I love Rust, but I think my biggest growing gripe is its current lack of reasonable compile-time capabilities. TIL that you can’t use an associated const of a trait as a const generic parameter. It counts as a const generic “expression” even though it’s just a value. WTH?!

We're nearing the new year, so time for another Jan 1st Q&A! Ask questions at wewerewondering.com/event/01KDDA... — none too big or small. I'll get to as many as I can, and upload the recording after the fact. Stream starts 1/1/26 at 2:30p UTC @ youtube.com/live/g1ZgInF.... Hope to see you there ❤️

Picture of M31 taken with our new telescope. This is so much better than any space photography I've ever done in the past it's not even funny. Interested to really learn to use this thing!

Christmas surprise; I fell and chipped my front tooth this morning. Luckily, the dentist was able to make an emergency visit. It was a small chip so it was filed down and looks alright. Not the best start ever to Christmas eve, but thanks to the kindness of the dentist, it will be OK.

I wonder if @fasterthanli.me knows of any cute way around this: bsky.app/profile/robp...

Rust feature I wish existed; initialize const based on generic parameter: ``` fn foo<R: Bound>(r :R) { ... const IS_IMPL: bool = TypeId::of::<R>() == TypeId::of::<ConcreteImpl>(); ... } ``` Why isn't this supported?

Streisand effect, let's gooooo!!!

Bari Weiss doesn't want you to see this... x.com/i/status/200...

Nice! Somebody had to say it: www.justfuckinguseneovim.com

Peter Theil knows about the antichrist!

So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

We relied on pyranges (v0) for a while in pyroe (which made splici/splicu transcriptomes for alevin-fry). It was nice to use, but many breaking changes eventually led us to rewrite what we needed in Rust in grangers (crates.io/crates/grang...). I'm happy to see v1 & that it's Rust-powered!

I appreciate that the Rust compiler recognizes that I am not good at spelling ...

“The radio plays what they want ya to hear. Tell me it’s cool; I just don’t believe it.”

Yea, it's because Biden was actually attempting to govern the nation competently and legally. Trump, OTOH, is flagrantly breaking the law and doing everything he can to destroy the republic. 36% is an insanely high approval rating for someone actively trying to end the American experiment...

GPT-5.2 Lies About Reading your Documents blog.stephenturner.us/p/chatgpt-li...

I am not all in on AI. Actually, I'm incredibly skeptical of the current AI hype. Nonetheless, I think eliminating the stats department is insanely foolish. It's like a microcosm of how the US itself is attempting STEM seppuku. U of N needs new leadership, immediately. Absolutely no confidence.

OMG.... samtools collate is taking *FOREVER*. WTH?

Rust 1.92.0 has been released! 🌈 🦀 This version adds RwLockWriteGuard::downgrade(), adds Location::file_as_c_str(), improves diagnostic and validation for various attributes, no longer warns for unused Result<(), Infallible>, and more! Check out the announcement: blog.rust-lang.org/2025/12/11/R...

My first Rust toy tool (just for learning purposes)!!! The performance (both time and memory) is good! Rust is hard to learn, and I still need more practice! github.com/shenwei356/f...

If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...

The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/

Brown to Panda Nano conversion #2 now underway!

🧬Explore the latest from Bioinformatics Advances: “Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.”   Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292 Author: @ducktapeprogrammer.bsky.social

Oh thank god the Chiefs lost!

And if you have a .fastq.gz.mim already present, you get another up to 2x speedup (or more with >6 cores).

The sour grapes ex-academic over on the other site is utterly insufferable. The wholesale dismantling of American science is OK, and deserved, in fact, because the existing system has structural problems. That's a total non-sequitur, bro.

Great points! I'll also note that even when instructions do ask me to evaluate a candidate by my own department's standards, I include specific and detailed caveats where they apply (e.g. it makes little sense to evaluate a med school candidate on my (hard $, CS) dept's teaching expectations).

Great question! 1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.

Kudos to MCPS for making the right call and opening schools on time today!

Ok, this is a first. I have a fastq file with an accession that I *can not find anywhere*. That is, the file has an SRR#, that is embedded in the read headers (and matches the file name), but I can't find this file anywhere (ENA/SRA/etc.). Has anyone ever encountered this?

Current AI agent assessment for coding: ChatGPT: absolute trash for anything but plotting Gemini 3 (via antigravity): made nice suggestions, then proceeded to totally break the code Claude: chatty and hit or miss, but reliably much better than others and often actually useful.

I have to say, Lamar Jackson is an elite quarterback, absolutely! However, this Lamar Jackson (random part of leg/foot), who skips practice all the time and can't throw touchdowns... not a fan of the second dude.

I'll be giving a talk to a CS club at a local high school in January. I welcome any suggestions of topics / activities that people have had success with in such a group. I want to talk about CS (not just AI) and it'd be cool to work in some genomics!

Dear MCPS, I'm closely monitoring your "closely monitoring" nonsense...

github.com/bede/deacon For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️

We now have feature parity in Rust (index construction and reading). Multithreaded decompression and parsing is also about 30% faster than C++! Checkout the mimrs directory in the GitHub repo!

It warms your heart to see one if your favorite devs start to star a bunch of dev-related Rust crates.

We now have a working proof-of-concept implementation of the mim-enabled fastq parser in Rust. It uses needletail for the actual parsing and is *already* ~30% faster than the C++ implementation! Very excited about where this will go! cc @curiouscoding.nl

GFF was originally conceived of as an interchange format for chaining together gene subfeatures (splice sites, promoters, exons, etc) predicted by various specialized tools (HMMs, decision trees, neural nets, SVMs); rather like GENSCAN, but with the idea you could mix & match subfeature predictors

"Sure, bedtools is great and happily used by literally everyone, but, it could be bedder" That takes some serious courage. Kudos Brent and @aaronquinlan.bsky.social !

The MCPS school decision today was so bad they needed to apologize. Thanks for the apology, but it's meaningless without real change. You consistently fail MC parents & students with these poor decisions. Please, do better! If you have to subdivide the county into several districts, then do it!

The Montgomery County, MD school district should be at least 4 separate school districts. Does anyone know the proper people to contact to propose such an initiative?

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Show me an administration that cares and I'll show you an administration that isn't in power in the US. Wouldn't it be ironic if a federal judge ordered a stop to this, brining about the 10th or so full-blown constitutional crisis of year 1 of the last presidency of the US republic?

After watching that painful Ravens game on Thurs. It's glorious to see the Bills take the Steelers to task!

@profanity.accountant, let's take account.

I can't stay quiet about what RFK jr is doing to the CDC and FDA: stevensalzberg.substack.com/p/dont-trust...

They should just have no tips at all. Actually, having a livable wage for service industry workers and no tips is a hugely progressive idea. Tipping culture hurts consumers, and many servers. It really just helps businesses defray the real costs and risks of employment to the whims of customers.