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.

Australian palaeoenvironments and biodiversity to be reconstructed through metagenomic analysis of sedimentary ancient DNA by national collaboration with Indigenous partners

Dr Vilma Pérez uses environmental DNA techniques to understand when and how environments have changed and responded to disturbances

A fascinating new project now has access to the specific computational resources required to build high resolution records of Australia’s changing ecosystems over the past millennium. The research will reconstruct Australian palaeoenvironments and biodiversity using metagenomic analysis of sedimentary ancient DNA collected from mainland Australia and the Torres Strait Islands as part of codesigned projects involving leading Australian researchers and Indigenous partner organisations. Streamlined bioinformatics analysis pipelines will be essential to process the large volume of samples expected to come in from this collaboration.

Sedimentary ancient DNA (sedaDNA) analysis is a transformative tool for studying past biodiversity and its responses to environmental, climatic, and human-induced change. The project aims to build capacity for the growth of sedaDNA research in Australia by automating bioinformatic analyses into a single Nextflow pipeline that can easily produce a robust and reproducible taxonomic profile of both modern and ancient target species found in sediment samples. BioCommons was keen to support the research with access to both ABLeS and our Australian Nextflow Seqera Service. 

This project is part of the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures (CIEHF) which seeks to create a lasting impact by integrating Indigenous and Western knowledge frameworks to model environmental, cultural, and historical change in Australia over the past millennium and into the near future. 

Dr Vilma Pérez is an environmental microbial ecologist at the Australian Centre for Ancient DNA, The University of Adelaide, who can now access the national computational infrastructure she needs for her research after being onboarded to BioCommons’ ABLeS and Seqera services. Vilma's expertise in using environmental DNA techniques to understand when and how environments have changed and responded to disturbances will be put to good use in CIEHF’s novel genetics research program.

Led by CIEHF Chief Investigator Assoc Prof Ray Tobler from the Evolution of Cultural Diversity Initiative at the Australian National University, the research program will use high-resolution landscape genomic analyses of selected Australian native flora and fauna, as well as ancient DNA recovered from archaeological sediments (sedaDNA).

This work will help reconstruct past Australian ecosystems to understand how biodiversity, from microbes to plants and animals, has changed over time, and how it has responded to environmental shifts, including Indigenous Australian landscape management practices that have helped care for Country for thousands of years.

Gaining access to the right computing infrastructure is one thing, but appropriate computing and data management mechanisms are needed to ensure that Indigenous genomic data resources are ethically managed to the benefit of Indigenous Australians. Mutual partners, Bioplatforms Australia, were able to connect CIEHF with colleagues at the National Computational Infrastructure (NCI) who are working with the National Centre for Indigenous Genomics (NCIG) to host their sensitive sequencing data. Given Indigenous genetics research requires unique ethical approaches, NCIG is leading the way in building a genome resource for the research community under Indigenous Governance and will no doubt have many insights to share. 

As part of our ongoing support for CIEHF, Dr Ziad Al Bkhetan, Product Manager - Bioinformatics Platforms at BioCommons, and Dr Kelly Scarlett, Manager - Partnerships and Engagement at Bioplatforms Australia will participate in an upcoming sedaDNA workshop hosted by CIEHF researchers at the University of Adelaide.

This workshop sits within the Genomics research stream which is part of a suite of nine chosen to ensure a holistic, interdisciplinary approach. Find out more about how CIEHF’s research streams are addressing unique environmental, cultural, and historical complexities of Australia through an integrated approach, leveraging both Indigenous knowledge systems and researcher’s fields of expertise. 

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.

Introducing the Australian Tree of Life Informatics Capability

Powering research and decision-making for Australian biodiversity and agriculture

Reposted from Bioplatforms Australia

The Australian Tree of Life Informatics Capability is establishing a new digital framework to bridge the gap between the generation of genomics data and its application in on-the-ground actions. This program will equip researchers and decision-makers with the tools to leverage cutting-edge genomics technologies, enabling them to more effectively manage and safeguard Australia’s precious biodiversity and agricultural resources.

Australia is one of a few megadiverse regions in the world. It is home to around 10 percent of the world’s species, with around 80 percent of Australia’s native species not occurring naturally anywhere else. National strategic plans for biodiversity and biosecurity emphasise the importance of making informed, data-driven decisions to support this unique environment and the primary industries that flourish in it.

Various endeavours, including the Bioplatforms National Initiatives, are currently producing essential genetic and genomic data, such as reference genomes. Whole genome sequencing acts as a cornerstone resource, facilitating discoveries such as identifying previously unknown species, uncovering novel genes for innovative applications, and understanding organism functions in nature and agriculture, and exploring their variability and interactions.

Generating genomic data for all relevant Australian species, and making it relevant to real-world application is an immense undertaking, requiring that we intensify our efforts. Our challenge is to develop a system that continues to foster enhanced collaboration, expedites data generation, assembly and analysis, and provides specialised platforms tailored to effectively deciphering this data for real-world use.

The Australian Tree of Life Informatics Capability is addressing this challenge by establishing two new infrastructures:

 1. The Australian Tree of Life – Genome Engine

The Genome Engine will accelerate the assembly and annotation of referential genomic data for species relevant to Australia. Building on existing Bioplatforms investments in data generation (via National Initiatives) and data analytics services (via Australian BioCommons),  it will allow Australian species to be studied from molecular to population scales. Researchers will be provided access to automatically produced genome assemblies, annotations and published Genome Notes soon after the raw sequencing data has been created.

The infrastructure will leverage approaches developed by the UK-based Wellcome Sanger Institute’s Darwin Tree of Life project and Galaxy infrastructure supporting the Vertebrate Genomes Project, bringing their workflows and methodologies to Australia.

 2. The Australian Tree of Life – Applied Data Laboratories

Applied Data Laboratories will generate meaningful and actionable information for decision-makers based on genomic resources, such as those made available by the Genome Engine.

Applied Data Laboratories will be developed in consultation with end-user communities such as those involved with the Plant Pathogen, Pest Management, and Functional Fungi Bioplatforms National Initiatives. Our objective is to allow more researchers, industry and government professionals, and policy makers to harness the power of genomics to inform on-the-ground actions that secure Australia’s primary industries, nature, and biodiversity.

This work will build on a concept from the Threatened Species Initiative (TSI), where Bioplatforms, in partnership with the University of Sydney and RONIN, has invested in the development of the TSI Biodiversity Portal. Scheduled for release in mid-2024, the Portal will empower threatened species managers to sequence and interpret population genetics data, generating reports tailored to inform species recovery actions.

Together, this digital capability will help to bridge the gap between generating and applying genomic data, significantly improving Australia’s capacity to leverage recent advances in next-generation sequencing. This will play a crucial role in preserving our unique biodiversity and safeguarding Australia’s primary industries, food systems and environments.

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This digital research infrastructure initiative is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS). 

For further information and updates, please contact:

Dr Nigel Ward – A/Director – Platforms, Australian BioCommons

nigel@biocommons.org.au

Sarah Richmond – General Manager Science Program, Bioplatforms Australia

srichmond@bioplatforms.com

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

Funding boost to bring game-changing growth to BioCommons

Australian BioCommons is poised to undertake a period of significant growth following the Department of Education’s announcement of crucial new funding to Australia’s National Collaborative Research Infrastructure Strategy (NCRIS). This will deliver a variety of game-changing national infrastructure developments to support omics-based life science research, with Bioplatforms Australia allocating funding to the BioCommons over the 2023-27 period in three growth areas:

• Integrated analysis platforms for omics research through the development of a ‘BioCloud’ - a unified set of ‘research context aware’ digital services tailored to meet the requirements of life sciences researchers to work with molecular biological data, using bioinformatics tools and workflows on a variety of infrastructures.

• Foundational infrastructure for accelerating biodiversity research and conservation (Australian Tree of Life (AToL) Data Laboratories) bringing together national ‘omics data with multidisciplinary data (environment, climate, trait) and connecting these to build a portfolio of transparent and repeatable analytical tools supporting deeply informed biodiversity and biosecurity management decisions.

• A translational human ‘omics data infrastructure program (GUARDIANS) to drive a step change to cutting-edge national digital research infrastructure and unlock Australia’s potential in human ‘omics research through the provision of secure, scalable, and integrated data and analytics platforms.

These three projects will be delivered in collaboration with the growing network of research consortia and delivery partners established by the BioCommons during its first phase. 

This exciting announcement builds on a 2023-28 extension to the BioCommons project that is already underway. Having delivered significant outcomes in the first 5-year term, the contractual agreements required for a further 5 years of continuity are currently being bedded down. This will ensure ongoing support for critical national services and community building activities.

Planning for the three growth areas is already underway and will intensify over the next six months. Discussions will broaden to include key partners soon, with a view to formalising initial projects and engagements in early 2024. Expect to see many exciting announcements, invitations to participate, and new opportunities to join BioCommons activities in the near future.

The outcomes of the NCRIS 2023 Funding Round are published on the Department of Education website.

The Australian BioCommons is supported by Bioplatforms Australia. Read their announcement: Bioplatforms Secures Crucial Funding from NCRIS Program to Propel Frontier Omics Technology.