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Seth Stadick

@ducktapeprogrammer.bsky.social
814 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
> rather than a regular compiler. He was just blissfully unaware that macros were great for defining a language, but once they had it, they should have built a compiler. ... sounds familiar
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Seth Stadick @ducktapeprogrammer.bsky.social · 28/08/2026
> I remember the director of that division once telling me, "we are the greatest users of computing at Bell Labs. We use more time than anybody else. We depend on it much more." And that was because they're using a macro-processor, which runs slow by about a factor of a hundred,
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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
It's a weird phenomenon to find myself re-wording things that I have written, just to avoid AI-isms.
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
My hourly switch between "AI is amazing and changing everything" to "this is heresy and we should burn it all down, code was meant to be typed" is getting exhausting! But I'd love to see what you've got when you're ready to get it out there!
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
Because I'm feeling particularly AI conscious right now, just want to say that "Big caveat" was actually my own wording here. I'm that original it seems 🫥
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
I haven't decided how I want to go about an actual response to that polars article yet, but here's the VERY unofficial numbers for the datasets in that blog post SuperIntervals still wins in some cases, but returns results in reverse ordering. If that doesn't matter, SuperIntervals is the fastest
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
Big caveat - rust-lapper won't work nicely for insertions. But on the datasets in that polars article, lapper-v2 is 1.35x to 1.8x faster than coitrees, including construction time. Thanks for pointing out that link, fixing it!
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
Perf: This should generally be 1.5x faster than the original rust-lapper, and 76-90x faster on the worst case scenarios. Huge thank you to the bio-polars team that put out this blog post which inspired the second look at rust-lapper biodatageeks.org/polars-bio/b...
biodatageeks.org
Interval operations benchmark — update September 2025 - polars-bio
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
While the ideas were mine (and lean heavily on ideas from super-intervals), the implementation in this case was nearly 100% AI written. While I've reviewed it all, tested it all, etc, I still have mixed feelings about shipping AI generated code in a repo that was previously human-only.
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
Why beta? This is a drastic change from the original rust-lapper, and while I've tested it every way I can think of, I'd still rather not pull the rug out on people who use this and don't have appropriate version guards set up.
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Seth Stadick @ducktapeprogrammer.bsky.social · 20/08/2026
The main change is adding 32-interval block index that allows for skipping, as well as doing simd comparisons when there are some matches present, while maintaining forward ordered iteration on query. See the PR for details: github.com/sstadick/rus...
github.com
Add a portable SIMD block index for forward overlap queries by sstadick · Pull Request #27 · sstadick/rust-lapper
A note on AI 🤖 I used agents extensively to benchmark possible implementations and explore different indexing methods. The two key ideas, the block-based index and the SIMD overlap masks, were, sur...
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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 · 19/08/2026
Are they friendly enough to scan a copy?
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
Lastly, I'm a contributor to the `pixi-build-mojo` backend, which is what @prefix.dev can use to build Mojo projects: pixi.prefix.dev/latest/build... And allows you to install dependencies directly from GitHub, which is really cool!
pixi.prefix.dev
pixi-build-mojo - Pixi
Pixi Documentation — Next-gen package manager for reproducible development setups
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
mojopt - A Mojo library for parsing CLI args based on the Rust Structopt crate. github.com/sstadick/moj...
github.com
GitHub - sstadick/mojopt: Structopt inspired command line arg parser in Mojo
Structopt inspired command line arg parser in Mojo - sstadick/mojopt
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
extramojo - Things I missed in the Mojo stdlib, such as Rust-like Reader/Writer, BitVec, bstr, etc github.com/ExtraMojo/Ex... Docs site here: extramojo.github.io/ExtraMojo/ex...
github.com
GitHub - ExtraMojo/ExtraMojo: A library of nice to have things not found in the current mojo stdlib
A library of nice to have things not found in the current mojo stdlib - ExtraMojo/ExtraMojo
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Seth Stadick @ducktapeprogrammer.bsky.social · 18/08/2026
hat - a thin wrapper for pixi for a more cargo like interface to working with mojo projects github.com/sstadick/hat
github.com
GitHub - sstadick/hat: Thin wrapper over pixi to be used as a mojo build tool.
Thin wrapper over pixi to be used as a mojo build tool. - sstadick/hat
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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
github.com/modular/modu... It really is there! 🔥
github.com
modular/KGEN at main · modular/modular
The Modular Platform (includes MAX & Mojo). Contribute to modular/modular development by creating an account on GitHub.
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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
Notably, phase 2 should start soon, which has the two things I'm most excited for: concurrency and pattern matching. mojolang.org/docs/roadmap...
mojolang.org
Mojo roadmap | Mojo
A summary of our plans and priorities to improve the Mojo language.
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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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Reposted by Seth Stadick
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
What I'm adding essentially a forward iterating version of super-intervals, where I have 32-interval blocks with forward skipping links, along with simd checks for all intervals in each block of 32. Substantially more complex than the original lapper sorted list+binary search.
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Seth Stadick @ducktapeprogrammer.bsky.social · 28/07/2026
The speedups roughly 1.5x faster on the general cases and ~76x faster on the worst case in that benchmark post. Lapper as an idea originates from @brent-p.bsky.social, and a large part of its uniqueness is how simple it is.
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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
An optional compile-target that offers a lot of guarantees seems like it can only be a good thing though? Having watched a lot of his interviews, I read his Rust jabs as knowing what everyone is going to poke at than genuine malice on his part. But agree that it doesn't present well in isolation.
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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 · 16/07/2026
I'm glad there is at least one group Zigging while the rest of us are Zagging, at least so we have a control group 😂
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Seth Stadick @ducktapeprogrammer.bsky.social · 16/07/2026
Certainly someone could Zag and add more features, but often the most important design choices are in what isn't there, and that's a lot harder to curate.
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Seth Stadick @ducktapeprogrammer.bsky.social · 16/07/2026
I'm not sure. The Zig project has put a lot of work into specifically not being beholden to anyone, or any timeline. And in that vacuum, why not spend the human time to do things?
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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
The article is about pharma, but I feel like it’s generally applicable to ideation in the bio space right now. Companies with the best infra will scale better.
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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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Seth Stadick @ducktapeprogrammer.bsky.social · 13/07/2026
Super impressive numbers down the thread! What did you start off with before moving to wgpu? cuda-oxide and CubeCL have been on my list to try for a while but just haven’t had the time.
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