The Aussie Outpost of BioHackathon 2024 was a blast! Here's why:
BY George he, Master of Genomics and Health student, The University of Melbourne
Allow me to set the scene for one of the most exciting events I attended to this year:
ELIXIR's 2024 BioHackathon: Aussie Outpost
Destination? Brisbane, in one of the city centre’s most defining towers, overlooking an expansive landscape and its glorious river network.
Twenty hackers from around the nation converged here, bringing a wealth of experience in bioinformatics, life sciences, and software engineering to collaborate on projects tackling critical challenges in the bioinformatics world. Many of the projects focused on enhancing data integrity, interoperability, and usability, developing better practices for research and data sharing.
As for me? I was grateful for the chance to participate, to meet and work with established professionals in their fields, and, I must say, we had a terrific time. I had only entered the world of programming last year during my Master’s degree and had recently completed a subject on database systems and information modelling. But, one of the definitive moments of the hackathon for me was moving between projects and quickly adjusting to the new one. What I thought would take me all night to grasp, I picked up in just five minutes! My studies and experiences had placed me in the perfect position to dive into the project quickly. All the knowledge I’d gained over the year came flooding out for me to apply.
You might be wondering at this point, what exactly did we achieve at this BioHackathon?
Of the three projects the outpost was collaborating on (Project 31: Executable Metadata Mappings to FAIRify Biodiversity Genome Annotations, Project 11: Galaxy CoDex, and Project 8: Data Model Converter), I was fortunate enough to move between Project 11 and Project 8. By doing so, I absorbed so much knowledge about the Galaxy platform while applying the programming and database modelling skills I had been developing. It was also a general pleasure, and a unique experience, to watch a multifaceted team come together, communicate, and collaborate with our international counterparts.
Galaxy CoDex focused on ensuring the future sustainability of the well-established open-source Galaxy platform for data analysis. As a continuing project from the previous year, I had the guidance of Gareth and Mike, who are both highly respected in the Galaxy community. They patiently brought me up to speed on the use of Galaxy and its benefits for data analysis. The project centred on helping users find the right tools to analyse their data and improve workflows by adding appropriate metadata to the underlying code. Instead of manually searching through thousands of tools available on the platform, metadata annotations would improve tool suggestions and allow custom workflows to be created automatically. This would increase the searchability and usability of Galaxy tools. I learnt a great deal about the Galaxy Project platform, the importance of metadata and tool annotation best practices, and brushed up on my GitHub skills, even contributing small updates to the project.
Josh and Christian presenting the Data Model Converter to the rest of the group.
In Data Model Converter, our team created a functional web application to convert between two clinical data models (FHIR and OMOP), becoming a valuable tool for transferring patient data or supporting research across hospitals. I was impressed with how quickly I onboarded this project, as it was a practical application of my studies this year. On one hand, I had experience with creating custom Python classes during my data analysis internship; on the other, my knowledge of database systems and information modelling. Combining these experiences, I quickly integrated into the team and figured out how my skills could best meet their needs. I contributed by helping the team test the data converter’s robustness and drawing data modelling diagrams to help users understand how the converter worked. It was so rewarding to apply what I had previously learned in theory and assignments. This wouldn’t have been possible without the unique skills and experiences I’d gained over the year. How good’s that?
This BioHackathon was a BLAST. It felt fantastic to be involved in the bioinformatics community, to learn from and collaborate with like-minded individuals. I’m excited to see how these projects shape the bioinformatics community and look forward to participating in future BioHackathons, to meet even more people in Australia and beyond!
If George’s experience has got you excited for future BioHackathons, subscribe to the Australian BioCommons newsletter to make sure you hear about the next one!