New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵

I have some large changes queued up for rust-lapper to address the worst-case in these benchmarks: biodatageeks.org/polars-bio/b... BUT, it's now a fundamentally different data structure. The API is the same for using it. Do I release as a v2 of rust-lapper, or release as a brand new crate?

Interval operations benchmark — update September 2025 - polars-bio

biodatageeks.org

July Scientific Computing in Rust scientificcomputing.rs/monthly/2026...

Scientific Computing in Rust

the Scientific Computing in Rust annual workshop and monthly newsletter.

scientificcomputing.rs

TIL `find` has an query opt level: -Olevel Enables query optimisation. The find program reorders tests to speed up execution while preserving the overall effect; that is, predicates with side effects are not reordered relative to each other. ...

"Once this is implemented then, in a twist of fate, Zig will become one of the only toolchains capable of producing actually memory safe executables" At 1-6x performance penalty. BUT, still very cool and interesting way to do this. codeberg.org/ziglang/zig/...

introduce an actually memory safe (unlike Rust) compilation mode inspired by Fil-C

Based on prior art: [Fil-C](https://fil-c.org/) Currently Zig has: ```zig pub const Optimize = enum { /// Safety checks enabled. Optimize for bug detection, accurate debug info, /// and compilation speed (in that order). debug, /// Safety checks enabled. Optimize for runtime per...

codeberg.org

... I think I actually liked writing all the stupid little glue scripts.

To be clear: I think this is cool because it means more money going into biotech related software. The same way companies are suddenly ready to pay to have good data storage practices and slap APIs on everything, they may now pay attention to their lab infrastructure.

Seth Stadick@ducktapeprogrammer.bsky.social · 3w ago

> AI changes this equation in the same way machine tools changed manufacturing or cloud computing changed software deployment: by collapsing the marginal cost of experimentation. mattshlosberg.substack.com/p/biotech-is...

purplesyringa.moe/blog/quadrup... I have not seen likely/unlikely used in order to allow the cpu to parallelize loop instructions before. Very cool.

Quadrupling code performance with a "useless" if

So I was optimizing a domain-specific compressor the other day, as one does. One important problem was chunking the input string and optimally choosing the most compact encoding for each chunk (differ...

purplesyringa.moe

> AI changes this equation in the same way machine tools changed manufacturing or cloud computing changed software deployment: by collapsing the marginal cost of experimentation. mattshlosberg.substack.com/p/biotech-is...

Biotech Is Entering Its Netflix Era

AI Just Created a Bigger Problem Than Cancer

mattshlosberg.substack.com

Jess Smith@nanojess.io · 3w ago

This is pretty much spot-on and it make all these lab-in-the-loop companies look prescient. My experience from doing this sort of work is that it's the boring sample chain-of-custody and metadata tracking stuff that will widen/narrow the bottleneck

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

arXiv cs.DS Data Structures and Algorithms@csds-bot.bsky.social · 4w ago

Ragnar Groot Koerkamp, Stefan Hermann, Peter Sanders, Stefan Walzer: Non-minimal k-perfect hashing: Tight lower bounds and an application to fast static hash tables https://arxiv.org/abs/2607.07257 https://arxiv.org/pdf/2607.07257 https://arxiv.org/html/2607.07257

There are going to be WILD internal code bases in 5 years, given how bad some of the “one person built their own world over 10 years” already is inside companies.

Kevin Riggle@kevinr.free-dissociation.com · last mo.

This is the Curse of LISP in action that I've been worried about happening too with LLMs by the way. It's so easy for one person to build a whole project, that they all do, but there's never any need to work together, so nobody does, nothing gets mindshare and eventually everything dies on the vine.

This is the Curse of LISP in action that I've been worried about happening too with LLMs by the way. It's so easy for one person to build a whole project, that they all do, but there's never any need to work together, so nobody does, nothing gets mindshare and eventually everything dies on the vine.

Yearly reminder to not use the default hashmap in rust unless you really do need the hashdos protections. nnethercote.github.io/perf-book/ha...

scientificcomputing.rs/2026/ Scientific Computing in Rust Annual (free) Workshop coming up on July 8!

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the Scientific Computing in Rust annual workshop and monthly newsletter.

scientificcomputing.rs

Shade throwing quote aside - that was a fantastic post about the evolution of mutability tracking / language design.

Seth Stadick@ducktapeprogrammer.bsky.social · last mo.

Software development being at best protoscientific, the failure of object-oriented abstraction to achieve its goal did not stop it from becoming the dominant practice. - without.boats/blog/referen... lol

docs.rs/dtolnay/late... I’m not sure how I made it this long without seeing this framing: - &T: shared reference - &mut T: exclusive reference

Qualcomm has bought Modular: www.modular.com/blog/qualcom... Time to see how strong that commitment to open sourcing the compiler for Mojo really is.

Modular: Qualcomm to Acquire Modular

NEW YORK – June 24, 2026 – Qualcomm Incorporated (NASDAQ: QCOM), a connected computing leader at the center of the AI era, today announced that it has reached an agreement to acquire Modular Inc, stre...

modular.com

nathan.rs/posts/gzip-lm/

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

Solving a chess puzzle with Claude and Prolog https://www.johndcook.com/blog/2026/06/11/prolog-claude/

Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone

I've been telling people for 25 years that Jane Street is not interested in formal methods. No more! And we're actively hiring to form a new formal methods team! blog.janestreet.com/formal-metho...

Formal methods and the future of programming

I’ve been telling people for the last 25 years that Jane Street as an organization was just not interested in formal methods.

blog.janestreet.com

github.com/sstadick/str... Stay in the code. Avoid context switching. That was the whole goal of this endeavor. I wanted to be able to use agents for things like search, one-off questions, and small patches without stepping out as abstracted as something like claude. github.com/sstadick/str...

New Zig Devlog about ELF linker improvements, featuring 30ms rebuilds of a Tetris game. Incremental is coming and y'all not ready. https://ziglang.org/devlog/2026/#2026-05-30

github.com/sstadick/ref... A tiny template crate based on github.com/facet-rs/facet. Do we really need another template engine? No. But I needed one and wanted to explore facet, so here we are!

In case you don't follow it already, reminder that this exists! scientificcomputing.rs/monthly/

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the Scientific Computing in Rust annual workshop and monthly newsletter.

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This seems like an awesome opportunity for people looking to pick up Rust experience and contribute to a very cool project! I hope for typst to become the standard for writing structured scientific and mathematical documents, saving us from the tyranny of LaTeX and the insanity of Word!

Typst@typst.app · 2mo ago

Get paid to work on Typst by joining our new limited project PDF Forms. It's a great opportunity to get professional experience for Rust through open source contributions this summer. More information on how to apply at typst.app/jobs/.

raw.githubusercontent.com/yugr/rust-sl... Interesting deep dive in the performance effects of various Rust features, done by using a fork of Rust where they turn features on and off, vs a suite of C/C++ benchmarks where they enable/disable similar checks. Lots of great references linked throughout

Memorial Day weekend project: port CaPS-SA parallel suffix array construction algo to Rust (crates.io/crates/caps-sa)! I also have a branch to integrate this into the ruSTAR-aligner, getting a *byte-for-byte* STAR compatible index on the human genome with just 10.7GB of RAM in ~18min (32 threads).

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

crates.io

WHEEEEEEEEEE github.com/rust-lang/ru...

alloc: stabilise `Allocator` by nia-e · Pull Request #156882 · rust-lang/rust

Stabilise a bare-minimum (dyn-incompatible, but could be in the future) Allocator trait, alongside Box::new_in(), Vec::new_in(), the System Allocator impl, and a blanket impl of Allocator for T: Gl...

github.com

nia (cia asset)@nia.is.fckn.gay · 2mo ago

CHAT WE HAVE STABLE ALLOCATORS