Building bridges for better data sharing: ENA experts empower Australian researchers in data submission

Participants of the in-person roundtable came from around Australia to meet the ENA team

For two weeks in March and April 2025, Australia’s life sciences community had a unique opportunity to engage directly with the European Nucleotide Archive (ENA) team. In a first-of-its-kind initiative, Dr Joana Pauperio (Biodiversity Curator, European Nucleotide Archive, EMBL’s European Bioinformatics Institute) and Maira Ihsan (User Support Bioinformatician, European Nucleotide Archive, EMBL’s European Bioinformatics Institute) visited Australia to deliver an intensive series of seven workshops and four roundtable discussions, aiming to enhance Australian researchers’ skills in submitting and retrieving genomic, metagenomic, and environmental DNA (eDNA) data to/from international repositories.

Organised by Australian BioCommons, the visit built technical capacity and opened a direct dialogue between the ENA and the Australian research community about the future of data submission, retrieval, and brokering. High-quality data submission to international archives like the ENA ensures that Australian-generated genomic and environmental data can contribute to global research efforts. Yet, challenges in submission processes, metadata preparation, and understanding of repository workflows can act as barriers. Bringing ENA experts together in person allowed Australian researchers to receive tailored, hands-on guidance, overcoming time zone challenges and helping the ENA team witness firsthand the hurdles local researchers face.

Workshops: Hands-on learning and capacity building

Across six data submission workshops, participants learned various data submission pathways (e.g., via Webin-CLI, programmatic, and command line) to submit:

• Raw reads, genome assemblies, and annotations

• Metagenome-Assembled Genomes (MAGs)

• Environmental DNA (eDNA) data

A data retrieval workshop provided an opportunity for participants to practice retrieving different data types from the ENA using various tools and protocols.

Feedback was welcome at all times by providing a living document for queries that were addressed during and after the workshop, and breakout rooms for 1:1 discussions were available.

Roundtables: Listening to the community

One in-person and three online roundtable discussions were also hosted to facilitate direct communication between ENA and Australian researchers.

In-person Roundtable

This meeting between invited members of Bioplatforms Australia, Bioplatforms Australia Data Portal, Australian Reference Genome Atlas (ARGA), the Australian Tree of Life project, and the ENA teams focused on information exchange and potential collaboration in the global biodata landscape. Key topics included data brokering to ENA, species taxonomy, and the possibility of establishing an Australian node within the International Nucleotide Sequence Database Collaboration (INSDC). The immediate next step identified was to further explore data brokering. The roundtable provided a valuable forum for discussing opportunities and challenges in collaborating with the ENA and enhancing Australia's contribution to international data repositories.

Genomics Roundtable

The meeting facilitated discussions on topics including Genome assembly and annotation efforts at scale in Australia, ENA's role as a global repository and challenges in annotation submissions to INSDC. It aimed to improve understanding of data publication options and ENA submission processes.

MAGs Roundtable

The meeting facilitated discussions on topics including the use of MAGs in Australia, the role of ENA+MGnify as a global repository, challenges in mass submission of MAGs, issues with submitting MAG data for organisms not represented in the NCBI Taxonomy, and suggestions for improvement.

eDNA Roundtable

The meeting facilitated discussions on topics including eDNA use across various sectors, Australian eDNA reference library initiatives like the National Biodiversity DNA Library (NBDL), making eDNA data FAIR (Findable, Accessible, Interoperable and Reusable) and the ENA as a global repository for eDNA data, data interoperability between resources, and data sharing with third-party platforms like GBIF.

Looking ahead

The momentum generated by the workshops and roundtables will continue through:

• The creation of self-paced training materials: by converting the workshop content and hosting it on the EMBL-EBI training website to ensure researchers have access to training when they need it

• Efforts to explore an Australian data brokering pathway as part of the Australian Tree of Life (AToL) project

• Strengthened connections between Australian researchers and INSDC repositories

By bridging expertise across continents, the collaboration between ENA and the Australian life sciences community is helping ensure that Australian research continues to have a strong, visible impact on the global stage.

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.