I'm Jakob, a biologist-turned-programmer, happy in my role as a research software engineer.
I work as an assistant professor at CPR, Copenhagen University researching metagenomics with particular interest in virus- and plasmid metagenomics. Biologically, my interests are in phylogenetics, molecular evolution and sub-genomic replicons. On the computer science side, I'm a Julia, Rust and Python enthusiast, contributing to BioJulia and Julia. I particularly enjoy writing optimized and generic software packages for bioinformatics.
Blogposts
- What scientists must know about hardware to write fast code
- On the performance and design of BioSequences compared to the Seq language
- An introduction to writing machine-generated parsers with Automa.jl
- What's bad about Julia?
- What's great about Julia?
- How to optimise Julia code: A practical guide
Selected repositories
- Vamb - variational autoencoders for metagenomic binning
- Beginner's Python for Biological Scientists [WIP]
- ScanByte.jl - find a byte in a chunk of memory - fast.
- Alen - simple terminal alignment viewer.
- LibDeflate.jl - bindings to the fast de/compression library libdeflate
- StackCollections.jl - optimized, fixed-bit collections in Julia
- MinHash.jl - efficient, generic minhashing.
Maintainer