Ragnar {Groot Koerkamp} 🦋
@curious_coding
PhD on high troughput bioinformatics @ ETH Zurich; IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography https://bsky.app/profile/curiouscod
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I made reddit.com/r/bioinformati… I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself. If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)
Barbell is out now: a new demultiplexer with much higher accuracy than eg Dorado. See the bsky threads for more: bsky.app/profile/curiou…
Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data biorxiv.org/content/10.110… #biorxiv_bioinfo
And still probably 95% of programmers are like "don't worry about the low level details, the compiler will take care of it"
I was curious whether compilers would convert a naive loop implementation of "set range of bits in u64 to 1" into O(1) bitwise ops. Answer: MSVC compiles the loop into a loop. Clang's output is bonkers: 418 bytes long, branches everywhere, 256-bit SIMD operations get involved?!
How can you gain a 40x increase in throughput over the #Rustlang standard library implementation? In 15 minutes, @curious_coding will show how to exploit what modern CPUs offer so you can achieve faster binary search. Join here > ow.ly/l8pl50XgfYT #ScyllaDB #P99CONF
i want knowledge to be passed by reference not by value
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (nature.com/articles/s4158…).
How can you achieve 40x faster binary search? @curious_coding's #P99CONF talk will dive into everything that modern CPUs have to offer in order to gain 40x increased throughput over the Rust standard library implementation. Save your spot here > ow.ly/oT8X50XbeTo #ScyllaDB
I'm having a talk on "40x faster binary search" at #p99conf next Wednesday, Oct 22! Register now :) p99conf.io
It’s a bit easier to just explain how we got here. In the old days, memory and CPU ran at the same speed. The laws of physics make it incredibly hard to ramp up the MHz of the CPU while keeping physically separated memory chips in sync. The distance is just too far for the…
The question: "Why do CPUs have multiple cache levels?" often gets many CS students and professionals thinking and researching. This article from Fabian Giesen narrates a "cache story" in a relatable way, only to delve into the details - a must-read! fgiesen.wordpress.com/2016/08/07/why…
Asymptotically, O(n^(1/3)) isn't quite achievable in this universe for a variety of reasons, and you have to be pretty clever to even get O(n^(1/2)). If you fill space with memory cells that don't collapse into a black hole then memory access actually takes O(n) time!
Memory access is O(N^[1/3]) vitalik.eth.limo/general/2025/1…
I am calling for a moratorium on new tote bags. We all have more than enough tote bags already. Stop giving me tote bags at conferences. I do not want or need any more tote bags. See also: water bottles
So tired of this.
No longer interested in a H1-B visa? You can work for @PacBio as a Bioinformatics Software Engineer even from Europe. Apply today! pacbio.wd12.myworkdayjobs.com/en-US/PacBio-/…
It seems a common experience in the lives of people with high agency is that they, at some point, metaphorically, lean against a wall and discover that there is a hidden door.
☕ there's a Dijkstra for everything: cs.utexas.edu/~EWD/transcrip…
I started using `rebase` instead of `merge` and now I understand why people were telling me to use rebase
I’m in an airport and the guy next to me has been watching videos with NO HEADPHONES. It’s so annoying. I finally took out my phone and started doing the same. But I made sure to slowly increase my volume over his. He looked over at me like he was super annoyed. And then turned…
In the beginning linkers were created. This has made a lot of people very angry and been widely regarded as a bad move.
The C/C++/ObjC separate compilation architecture is one of the most underappreciated PL innovations of all time
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