Australian Outpost of BioHackathon Europe connects researchers to help shape global bioinformatics advances

A diverse collection of Australian researchers gathered in Brisbane for the latest edition of ELIXIR’s BioHackathon Europe. Thanks to the ongoing collaboration between Australian BioComons and ELIXIR, Australian life scientists had a powerful opportunity to shape global bioinformatics advancements, while networking with other life scientists both at home and abroad.

From 4 - 8 Nov, 18 keen Aussies worked from 12 - 9:30 pm each day to allow overlap with the European participants. This year our group worked across three projects:

One team developed a prototype data model converter that makes it easy to switch between data models for a given biomedical cohort. The team built mappings between common data formats OMOP and FHIR and central ‘meta cohort’ format, plus made a front end interface that enables data upload, selection of the data model, selection of the data format, and download of the converted dataset. This team was highly collaborative, with members from the BioCommons Human Genome Informatics team, software and bioinformatics engineers from Children’s Cancer Institute (CCI), bioinformaticians and data scientists from the Sydney Informatics Hub, and a University of Melbourne Masters of Genomics and Health student. 

A particularly diverse team with representatives from BioCommons, Melbourne Bioinformatics, Curtin University, University of Sydney (Threatened Species Initiative), University of Tasmania, Symbio Labs, and QUT contributed to the FAIRtracks metadata schema. Their wide range of experience across conservation, agriculture and biodiversity was a new angle for a project that had previously focused on human data. The Aussies built many new connections and had a strong influence on the extension of the FAIRtracks schema into the life sciences.

Another team worked on was a key component of a larger European effort to ensure the global Galaxy project is sustainable and resources remain clearly accessible. Building the ‘Galaxy Codex’ led to major improvements in the findability of Galaxy resources such as tools, workflows and training material across microbiology, single cell omics, and proteomics.

Outside of the project work, the local team spent plenty of time getting to know each other and building their professional relationships, plus ate plenty of Spanish food to feel more connected to the Barcelona event! Dr Tim White, Data Science Software Engineer at the Sydney Informatics Hub, found collaborating in real time invaluable:

Typically in software development we are presented with the final product and don’t get to see the drafting process. It was fantastic to collaborate with the CCI software engineers to develop the code together and share what we consider at each stage of development.

Meanwhile, Dr Christian Fares, Senior Software Engineer at CCI, said their team found significant benefit from working outside of their usual area:

Our day to day roles wouldn’t normally encompass data model conversion, so we gained fantastic experience in a new area. We’ve been intending to learn more about the FHIR data standard, so attending the Aussie Outpost was a great opportunity, and we’ll be sharing our learnings with the rest of the CCI team soon.

 We'll be bringing together another team for the next BioHackathon Europe in Nov 2025 - keep your eyes peeled for our call for applications mid next year! In the meantime, read ELIXIR’s summary of BioHackathon Europe 2024.