Ragnar {Groot Koerkamp} 🦋 @curious_coding
PhD on high troughput bioinformatics @ ETH Zurich; IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography https://t.co/wBv2zN4F80 curiouscoding.nl Zurich Joined October 2021-
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Sassy: Fuzzy Searching DNA Sequences using SIMD academic.oup.com/bioinformatics…
@jpelbers @heufd4 Rick made Barbell for demultiplexing+trimming. I'm not actually sure if it supports just trimming though. It might make sense to add this to sassy directly. The hard part is choosing all the thresholds usually (# errors; dist to end; overhang cost). github.com/rickbeeloo/bar…
To all folks dealing with biological data: do you ever need to check if your reads contain barcodes/adapters/primers/...? Or off-target matches? Sassy is the tool to use! A super fast implementation of "approximate string matching" with a grep-like CLI. curiouscoding.nl/posts/sassy/
As said before, this is a super useful (and *fast*) tool, that we've already been using quite a bit for troubleshooting spurious primer matching and the like. Warmly recommended!
To all folks dealing with biological data: do you ever need to check if your reads contain barcodes/adapters/primers/...? Or off-target matches? Sassy is the tool to use! A super fast implementation of "approximate string matching" with a grep-like CLI. curiouscoding.nl/posts/sassy/
@heufd4 ❤️ Basically "fuzzy grep for fasta files": search fasta/fastq files for short DNA patterns to verify that they are present/absent in the data in the right places, and what kind of errors there are.
As often: the SimdQuickHeap is a conceptually very simple data structure that thus can be easily optimized using SIMD, leading to pretty big speed gains.
New preprint! The SimdQuickHeap is the fastest priority queue, by far. 2x faster than a radix heap, and up to 10x faster than binary heaps. Coauthored with Johannes Breitling and Marvin Williams.
SimdQuickHeap: The QuickHeap Reconsidered Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams arxiv.org/abs/2604.25681 [𝚌𝚜.𝙳𝚂]
New preprint! The SimdQuickHeap is the fastest priority queue, by far. 2x faster than a radix heap, and up to 10x faster than binary heaps. Coauthored with Johannes Breitling and Marvin Williams.
OMG! By popular demand (🤗) I'm going to speak at P99 again! This time about the SimdQuickHeap preprint that just came out: the fastest priority queue by 2x (or 10x comparing to a binary heap).
We've been working hard behind the scenes to bring you an unforgettable P99CONF 2026. Registration is now open, so take a look at who is coming back and the new speakers we have on board > p99conf.io/2026/04/01/be-… #ScyllaDB #P99CONF
SimdQuickHeap: The QuickHeap Reconsidered Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams arxiv.org/abs/2604.25681 [𝚌𝚜.𝙳𝚂]
@valigo Getting good at GPU programming will make you a better coder on modern CPUs. A throughput-oriented mentality, while critical on GPUs, is also a way better way of coaxing better performance out of the wide, deeply-pipelined, SIMD-enabled monstrosities that are modern CPUs.
@slimjimmy @sasuke___420 5s with avx2 curiouscoding.nl/posts/1brc/
Me 15 years ago, as a PhD student: “It seems like all the interesting questions have been answered & there are no useful studies left to do.” Me now, as a funder focused on evidence-based criminal justice policy: “The biggest constraint we face is finding researchers with time to engage in important new projects.” Truly, this is the most pressing problem I have. I need an army of scholars who understand causal methods & who would jump at an opportunity to study a program or policy. Would you like to help? Email me. 🙏
Microsoft has set a goal to “eliminate every line of C and C++ from Microsoft by 2030.” What are they going to try to replace that C & C++ code with? You guessed it. Rust. And they’re going to use AI to do the “Rust re-write” at an insane speed. “Our strategy is to combine AI *and* Algorithms to rewrite Microsoft’s largest codebases. Our North Star is “1 engineer, 1 month, 1 million lines of code”. You read that right. One million lines of code, per engineer, per month. Pure insanity. This kind of decision making is common among those with a deeply held, delusional faith in the Cult of Rust. Take battle tested code, and re-write it (without a clear benefit to the end user) at a recklessly rapid rate. Then force others to adopt that rewritten code before it is ready or properly tested. All while holding a delusional belief that your new Rust code is superior in all ways, and is inherently bug free thanks to the divine nature of Rust. We learned this from a post by Galen Hunt, Distinguished Engineer at Microsoft Research. linkedin.com/posts/galenh_p…
The experience of having some muddy mess of a hundred line function with goofy "do things one way here, then do almost the same thing somewhere else, then ..." become clear and turn into a 20-line clean "computer science" type function with nice clean data structures is bliss.
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383 Followers 184 Following I quit. Follow @jnalanko at Bluesky or at https://t.co/LNG33M1Djo. Jarno was not an algorithm. Jarno was a computer scientist. He knew how to write programs. -GPT2.
Carl Kingsford @ckingsford
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