alt Hacker NewsThis is interesting; thanks for sharing! I have been curious about the adoption of Rust in computational biology. I know that the folks at Saint Jude's [1] are also using Rust for their 'omics research.
Replies
We rewrote Nextclade in Rust and are very happy. Works nicely both for CLI and client side browser with wasm.
There is a relatively widely adopted tool (100+ citations, >500k invocations collected via telemetry) for mass spectrometry-based proteomics written in Rust, and quite a few others in the works.
I'm building a structural bio crate system in rust (na_seq, bio_files, bio_apis, dynamics and some more specialized). No one is using it AFAIK other than myself. I am using it to build a GUI multi-purpose structural bio GUI program called Molchanica.
Note that this doesn't have much overlap with the traditional bioinformatics workflows like the OP (Rosland), or the one you linked to seem to be focused on.
Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community.
Nature even wrote a feature article about it a couple years ago:
Why scientists are turning to Rust
https://www.nature.com/articles/d41586-020-03382-2
They mention the Rust-Bio [1] project by well known Snakemake author Johannes Köster & co, and there are some other widely used libraries like needletail [2] and noodles [3].
A cool smaller tool developed by performance wiz Ragnar Groot Koerkamp which was just published is Sassy [4] [5]. He has also been involved in developing some high performance SIMD based stuff (minimizers) [6].
[1] https://github.com/rust-bio/rust-bio
[2] https://github.com/onecodex/needletail
[3] https://github.com/zaeleus/noodles
[4] https://github.com/RagnarGrootKoerkamp/sassy
[5] https://academic.oup.com/bioinformatics/article/42/5/btag244...
[6] https://github.com/rust-seq/simd-minimizers