2026-08-13 –, Room 4
Julia is a fantastic language for bioinformatics. But why? What about bioinformatics makes Julia so suitable? On which bioinformatics problems have Julians focused their efforts to far? And if Julia is so useful for bioinformatics, why isn't it more popular? This talk presents the state of affairs of programming in modern bioinformatics and where Julia fits into that.
Bioinformatics is a perfect example of a discipline suffering under the two language problem: Our datasets are huge and our algorithms demanding, yet the majority of our code is written by scientists, not software engineers. Our code requires both performance, and also introspection and interactivity, and the line between exploratory data science and demanding production code is hazy.
For this reason, myself and others have found Julia to be a good tool. The Julian bioinformaticians have created a selection of great packages, and several of us have been using Julia in our research for years. Yet Julia has never taken off in our field, and bioinformatics remains dominated by Python and increasingly Rust, neither of which make any attempt at solving the two language problem.
In this talk, I will cover what particular requirements bioinformatics, as a discipline, demands from a programming language. What computational problems bioinformaticians tend to face, and why Julia is a good fit. I will briefly touch on the current, and possible future state of bioinformatics software in Julia. Finally, I will attempt to answer why Julia, despite its important advantages, have remained niche in the field, and speculate on how Julia can continue to provide value as a niche programming language.
I am a research software engineer from Copenhagen, Denmark.
I currently work for the Danish health authorities, writing software for pathogen surveillance. I am trained as a molecular biologist, and have previously been working as an academic researching bioinformatics.
I program in Python, Rust and Julia, and am an active developer in the BioJulia ecosystem. I write Julia packages for efficient I/O and parsing, and foundational bioinformatics functionality such as BioSequences and Kmers.jl.