This is one of my favorite new interactions with coding agents: "hrm, the test failed. Let me look why" "Oh, it's because of X. I was doing it like Y, but I should be doing Z; I see that clearly now." Meanwhile, I told it explicitly to avoid the Y footgun by doing Z in at least 4 places.

What's your biggest practical issue with large gzip files? I've been polishing the mim API and CLI the last few days and could integrate it in some tools.

There's meta-cognition, which is most often thinking about your own thinking. What do people call it when they watch AI models talk to themselves (Opus/Codex), and then think about the model's own "internal" monologue?

US science is in trouble, and it doesn't have to be stevensalzberg.substack.com/p/making-ame...

So i've been doing this, and spamming another thread with updates. I will move that over here now. I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.

I think this oversimplifies several possibilities. First, not all people have the same notion of wonderful place to live. Second, the market is not always a true reflection of value. Third, extreme distortions in the local economy along with employers disallowing remote work has big implications.

Counterpoint: I don't want a slimmer macbook pro. I think I'll go with the M5 Max before the redesign. www.creativebloq.com/design/produ...

This is a very interesting and relevant PPoPP paper from this year for genomics folks! dl.acm.org/doi/10.1145/... BWA-compatible (identical) output w/o the massive index size increases of BWA2 or BWA-MEME... & faster than both. To boot, no requirement for special hardware; it uses SIMD on CPUs.

Put in a request to order some equipment on Jan 20. The university still hasn't placed the order. Since then, the main hardware price has increased about $1,500. How do I convey that time is literally $, and that it's critical to order ASAP?!!

And a pedophile.

Or malicious incompetence!

$ jj describe -m "Hello, world!"

I wonder if this is the kind of project that @anthropic.com might be willing to sponsor? If so, please let me know how to get in touch!

Community service: Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent. github.com/RagnarGrootK...

@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...

I have to believe in the many worlds hypothesis because, somehow, we ended up in the worst of all possible worlds. I have to believe worlds that evaded this horrific fate must exist.

I think that all of the decision makers for @montgomerycountymd.bsky.social should be sent (at tax payer expense) to spend the rest of the winter in and around Boston, with a duty to report back what the shape of competence looks like, and a concrete (snowcrete?) plan to improve their operations!

Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240

No @mcdotnow.bsky.social schools; it is not reasonable to cancel school again tomorrow. You've and an *entire* week to perform snow and ice removal. Businesses are open, Universities are open, recreational activities & museums are open. Children need to return to school tomorrow! This is wrong.

I'm looking to update the SRA growth curve for the intro lecture of my computational genomics course, and I noticed that the data traces provided by SRA end in 2024 ... Does anyone have an idea what's up here or how to get more up-to-date data? www.ncbi.nlm.nih.gov/sra/docs/sra...

I cannot begin to convey how frustrating it is that different systems choose subtly different default installation paths (e.g. `lib` vs `lib64`, even though they are both 64-bit systems) when building the *same* project (in this case zlib-ng) from source. WHY?!?!

E.g. here anaconda.org/channels/con...

Ok a new bioconda recipe question. Any idea why the build system seems unable to find the package ‘zlib-ng-compat’, despite the fact that this package clearly exists on conda forge?

I have a better idea, why don't @montgomerycountymd.bsky.social schools explain why they've cancelled school for an entire week for ~7" of snow, and why it's not a deriliction of their duties? I think it's time for some new leadership, some legal action, or both... mocoshow.com/2026/01/29/m...

What nonsense. You do what you want, Carl, but I think silencing yourself for being called out for such imagined "transgressions" is counterproductive. Personally, I feel people going around policing such speech calling out fascism, and insufficient responses to it, are "problematic".

Frankly, it's probably time that @montgomerycountymd.bsky.social scools face some kind of legal action for their deriliction of duty. It's come to be expected, but it's so incredibly disappointing.

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

Generating minimum-density minimizers https://www.biorxiv.org/content/10.64898/2026.01.25.701585v1

Let's be clear. School closures have already been preemptively made until (including) Thurs. Pushing closures, or even delays, any further than than is simply abuse of the system and deriliction of duty on the part of @montgomerycountymd.bsky.social's schools! mocoshow.com/2026/01/27/s...

I often think about design decisions and implementation details while doing my cardio (stationary bike). Is it the case that AI agents will let me interactively direct that design and implementation *during* my cardio? Testing that now!

I can see that @montgomerycountymd.bsky.social schools are back to their wanton irresponsibility, preemptively cancelling school on THURSDAY! Honestly, it's shameful. I live on a tertiary road & it has already been cleared. I could even understand cancelling tomorrow, but Thurs. a a bridge too far.

Awesome! Looking forward to your guys' feedback :).

Today's journal club led by @imartayan.bsky.social and Lucas Robidou. 👋🏻 @robp.bsky.social @jermp.bsky.social

As my snowstorm project, I finally read up on how to solve a rubick's cube, and got some practice. I'm not going for speed or anything, but now I feel like I have a solid understanding of the principles and strategies. It's cool!

The little pieces sticking off this ball are like real-life surface normal vectors.

They are trying to distract from the fact that the administration is violating a direct congressional mandate to stop protecting pedophiles, because the administration is shielding pedophiles!

If you intend to record ICE on your phone, make sure mobile data upload to the cloud is enabled.

Happy to share I recently received the ETH Doctoral Medal. More information on LinkedIn: www.linkedin.com/posts/canfir... @safari-eth.bsky.social @omutlu.bsky.social

Optimizing sparse and skew hashing: faster k-mer dictionaries https://www.biorxiv.org/content/10.64898/2026.01.21.700884v1

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster! www.biorxiv.org/content/10.6...

Rust 1.93.0 has been released! 🌈 🦀✨ This release includes a new musl version for the *-linux-musl targets, adds support for #​[cfg] inside asm!(), and adds [T]::as_array, VecDeque::{pop_front_if, pop_back_if}, Vec/String::into_raw_parts, fmt::form_fn, and more! ✨ blog.rust-lang.org/2026/01/22/R...

Rust 1.93is out! blog.rust-lang.org/2026/01/22/R...

Great resource! However, I must say that if I was ever in a position of administrative authority over such things, the first thing I would do would be to put a hard cap on the number of format changes that biosketches can require. No more than one format change per decade!

🦀🦀

The fact that we might possibly, or not, be getting 0-128” of snow this weekend puts me in a quantum superposition of having either far too much, or far too little toilet paper, bread and milk.

Oh noes; Bioinformatics name collision! www.biorxiv.org/content/10.6... collides with pubmed.ncbi.nlm.nih.gov/29936185/

Plus, the name is already obvious "STARS" (can be abbreviated "STA-RS"!

Any bioinformatics friends out there have a huge load of AI code credits & want to try smth crazy (but amazing if it works)? What if we ask Claude to port STAR to Rust? Current development and maintenance on this central tool has largely stalled, but I think a lang change would reinvigorate it!

Crazy idea. What if we just didn’t sell the plurality of all of the world’s memory to the AI companies? Or what if we charged them a massive “negative externality” tax to acquire it in large quantities?