Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

#rustlang PSA: you probably don't want #[allow(dead_code)], you probably want #[expect(unused)]

Any recommendations for a github CI plugin for performance monitoring? Thinking of using github-actions-bench [0] which makes decent plots, in combination with maybe iai [1] for measuring CPU cycles (wall-time is too flaky in GH actions). 0: github.com/benchmark-ac... 1: github.com/bheisler/iai

Excited to say that we're looking to hire someone to focus on OxCaml education! We're doing enough to change the language that we have a pretty big internal education task ahead of us, and we want to hire someone to focus on it! Please share this with others! www.janestreet.com/join-jane-st...

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

Some very interesting preliminary benchmarks between Stringzilla and some Rust libs from Ash: x.com/ashvardanian... Including some alignment comparisons.

Perl 👀 x.com/jxmnop/statu... To be fair, Perl was the OG write only vibe coding language.

Another deep dive in the technology behind Conda package managers: file linking! Did you know that there are symlinks, hardlinks and reflinks? Reflinks are the best – copy on write is space efficient and isolates the cache. Learn more: prefix.dev/blog/what-l...

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

TIL - zless linux.die.net/man/1/zless

Q3 Mojo roadmap looking awesome! Highlights: - apple Silicon GPU Support - requires clauses - struct extensions forum.modular.com/t/mojo-q3-ro...

@steveklabnik.com Did you write an article about ways you wish Rust Iterators had evolved differently? Or remember who wrote that? Mojo is about to start in on its iterator abstraction and I was looking for lessons learned from Rust, but can't find that article. I might be imagining this it 😬

Looking for papers to cite for tight definitions of global alignment, semi-global alignment, and mapping... I would probably be the person to ask, yet here we are.

Catching up on some releases: Perbase 0.10.3: bugfix for --mate-fix when MAPQ scores are equal github.com/sstadick/per... rust-lapper 1.2.0: fix to the BITS count algorithm for 25-30% improvement in perf github.com/sstadick/rus...

Happy if-let-chain stabilization day to all those who celebrate!

ExtraMojo update is live! Two added datastructures with BitVec and BBHash. Updated for Mojo 25.4. extramojo.github.io/ExtraMojo/Ex... extramojo.github.io/ExtraMojo/Ex... github.com/ExtraMojo/Ex...

ish v1.2.0 released and available via conda! github.com/BioRadOpenSo... Updates to Mojo 25.4 Bugfix for AVX512 on short queries Improvement for saturating arithmetic to use LLVM intrinsics.

FastGA: Fast Genome Alignment https://www.biorxiv.org/content/10.1101/2025.06.15.659750v1

Why do some have a shit time with LLMs for programming while others love it? To succeed, the latter group tacitly creates tons of scaffolding and gain weird new skills. While it works, this posts explains how doing all that is an incidental consequence of bad interaction design in coding AI agents.

Mojo 25.4 is out! This is the version where the beta version of Python bindings is live 🔥 docs.modular.com/max/changelog/

And here's a blog post, announcing the release! blog.janestreet.com/introducing-...

Well worth 10 minutes to read this. I had no idea that's how they worked.

Yearly PSA: you probably don't actually want to be using the builtin HashMap hashing algo in Rust stdlib. nnethercote.github.io/perf-book/ha...

It's very cool to me that this is possible. Mojo doesn't have saturating add/sub ops (yet). But you can add them yourself with inline llvm intrinsics. Delivering on the promise of "moving the magic out of compilers and into libraries". Notably, this implementation will work for both scalar simd.

I presented on ish at the Modular Community meeting today! It’s geared toward non-BFX people and covers what ish does at a high level. youtu.be/1Q4RNVOSAH0?...

ish is a grep-like CLI tool that uses optimal alignment instead of exact matching. It’s record-type aware, supporting line, FASTA, and FASTQ records. Built in Mojo as a proof of concept for bioinformatics. 🧵1/5

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

“A program is a shared mental construct that lives in the minds of the people who work on it. If you lose the people, you lose the program. The code is merely a written representation of the program, and it's lossy, so you can't reconstruct a program from its code.” gist.github.com/onlurking/fc...

Always odd to imagine that some of the superstar engineers I look up to also have managers and meetings and are generally normal people. > I summarize each week for my manager. www.brendangregg.com/blog/2025-05...

ohadravid.github.io/posts/2025-0... - MaybeUnit to avoid needless initialization - Using zerocopy::AsBytes to compare a struct with multiple fields instead of the default PartialEq

new #rustlang crate drop: iddqd! ID-based maps where keys are borrowed from values. Four maps are included: IdOrdMap, IdHashMap, a bijective (1:1) BiHashMap and a trijective (1:1:1) TriHashMap. At Oxide we've found this pattern to be very useful. iddqd is no-std compatible, too! docs.rs/iddqd

Great post from @bernsteinbear.com! bernsteinbear.com/blog/simple-...

Some great nuggets of info: vec[0; len] uses a specialized alloc_zeroed call Pre slicing and custom type that checks range to avoid bounds checks inside loops Discussion on stack size being larger in rust and how that changes optimizations Move panic and string fmt out of inlining

You know what's just awesome? When someone is working on a method and they ask the authors of a "competing" method to merge in the changes that they, themselves, proposed to make the competition look better in the benchmarks. Kudos, @curiouscoding.nl : github.com/Martinsos/ed...

Oxide’s Compensation Model: How is it Going? oxide.computer/blog/oxides-...

Moving the counter back to zero days since parsing fasta/fastq was the bottleneck.

Moving the counter back to zero days since FASTA/FASTQ parsing was found to be the bottleneck.

🎉 I've bumped github.com/facet-rs/facet from "highly experimental" to just "experimental" — it has a pretty well-designed set of types, the derive macro is quite capable already, the JSON read+write crates are iterative (!!), go play with it!

🦀 Hello World! The Rust project now has an official presence on Bluesky! ✨ We'll be posting the same on our Mastodon and Bluesky accounts, so you won't miss anything on either platform.

Read this paper from Twitter/X and it was a good read. academic.oup.com/bioinformati...

As someone actively getting up to speed on alignment methodology, @curiouscoding.nl's work has been invaluable. I keep going back to it when reading other sources. I can't wait for the full thesis 👀

Is this finally the breakthrough for io_uring for general use in Rust? chesedo.me/blog/monoio-...

"...asking if there was any documentation for developers to onboard the new code base. Ginsparg responded, “I learned Fortran in the 1960s, and real programmers didn’t document,” which nearly sent me, a coder, into cardiac arrest."

The next version of Rust might be one of the most transformative to the Rust ecosystem due to support for up-casting of trait objects. This makes `Any` significantly more powerful and potent!

"This essay introduces the term hardware lottery to describe when a research idea wins because it is suited to the available software and hardware and not because the idea is superior to alternative research directions." arxiv.org/abs/2009.06489

Thanks to all the helpful replies I found a way to solve my issue. If anyone else runs into it, here is how you can efficiently use FromStr on a String with a no-op path for String to String: lucumr.pocoo.org/2025/3/23/fr...

Wow, these crates seem to provide some very serious new functionality in rust! I wonder if anyone has experience with them yet: www.reddit.com/r/rust/comme...

Rob Landley wrote what I believe to be the most accurate historical retelling of how we ended up with a mess on the file system. That retelling also has a lesson at the end about bureaucracy :) lists.busybox.net/pipermail/bu...

This is very cool work and I'm happy to see it published. Vcfexpress by @brent-p.bsky.social and @aaronquinlan.bsky.social allows building (essentially) arbitrary VCF filters expressed in lua code with parsing & eval powered by rust! academic.oup.com/bioinformati...

The Rust macros we've all been waiting for? There must be a catch... github.com/wdanilo/eval...