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Reposted by Ragnar {Groot Koerkamp}

Sophie Huiberts @sophie.huiberts.me · 16h

found an IRL linear program, took some pictures

4 photos showing the same thing from different angles. a convex polyhedron made of glass, with black edges, is held in two hands. the hands wear white gloves, the polyhedron is wider than it is tall or deep. width is around 4 hands, other dimensions are about one and a half. inside the polyhedron is a orange ping pong ball, and is has found its resting spot at the bottom vertex. hence it solves the LP of minimizing height subject to being inside the polyhedron

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 21h

So what's the equivalent of `perf record && perf report` on a MacBook?

I want to see the generated assembly and which lines are hot.

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Reposted by Ragnar {Groot Koerkamp}

Camille Marchet ⚡ @camillemrcht.bsky.social · 1d

Wat

a close up of a hamster 's face with its mouth open .

ALT: a close up of a hamster 's face with its mouth open .

media.tenor.com

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Reposted by Ragnar {Groot Koerkamp}

Adam Phillippy @aphillippy.bsky.social · 1d

Funny story, though, we found this gene in NCBI databases, but it was annotated in Streptococcus pneumoniae! This is surely human contamination in a bacterial strep sample that was not properly filtered. Lesson: use CHM13, or better yet a pangenome, when filtering for human contamination...

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Reposted by Ragnar {Groot Koerkamp}

Camille Marchet ⚡ @camillemrcht.bsky.social · 2d

Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...

‘Google for DNA’ brings order to biology’s big data

MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.

www.nature.com

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Reposted by Ragnar {Groot Koerkamp}

Ewan Birney @ewanbirney.bsky.social · 2d

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Staff Scientist

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

embl.wd103.myworkdayjobs.com

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 2d

_platform_memset_pattern16*, in case anyone besides me will ever google this

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 2d

The fight against the _platform_memset_platform16 continues until all u32x8::splat() have been purged...

(Turns out wide's `transmute([X; 8])` into `[u32x4;2]` has very bad codegen that prevents inlining and loop hoisting 😭)

A screenshot of a flamegraph, showing that 28% of Deacon's runtime is just splatting constants

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Reposted by Ragnar {Groot Koerkamp}

Rob Patro @robp.bsky.social · 3d

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

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Reposted by Ragnar {Groot Koerkamp}

Travis Wheeler @wheelerlab.org · 3d

Dream postdoc - Rob's science is excellent (and he's pretty great, too)

Rob Patro @robp.bsky.social · 3d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 3d

Bulk operations / batching is the future of high throughput libraries!

Nice to see boost doing this :)

Boost C++ Libraries @boost.org · 4d

Learn about the implementation of high-performance bulk operations in Boost.Bloom:

bannalia.blogspot.com/2025/10/bulk-operations-in-boostbloom.html
boost.org/libs/bloom

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Reposted by Ragnar {Groot Koerkamp}

Manoel Horta Ribeiro @manoelhortaribeiro.bsky.social · 6d

Computer Science is no longer just about building systems or proving theorems--it's about observation and experiments.

In my latest blog post, I argue it’s time we had our own "Econometrics," a discipline devoted to empirical rigor.

doomscrollingbabel.manoel.xyz/p/the-missin...

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Reposted by Ragnar {Groot Koerkamp}

Bede Constantinides @bedec.bsky.social · 4d

Deacon 0.11.0:
- Local server mode
- Ultra-careful handling of non-ACGT
- Faster indexing & index loading
- Denser index now stores k-mers not hashes
- xxHash & FxHash replaced with rapidhash::fast
- Bug fixes

Thanks @curiouscoding.nl (and others!) for contributions
github.com/bede/deacon/...

Release 0.11.0 · bede/deacon

Major release incorporating new features, fixes and peformance optimisations. Includes many PRs from @RagnarGrootKoerkamp, taking advantage of new features in simd-minimizers, packed-seq and parase...

github.com

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Reposted by Ragnar {Groot Koerkamp}

Ben Langmead @benlangmead.bsky.social · 4d

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

www.youtube.com

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 5d

Anyone here using rr debugger? looks cool

I'm scared of gdb though... am I missing out?

github.com/rr-debugger/rr

GitHub - rr-debugger/rr: Record and Replay Framework

Record and Replay Framework. Contribute to rr-debugger/rr development by creating an account on GitHub.

github.com

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 5d

crates.io/crates/fibon...

> fibonacci-numbers = "186.0.0"

> let fib_186 = fibonacci_numbers::VALUE;

crates.io: Rust Package Registry

crates.io

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 5d

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

GitHub - benchmark-action/github-action-benchmark: GitHub Action for continuous benchmarking to keep performance

GitHub Action for continuous benchmarking to keep performance - benchmark-action/github-action-benchmark

github.com

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Reposted by Ragnar {Groot Koerkamp}

Bede Constantinides @bedec.bsky.social · 5d

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

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Matt Holt @holtjma.bsky.social · 5d

I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!

Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...

Some highlights in this thread:
1/N

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 5d

that's me :)

The only way unimportant tasks get done is by always working from non-important/non-urgent to urgent.
Then once the deadline of the most urgent thing passes, the list is empty!

news.ycombinator.com/item?id=4548...

Structured Procrastination (1995) | Hacker News

news.ycombinator.com

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 5d

Splitting into crates is usually better for compile times, but if you need code to be inlined across crates and then do full-lto on *all* crates instead of just the 3 that were split, yes it's going to be worse.

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Reposted by Ragnar {Groot Koerkamp}

Camille Marchet ⚡ @camillemrcht.bsky.social · 6d

French govt did cargo +nightly build --release -Z unstable-options

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 6d

ICYMI

vitalik.eth.limo/general/2025...

Memory access is O(N^[1/3])

vitalik.eth.limo

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Shubhendu Trivedi @shubhendu.bsky.social · 8d

¹'²'³'⁴ contributed equally, †‡§¶ equal advising, ¤▪︎☆♡♧ joint second authors. Each order determined by coin flip with ⌈log⁡2(n!)⌉ repetitions for fairness.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 7d

I was considering to have a look at optimizing full-lto, but then I realized this is part of LLVM, not wild 🫤