Solving the big international bioinformatics challenges from the comfort of home
The Australian Outpost of ELIXIR’s BioHackathon Europe, running for the fourth consecutive year, recently brought together 16 bioinformaticians from across Australia to the University of Melbourne for an intensive week of collaborative coding.
Facilitated by BioCommons’ ongoing partnership with ELIXIR, the event provided a unique opportunity for local experts to contribute directly to global bioinformatics projects, connecting with their local peers and linking into the main BioHackathon Hub in Berlin.
From 3-7 November, the Australian team worked from 12:00 - 8:30 PM AEDT each day to ensure overlap with their European counterparts. This year’s outpost dedicated its efforts to three key projects.
Team members collaborating during the BioHackathon
One team tackled the challenge of using BUSCO (Benchmarking Universal Single-Copy Orthologs) tools for phylogenomics. BUSCO genes are standard for assessing genome assembly and annotation completeness, but their use in phylogenetics is often challenged by gene duplication (paralogy). Representatives from BioCommons, University of Melbourne, University of Sydney, Curtin University, and University of Tasmania collaborated with peers around the world to build an automatic pipeline that explicitly resolves these paralogy events, which will result in larger, more informative datasets for biodiversity research.
Another team brought together experts from BioCommons, Curtin University, University of Melbourne, QIMR Berghofer, and University of Queensland to focus on expanding the benchmarking landscape for long-read transcriptomics. While foundational benchmarks for long-read RNA-Seq were established in 2020, the field has evolved rapidly since then with new tools and protocols. This project worked towards an updated benchmark, leveraging new datasets to ensure the reproducibility and comparability of modern transcriptomics research.
The final project brought together a ‘supergroup’ from the Australian Tree of Life (ATOL) and European Reference Genome Atlas (ERGA) projects, to tackle streamlining FAIR metadata for biodiversity genome annotations. Tom Harrop represented the Outpost in-person in Berlin, with Tiff Nelson co-leading the whole project from the Australian Outpost, along with participants from BioCommons, Melbourne Bioinformatics, University of Queensland, and QCIF. With thousands of reference genomes being generated globally, there is an urgent need for structured, automated ways to report metadata for genome annotations. This project worked on developing automated tools to process, validate, and deploy this metadata, ensuring it is harmonised and discoverable across global repositories.
Outside of the intensive project work, the local team built their professional relationships over lots of Melbourne’s coffee and terrible weather. Hacking paused for the ‘race that stops the nation’ (for approximately four minutes!) on Melbourne Cup day, and the event wrapped up with a celebratory German lunch at the iconic Hofbräuhaus Melbourne to feel more connected to their colleagues at the main site of the BioHackathon Europe.
“This was a fantastic event. It's rare to get the opportunity to work as part of a specialised software development team while in academic research. This was a great opportunity to learn the skills required to make my code more usable, work together to produce larger projects, and plan contributions amongst team members,” said Thomas Crow, University of Queensland PhD candidate and affiliate of the ARC Centre of Excellence for Plant Success in Nature and Agriculture.
“The event covered important pipeline and repo development skills I have been seeking for some time. That our collective work has also led to collaborations in Europe, potential publications and research impact make this event even more worthwhile. I am very excited to attend future events."
The collaboration continues, and we look forward to bringing another team together for BioHackathon Europe 2026. Be sure to watch for our call for applications in mid-2026 if you'd like to participate!
Read ELIXIR’s article about the event: Accelerating open science - the impact of the BioHackathon Europe
BioHackathon attendees avoiding the Melbourne weather
Celebratory German lunch at the iconic Hofbräuhaus Melbourne
Dialling in for discussions with Tom Harrop in Berlin
