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Seth Stadick

@ducktapeprogrammer.bsky.social
813 followers 486 following 346 posts

Bioinformatics. Rust. Mojo.

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Seth Stadick @ducktapeprogrammer.bsky.social · 09/09/2026
GPU kernels in Rust! developer.nvidia.com/blog/introdu...
developer.nvidia.com
Introducing CUDA Rust: Two Tracks for Writing GPU Kernels | NVIDIA Technical Blog
In September 2026, NVIDIA announced it is leaning into native GPU programming in Rust. CUDA C++ and CUDA Python are mature, enterprise-grade toolchains, and NVIDIA will be growing and maturing CUDA…
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Seth Stadick @ducktapeprogrammer.bsky.social · 09/09/2026
enums and match proposals for Mojo: github.com/modular/modu...
github.com
[mojo-lang] Add the pattern matching + enum proposals, NFC · modular/modular@0bcbbfe
This checks in the proposals for pattern matching and enums, for community discussion on the forums. PRDT-304 MODULAR_ORIG_COMMIT_REV_ID: f55f28046b394f62f40eb122241df148b4dee88f
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Seth Stadick @ducktapeprogrammer.bsky.social · 28/08/2026
ls -transubstantiationalist That works. tmpout.sh/5/2.html
tmpout.sh
Interview: Doug McIlroy ~ tmp.0ut Staff
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Seth Stadick @ducktapeprogrammer.bsky.social · 27/08/2026
🔥🔥🔥
Using noodles instead of htslib is fire
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Seth Stadick @ducktapeprogrammer.bsky.social · 25/08/2026
One of the most balanced articles I've read on how LLM usage and learning interact: larsfaye.com/articles/ai-... Well worth the 10 minutes to read it.
larsfaye.com
AI Coding will Prevent Expertise | Lars Faye
The need for ongoing friction in long-term skill formation.
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Seth Stadick @ducktapeprogrammer.bsky.social · 24/08/2026
Jupyter and REPL support for mojo via Jeremy Howard: github.com/AnswerDotAI/...
github.com
GitHub - AnswerDotAI/xmojo: Experimental interactive Mojo environment built on Modular's ORC compiler stack
Experimental interactive Mojo environment built on Modular's ORC compiler stack - AnswerDotAI/xmojo
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Seth Stadick @ducktapeprogrammer.bsky.social · 21/08/2026
A good write up on how the new fast floating point arithmetic in rust v1.98.0 can be used pythonspeed.com/articles/fas... releases.rs/docs/1.98.0/ (the `algebraic_*` methods)
pythonspeed.com
Faster floating point math with Rust’s new API
Compilers have a hard time optimizing floating point math. Rust has a new API to fix this.
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
rust-lapper v2.0.0-beta.1 is published! This is a large update to mitigate the worst case scenario where there are large intervals that envelope many smaller intervals. It's a lot faster (more details below), and keeps the same api, as well as the BITS implementation. crates.io/crates/rust-...
crates.io
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
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
github.com/microsoft/sn... There is a rust crate as well. tl;dr; Allocator that is great when allocations on one thread are freed by a different thread
github.com
GitHub - microsoft/snmalloc: Message passing based allocator
Message passing based allocator. Contribute to microsoft/snmalloc development by creating an account on GitHub.
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Seth Stadick @ducktapeprogrammer.bsky.social · 19/08/2026
These new chips (meaning all the Cerebras chips, not just this one) are so cool. I can’t wait till the older generation falls out of inference service so we can use it for other stuff
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
Now that it's open source, I can plug a few helper libraries I've been pulling along to 1.0! But first, the best spot to start is mojolang.org For looking for libraries: github.com/modular/modu...
mojolang.org
Mojo
The Mojo programming language
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
Mojo is now fully open source! www.modular.com/blog/mojo-op...
modular.com
Modular: Mojo🔥 is now open source!
The Apache 2.0 license is the gold standard for programming languages and compilers, because it provides great flexibility to be used in all sorts of applications. The LLVM extensions to the license f...
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Seth Stadick @ducktapeprogrammer.bsky.social · 14/08/2026
This is awesome
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Seth Stadick @ducktapeprogrammer.bsky.social · 13/08/2026
"<new format> is easily readable in any spreadsheet software or text file editor" Why do we keep doing this to ourselves.
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Seth Stadick @ducktapeprogrammer.bsky.social · 11/08/2026
Mojo 1.0 is out! www.modular.com/blog/modular... Compiler open sourcing still looks on track for sometime in the next few months.
modular.com
Modular: Modular 26.5: Mojo 1.0 is here!
Today, the Mojo language officially reaches 1.0: a milestone the language has been building toward since its first release in 2023. Mojo has grown into a general-purpose language with a vibrant develo...
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Rob Patro @robp.bsky.social · 29/07/2026
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... 🧵
Crop of the preprint's first page. The title is "seqproc: An
efficient, flexible, and concise tool for sequence geometry description and
transformation." Authors are Noah Cape, Elan Fisher, Daniel Liu, and Rob Patro.
The abstract introduces seqproc, EFGDL, and the antisequence execution engine.
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Seth Stadick @ducktapeprogrammer.bsky.social · 28/07/2026
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?
biodatageeks.org
Interval operations benchmark — update September 2025 - polars-bio
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Seth Stadick @ducktapeprogrammer.bsky.social · 27/07/2026
July Scientific Computing in Rust scientificcomputing.rs/monthly/2026...
scientificcomputing.rs
Scientific Computing in Rust
the Scientific Computing in Rust annual workshop and monthly newsletter.
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Seth Stadick @ducktapeprogrammer.bsky.social · 22/07/2026
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. ...
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/07/2026
"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/...
codeberg.org
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...
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Seth Stadick @ducktapeprogrammer.bsky.social · 15/07/2026
... I think I actually liked writing all the stupid little glue scripts.
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Seth Stadick @ducktapeprogrammer.bsky.social · 13/07/2026
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.
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Seth Stadick @ducktapeprogrammer.bsky.social · 13/07/2026
purplesyringa.moe/blog/quadrup... I have not seen likely/unlikely used in order to allow the cpu to parallelize loop instructions before. Very cool.
purplesyringa.moe
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...
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Seth Stadick @ducktapeprogrammer.bsky.social · 13/07/2026
> 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...
mattshlosberg.substack.com
Biotech Is Entering Its Netflix Era
AI Just Created a Bigger Problem Than Cancer
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/07/2026
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
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Seth Stadick @ducktapeprogrammer.bsky.social · 05/07/2026
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.
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Kevin Riggle @kevinr.free-dissociation.com · 05/07/2026
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.
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Seth Stadick @ducktapeprogrammer.bsky.social · 02/07/2026
Yearly reminder to not use the default hashmap in rust unless you really do need the hashdos protections. nnethercote.github.io/perf-book/ha...
nnethercote.github.io
Hashing - The Rust Performance Book
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Seth Stadick @ducktapeprogrammer.bsky.social · 02/07/2026
scientificcomputing.rs/2026/ Scientific Computing in Rust Annual (free) Workshop coming up on July 8!
scientificcomputing.rs
Scientific Computing in Rust 2026
the Scientific Computing in Rust annual workshop and monthly newsletter.
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Seth Stadick @ducktapeprogrammer.bsky.social · 29/06/2026
Shade throwing quote aside - that was a fantastic post about the evolution of mutability tracking / language design.
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Seth Stadick @ducktapeprogrammer.bsky.social · 29/06/2026
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
docs.rs
_02__reference_types in dtolnay - Rust
Accurate mental model for Rust’s reference types
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Seth Stadick @ducktapeprogrammer.bsky.social · 24/06/2026
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.com
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...
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Seth Stadick @ducktapeprogrammer.bsky.social · 17/06/2026
nathan.rs/posts/gzip-lm/
nathan.rs
Can gzip be a language model?
A while back I wrote about language modeling without neural networks, where I generated Shakespeare with an unbounded n-gram model: no weights, no training, …
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Reposted by Seth Stadick
Rob Patro @robp.bsky.social · 14/06/2026
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/
combine-lab.github.io
salmon
Fast, accurate transcript quantification from RNA-seq reads.
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Reposted by Seth Stadick
John D. Cook @johndcook.mathstodon.xyz.ap.brid.gy · 11/06/2026
Solving a chess puzzle with Claude and Prolog www.johndcook.com/blog/2026/06/11/p…
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Igor Martayan @imartayan.bsky.social · 15/06/2026
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
phd.martayan.org
Algorithm design and implementation for the scale of sequencing data
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Yaron Minsky @yminsky.bsky.social · 11/06/2026
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...
blog.janestreet.com
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.
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Seth Stadick @ducktapeprogrammer.bsky.social · 01/06/2026
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...
Example showing the StriderChat where the agent is walking the user through what a visually selected block of lua code does.
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Loris Cro ⚡ @kristoff.it · 30/05/2026
New Zig Devlog about ELF linker improvements, featuring 30ms rebuilds of a Tetris game. Incremental is coming and y'all not ready. ziglang.org/devlog/2026/#2026-05-30
ziglang.org
Devlog ⚡ Zig Programming Language
https://ziglang.org/devlog/2026/#2026-05-30
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Seth Stadick @ducktapeprogrammer.bsky.social · 29/05/2026
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!
github.com
GitHub - sstadick/refill
Contribute to sstadick/refill development by creating an account on GitHub.
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Seth Stadick @ducktapeprogrammer.bsky.social · 27/05/2026
In case you don't follow it already, reminder that this exists! scientificcomputing.rs/monthly/
scientificcomputing.rs
Scientific Computing in Rust
the Scientific Computing in Rust annual workshop and monthly newsletter.
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Reposted by Seth Stadick
Rob Patro @robp.bsky.social · 26/05/2026
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!
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Seth Stadick @ducktapeprogrammer.bsky.social · 26/05/2026
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
raw.githubusercontent.com
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Rob Patro @robp.bsky.social · 25/05/2026
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
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
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Reposted by Seth Stadick
nia (cia asset) @nia.is.fckn.gay · 24/05/2026
WHEEEEEEEEEE github.com/rust-lang/ru...
github.com
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...
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/05/2026
'Why? Because, if you're unable to type out what you have in mind to a certain degree of precision that means you didn't really have it in mind. You were hallucinating understanding, the same as an LLM.' haskellforall.com/2026/05/type... (In case you missed it on HN)
haskellforall.com
Type out the code
Freecoding improves broader programming proficiency
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Seth Stadick @ducktapeprogrammer.bsky.social · 17/05/2026
Hoping to see more about this at Computex in June: github.com/NVlabs/cuda-... I still can’t tell if it’s just an experiment, or a serious effort.
github.com
GitHub - NVlabs/cuda-oxide: cuda-oxide is an experimental Rust-to-CUDA compiler that lets you write (SIMT) GPU kernels in safe(ish), idiomatic Rust. It compiles standard Rust code directly to PTX — no...
cuda-oxide is an experimental Rust-to-CUDA compiler that lets you write (SIMT) GPU kernels in safe(ish), idiomatic Rust. It compiles standard Rust code directly to PTX — no DSLs, no foreign languag...
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Seth Stadick @ducktapeprogrammer.bsky.social · 10/05/2026
I have been writing a bit of Zig to see what their new async io model looks like (it's awesome), but have found that the language itself is just so much fun to work in. This is one of the most ergonomic design choices I could possibly think of for a formatter: matklad.github.io/2026/05/08/s...
matklad.github.io
Steering Zig Fmt
Two tips on using zig fmt effectively. Read this if you are writing Zig, or if you are implementing a code formatter.
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Seth Stadick @ducktapeprogrammer.bsky.social · 08/05/2026
The slab backed records really do speed up some workflows! Initial tests in perbase showed a 1.4-1.5x speed up on the path (base depth with mate fix) that makes the most use record data.
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Seth Stadick @ducktapeprogrammer.bsky.social · 01/05/2026
The slab based backing of records is a very cool idea that I'm excited to try out. Great write up. (yes this is meaningfully different that noodles)
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