agreement now into its fifth year, representatives from BioCommons and ELIXIR hosted an official side event, Euro-Australian research infrastructure collaboration in the molecular life sciences. Partners described fruitful outcomes for the global community, and key examples from BioCommons’ perspective were highlighted, including our enablement of:

• A  multi-week coworking session for Galaxy Australia and Galaxy Europe staff in Brisbane in 2023

• Shared product ownership of WorkflowHub between Australian and European colleagues

• Launch of Australia’s DReSA and incorporation of its codebase into ELIXIR’s TeSS

• The Australian Outpost of ELIXIR’s BioHackathon Europe in 2022, 23, and 24

• Codevelopment of genome assembly and annotation pipelines for biodiversity efforts

• Connection building to target efficient data publishing and re-use in a global context 

Presenters at this event included Kelly Scarlett from Bioplatforms Australia who set the context within the National Collaborative Research Infrastructure Strategy (NCRIS), Ondřej Hradil representing the European Strategy Forum on Research Infrastructures (ESFRI), Jeff Christiansen and Nigel Ward representing Australian BioCommons, Tim Hubbard representing ELIXIR, Fotis Psomopoulos representing CERTH and ELIXIR Greece, and Gerry Reilly representing BioFAIR UK.

To capture the international goodwill generated and the progress made during the ICRI conference, organisers published The Brisbane Statement. It encourages all research infrastructure (RI) stakeholders to actively consider the role of RIs in addressing global challenges, and how strengthening international RI collaborations can help solve them.

Australian BioCommons is supported by Bioplatforms Australia, which is enabled by NCRIS.

An international approach to harnessing AI opportunities in the life sciences

From left to right: Prof Ewan Birney, Andrew Gilbert, Dr Jeff Christiansen, Prof Andrew Lonie

Many of us are exploring the opportunities that AI brings to life sciences. Australian BioCommons and Bioplatforms Australia recently hosted Prof Ewan Birney, Deputy Director General of the European Molecular Biology Laboratory (EMBL) and Director of EMBL’s European Bioinformatics Institute (EMBL-EBI) at the University of Melbourne to share his views in a workshop: Exploring opportunities in Life Sciences AI. 

The workshop focused on existing activities in Australia and global AI developments, with a facilitated discussion on how to build effective collaborations between infrastructures and researchers in the AI-life sciences space, and what opportunities there are for Australia to collaborate more closely with the EU across life sciences infrastructure, data, informatics, training and research programs.

Prof Birney’s visit included a keynote address at the iconic Shine Dome in Canberra. Co-hosted by EMBL Australia and Bioplatforms Australia, the event included talks from international and Australian experts, and drew scientists and senior leadership from a range of organisations, including CSIRO, Monash University, UNSW, the Australian National University, the University of Canberra, the Australian Government Department of Education, NCRIS projects, Snow Medical and Research Australia, as well as postdoctoral researchers and students. Read more about Prof Birney’s presentation in EMBL Australia’s news item.

As well as helping BioCommons to coalesce its approach to facilitating AI application in life sciences, the visit has strengthened the connection between BioCommons and EMBL and has led to ongoing discussions about future cooperation. Meeting in person was an excellent opportunity to clarify our intersecting needs, and establish a foundation to work together more closely into the future.