Jakob Nybo Andersen
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.
Sessions
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.
Despite being a high-performance language, Julia's I/O functionality has been designed for convenience, and is neither robust nor efficient. I present an alternate I/O interface in BufferIO.jl, which has more well-defined semantics, and permits low level, high performance I/O operations.
Round table discussion on using Julia for computational biology: Use cases, limitations and concerns we should address, and where to focus our collective efforts.