Happy Easter!

I find it super frustrating, we were that close to modularity with Rust, and you port nice librairies with fine APIs to C? I'm judging you. 👀 If you wish to vibe code then Claude can interface the Rust for you instead?

let (pipe1_tx, pipe1_rx) = tokio::net::unix::pipe() .expect("ceci n'est pas une pipe");

The Treachery of Images

greyscale image with some light diagonal smears across the frame and a horizontal smear with an orange ellipse around it in the middle. the horizontal smear is the Orion spacecraft

everyone say hello to the artemis II crew

Screenshot showing the initialization of a perf counter that counts last-level cache misses. It then starts the counter, executes the function to be benchmarked, stops the counter, and reads its value.

Have I advertised perfcnt yet? It's awesome!

Super easy to add fine-grained perf counters benchmarks, for eg branch misses and last-level cache misses.

(These things are otherwise annoying to get from `perf stat`, because that includes benchmark setup and such.)

crates.io/crates/perfcnt

"The failures are the curriculum. The error messages are the syllabus. Every hour you spend confused is an hour you spend building the infrastructure inside your own head that will eventually let you do original work. There is no shortcut through that process..."

crates.io: Rust Package Registry crates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

There's multiversion, but it's only for auto-vectorization (IIUC) and doesn't help us:
We use `wide`, which determines at compile time using the target features whether `u64x8` is `m512i` or `(m256i, m256i)`, and then explicitly hardcodes SIMD intrinsics on those.

crates.io/crates/multi...

Sassy 0.2.2 binaries are now up on bioconda!

It has AVX2 and AVX-512 binaries bundles together into a single file using cargo-multivers (which in the process got some speedups as well).
This gives up to 2x speedup when using the --v2 flag when searching many equal-length patterns!

A full disc image of Earth, as seen from the Orion Crew Module. The planet is a pale blue, swirling with white clouds and glowing slightly lighter blue in place from reflected light. At lower left, a large brown landmass is Africa, with Spain and Portugal with twinkling lights where the planet curves. At top right, auroras glow in a thin green glow, just barely separated from the planet's surface. Earth is set against the black of space (pic: NASA/R.Wiseman)

More context on this #Artemis II image:

* This is the night side, lit by moonlight. You can see city lights in Spain & Portugal, & a sliver of day at lower right

* The Sun is entirely behind Earth, which makes it a kind of solar eclipse, but w/ Earth doing the eclipsing instead of the Moon:
☀️🌍🚀🌕

Bioinformaticians have been writing the same abstract for decades We have always been overwhelmed by the data explosion

We have always been overwhelmed by the current data explosion!

luispedro.substack.com/p/bioinforma...

1983

In the last two weeks, the world gained 2 new C++ ports of simd-minimizers, and 2 new Rust ports of FastQC.

Do with that information what you want I guess.

First RasQC commit: 3 days ago
github.com/Huang-lab/Ra...

Huh?!

RustQC and RastQC both released within hours of each other?

bsky.app/profile/bior...

Huh?!

RustQC and RastQC both released within hours of each other?

bsky.app/profile/bior...

Rusland trekt persaccreditatie van NOS-correspondent Geert Groot Koerkamp in NOS-correspondent Geert Groot Koerkamp verliest na dertig jaar zijn persaccreditatie in Rusland. Achtergrond en gevolgen op een rij.

Onze fantastische last man standing in Rusland ❤️‍🩹
www.nrc.nl/nieuws/2026/...

Reading the masto thread I can't help but think that it is extremely emblematic that all of this is written in TypeScript and contains almost all of the exact antipatterns we've been harping on and on for the past what, three decades?

Terrible error handling; no fail-fast; no input sanitization...

entire thread is incredible, but just absolutely screaming at claude code having \u2014 (unicode number for "em dash") baked into its source mastodon.social/@jonny@neuro...

The Four Color Theorem with Linearly Many Reducible Configurations and Near-Linear Time Coloring We give a near-linear time 4-coloring algorithm for planar graphs, improving on the previous quadratic time algorithm by Robertson et al. from 1996. Such an algorithm cannot be achieved by the known p...

4색 정리 새로운 증명이 arXiv에 올라왔습니다.
New proof of the four color theorem
by
Yuta Inoue, Ken-ichi Kawarabayashi, Atsuyuki Miyashita, Bojan Mohar, Carsten Thomassen, Mikkel Thorup
arxiv.org/abs/2603.24880

Computing k-mers in Graphs We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on...

Accepted to CPM 2026! In this paper, we consider the problem of k-mer counting in *graphs*. We show that it's #P-hard even in deterministic DAGs. But on Wheeler graphs, it's tractable -- easy in O(nk) time. We can also do O(poly(n) log k) but it gets complicated. #CPM2026
arxiv.org/abs/2509.22885

GitHub - fulcrumgenomics/fgumi: High-performance UMI tools for NGS data analysis High-performance UMI tools for NGS data analysis. Contribute to fulcrumgenomics/fgumi development by creating an account on GitHub.

We built fgbio years ago to support UMI-aware sequencing.

As datasets grew, the single-threaded design started to show its limits.

fgumi is the next iteration: same expected outputs, rewritten for performance and scale.

github.com/fulcrumgenom...

Blog post details below👇

arXiv and code highlighting using minted is a very unhappy marriage... again took me an hour to get it working.
(Probably some weird issue with latexmk vs pdflatex writing pygment files to different places?)

LipiCS on the other hand: so much love for that. It just works 😍

I got a little carried away making interactive plots using native SVG features. Then @jpelbers.bsky.social asked if it could run DOOM. It was probably a joke...but I took it as more of a challenge.

Anyway.
kuva doom -o doom.svg

Fully playable and fully contained DOOM inside an SVG

The basic idea of hash tables is that “the universe is a big place, but it’s mostly empty."

Hash tables, or how to leverage the sinking feeling of loneliness you get when you look at the sky

Is there a German word for the particular type of schadenfreude one feels watching the stock of RAM manufacturers plummet after OpenAI backed out of their deal to buy 41% of the global RAM supply?

You want a proof for the result that probing for positive queries is 1/eps and negative queries is 1/eps^2, right? With load factor 1-eps.

Just today I was wondering how this changes for cacheline-based probing, where each cacheline has k (eg 8) slots.
I'm curious if there is a result on this?

This seems like a very reasonable policy indeed.

Vibing wrappers might be annoying because nobody likes FFI and also nobody likes more complicated build processes

That said like you I'm of two minds here @curiouscoding.nl. While I do think contributing is the right default and should be praised, open source should equally be whatever people want it to be. Hard to be to confidently normative in either direction.

Maybe some of this is also just because C++ has much more of a redo-it-yourself culture than Rust.
I see that C++ is now becoming more safe (herbsutter.com), surely learning from Rust, so maybe us academics can do the same :D

(That said, myself I'm also more into reimplementing than PRing 😅)

A quick rant on people vibe-translating our Rust libraries to other languages

That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++.

I have two major issues with that: