Seth Stadick
@ducktapeprogrammer.bsky.social
Bioinformatics. Rust. Mojo.
hat: a cargo-like wrapper around pixi for managing mojo projects.
github.com/sstadick/hat
It literally just shells out to pixi and is meant to be very transparent! 100% compatible with pixi.
github.com/sstadick/hat
It literally just shells out to pixi and is meant to be very transparent! 100% compatible with pixi.
February 9, 2026 at 1:27 PM
hat: a cargo-like wrapper around pixi for managing mojo projects.
github.com/sstadick/hat
It literally just shells out to pixi and is meant to be very transparent! 100% compatible with pixi.
github.com/sstadick/hat
It literally just shells out to pixi and is meant to be very transparent! 100% compatible with pixi.
This essay keeps feeling more salient the more I work with various AI agents.
That's not to say that agents aren't massive enablers in some cases. There's just tradeoffs.
That's not to say that agents aren't massive enablers in some cases. There's just tradeoffs.
“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...
gist.github.com/onlurking/fc...
February 6, 2026 at 4:33 PM
This essay keeps feeling more salient the more I work with various AI agents.
That's not to say that agents aren't massive enablers in some cases. There's just tradeoffs.
That's not to say that agents aren't massive enablers in some cases. There's just tradeoffs.
Reposted by Seth Stadick
So anyway:
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
February 4, 2026 at 1:24 AM
So anyway:
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
Reposted by Seth Stadick
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...
January 29, 2026 at 10:37 AM
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...
Reposted by Seth Stadick
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
Reposted by Seth Stadick
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...
employment.utah.edu/salt-lake-ci...
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
employment.utah.edu
January 12, 2026 at 9:04 PM
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...
employment.utah.edu/salt-lake-ci...
Reposted by Seth Stadick
We ❤️ our users in academia – and we love to read their success stories.
PS: If you think your institute/company could benefit from Pixi as well, and you want to learn more, please reach out to us to plan something! We're looking forward to organize more workshops this year.
PS: If you think your institute/company could benefit from Pixi as well, and you want to learn more, please reach out to us to plan something! We're looking forward to organize more workshops this year.
January 9, 2026 at 10:25 AM
We ❤️ our users in academia – and we love to read their success stories.
PS: If you think your institute/company could benefit from Pixi as well, and you want to learn more, please reach out to us to plan something! We're looking forward to organize more workshops this year.
PS: If you think your institute/company could benefit from Pixi as well, and you want to learn more, please reach out to us to plan something! We're looking forward to organize more workshops this year.
December 12, 2025 at 1:40 PM
TIL that a single `*` is a valid SEQ in SAM spec.
It makes sense in retrospect, but I did not cover that edge case.
github.com/sstadick/per...
It makes sense in retrospect, but I did not cover that edge case.
github.com/sstadick/per...
December 11, 2025 at 3:33 PM
TIL that a single `*` is a valid SEQ in SAM spec.
It makes sense in retrospect, but I did not cover that edge case.
github.com/sstadick/per...
It makes sense in retrospect, but I did not cover that edge case.
github.com/sstadick/per...
Advent of Code Day 10: codeberg.org/sstadick/aoc...
The wall has been hit on part 2. I know what it is I don't know... I just need a few days to re-learn the math.
The wall has been hit on part 2. I know what it is I don't know... I just need a few days to re-learn the math.
day10: there was an attempt
Part a solved, Part b heat death of the universe.
codeberg.org
December 10, 2025 at 6:20 PM
Advent of Code Day 10: codeberg.org/sstadick/aoc...
The wall has been hit on part 2. I know what it is I don't know... I just need a few days to re-learn the math.
The wall has been hit on part 2. I know what it is I don't know... I just need a few days to re-learn the math.
@typst.app really is as good as the hype.
December 10, 2025 at 6:17 PM
@typst.app really is as good as the hype.
Not the first paper I've been a part of, but the first one I've ever written, organized, and executed! I learned a lot getting this one done.
Also, Mojo! 🔥 👇
Also, Mojo! 🔥 👇
🧬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
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
December 9, 2025 at 4:32 PM
Not the first paper I've been a part of, but the first one I've ever written, organized, and executed! I learned a lot getting this one done.
Also, Mojo! 🔥 👇
Also, Mojo! 🔥 👇
Advent of Code Day 9:
codeberg.org/sstadick/aoc...
Classic part B where I thought I had it solved.... and then two hours later figure out the trick.
codeberg.org/sstadick/aoc...
Classic part B where I thought I had it solved.... and then two hours later figure out the trick.
feat: day9 part 1 and part 2
M3
Spent a long time on part B. First try was to check every point on the boundary of the rectangle to see if it was inside the polygon by raycasting. That worked but was very slow and didn't scale u...
codeberg.org
December 9, 2025 at 4:27 PM
Advent of Code Day 9:
codeberg.org/sstadick/aoc...
Classic part B where I thought I had it solved.... and then two hours later figure out the trick.
codeberg.org/sstadick/aoc...
Classic part B where I thought I had it solved.... and then two hours later figure out the trick.
Reposted by Seth Stadick
🧬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
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
December 9, 2025 at 10:01 AM
🧬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
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
Advent of Code Day 8: codeberg.org/sstadick/aoc...
Time to go read up on the correct way to solve this one.
Time to go read up on the correct way to solve this one.
Torrent of song. In the end his mother did not quite abreast and.
The half-forgotten world of steel and concrete, of monstrous machines and terrifying weapons — a.
codeberg.org
December 8, 2025 at 4:14 PM
Advent of Code Day 8: codeberg.org/sstadick/aoc...
Time to go read up on the correct way to solve this one.
Time to go read up on the correct way to solve this one.
Advent of Code day6!
Nothing elegant about my approach today, just a "get it done before the kids wake up" solution.
Nothing elegant about my approach today, just a "get it done before the kids wake up" solution.
feat: day6 part 1 and 2
Nothing elegant in my solution for today.
Part 1:
```bash
❯ hyperfine --warmup 3 ./main
Benchmark 1: ./main
Time (mean ± σ): 4.0 ms ± 0.3 ms [User: 3.5 ms, System: 0.9 ms]
Range (min ...
codeberg.org
December 6, 2025 at 12:05 PM
Advent of Code day6!
Nothing elegant about my approach today, just a "get it done before the kids wake up" solution.
Nothing elegant about my approach today, just a "get it done before the kids wake up" solution.
A path to 1.0 for Mojo www.modular.com/blog/the-pat...
Modular: The path to Mojo 1.0
While we are excited about this milestone, this of course won’t be the end of Mojo development! Some commonly requested capabilities for more general systems programming won’t be completed for 1.0, su...
www.modular.com
December 5, 2025 at 9:44 PM
A path to 1.0 for Mojo www.modular.com/blog/the-pat...
Advent of Code Day 5: codeberg.org/sstadick/aoc...
Always a good time when you get to roll out the BITS algorithm!
Always a good time when you get to roll out the BITS algorithm!
feat: day5
M1 Pro
Part A
```
❯ hyperfine --warmup 3 ./main
Benchmark 1: ./main
Time (mean ± σ): 9.4 ms ± 0.4 ms [User: 6.8 ms, System: 2.9 ms]
Range (min … max): 8.1 ms … 10.5 ms 193 runs...
codeberg.org
December 5, 2025 at 9:25 PM
Advent of Code Day 5: codeberg.org/sstadick/aoc...
Always a good time when you get to roll out the BITS algorithm!
Always a good time when you get to roll out the BITS algorithm!
Advent of Code Day 3:
codeberg.org/sstadick/aoc...
Trying out codeberg with Zig migrating off of GitHub.
codeberg.org/sstadick/aoc...
Trying out codeberg with Zig migrating off of GitHub.
December 3, 2025 at 5:34 PM
Advent of Code Day 3:
codeberg.org/sstadick/aoc...
Trying out codeberg with Zig migrating off of GitHub.
codeberg.org/sstadick/aoc...
Trying out codeberg with Zig migrating off of GitHub.
Advent of Code Day 2!
github.com/sstadick/aoc...
12 says of advent of code feeling way more doable than the full month.
github.com/sstadick/aoc...
12 says of advent of code feeling way more doable than the full month.
feat: day2 partA and partB, day1 partA in perl6 by sstadick · Pull Request #2 · sstadick/aoc-2025
M3 Macbook Air
Part A:
❯ hyperfine --warmup 3 ./main
Benchmark 1: ./main
Time (mean ± σ): 35.5 ms ± 2.5 ms [User: 34.5 ms, System: 1.1 ms]
Range (min … max): 34.4 ms … 57.4 ms ...
github.com
December 2, 2025 at 12:07 PM
Advent of Code Day 2!
github.com/sstadick/aoc...
12 says of advent of code feeling way more doable than the full month.
github.com/sstadick/aoc...
12 says of advent of code feeling way more doable than the full month.
Reposted by Seth Stadick
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
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
It's advent of code season!
Day1, parts A and B. Going with Mojo this year:
github.com/sstadick/aoc...
Day1, parts A and B. Going with Mojo this year:
github.com/sstadick/aoc...
aoc-2025/day01/main.mojo at main · sstadick/aoc-2025
In Mojo. Contribute to sstadick/aoc-2025 development by creating an account on GitHub.
github.com
December 1, 2025 at 4:20 PM
It's advent of code season!
Day1, parts A and B. Going with Mojo this year:
github.com/sstadick/aoc...
Day1, parts A and B. Going with Mojo this year:
github.com/sstadick/aoc...