jakobnissen / csv.jl Goto Github PK

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

• BioSymbols.jl
• BioSequences.jl
• FASTX.jl
• Automa.jl