Lucas van Dijk

Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...

Population-scale Long-read Sequencing in the All of Us Research Program The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno...

>1,000 human genomes sequenced with PacBio HiFi, offering many new insights into human structural variation and its associations with disease. www.medrxiv.org/content/10.1...

Easier might be to use “basedpyright” which has built-in uv environment detection support.

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

I am grieving the barbarism that is going to unfurl from all this. People are going to die. Livelihoods gone. All to feed a corrupt kleptocracy.

I see every day up close how different it is from the first time around. There are no guardrails. A disaster. I’m sorry we have to live through this.

Exciting! Good luck tomorrow 🙌

Spain’s high-speed trains aren’t just efficient, they have transformed people’s lives | María Ramírez A fiasco like HS2 could never happen here – our fast train network is so popular that no Spanish government would dare give up on it, says journalist María Ramírez

Spain spent 57 bln euros to build its entire high speed rail network.

www.theguardian.com/commentisfre...

The efficiency of the market

What the actual fuck is this

And now officially out in Oxford Bioinformatics :)

academic.oup.com/bioinformati...

Thanks to @jdidion.bsky.social for writing 99% of the tree-sitter grammar at the heart of this extension. I made some modifications to ensure compatibility with Zed's WASM plugin system and fixed a few bugs in the C lexer extension.

Screenshot of the Zed editor showcasing syntax highlighting for the Workflow Description Language.

For those using WDL for their bioinformatic workflows: I wrote an extension for the @zed.dev code editor enabling syntax highlighting and integration with wdl-lsp. It also supports bash highlighting in command blocks.

Installable through the Zed extensions pane!

github.com/broadinstitu...

A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌

Diversity and consequences of structural variation in the human genome - Nature Reviews Genetics Collins and Talkowski provide a broad overview of structural variation in the human genome that covers their mutational properties, the dynamics of population genetics and functional consequences in d...

Diversity and consequences of structural variation in the human genome go.nature.com/4awEtaY #Review by Ryan L. Collins & Michael E. Talkowski @broadinstitute.org @harvard.edu @harvardmed.bsky.social

I feel this one 🤣

COMPUTER SCIENTISTS: "k" means one thousand and twenty-four
STORAGE MANUFACTURERS: "k" means one thousand
DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty

That looks super interesting and I would read that in a heartbeat!

Still in beta, so possible minor API changes ... but our Suffix Array library (in Rust) is ready for business. Builds on lovely ideas in CaPS-SA from @robp.bsky.social.

Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.

5/ In my experience, most of the time, you don’t need deep learning.

Often, simple methods like linear regression or random forests work well — especially for moderate-sized datasets.

Deep learning excels in image analysis & protein structure prediction.

I remember this blog: kobzol.github.io/rust/cargo/2...

But it was released earlier this year, so not super recent.

Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv?

ChatGPT when you ask it to write something clearly and succinctly:

"Salutations and felicitations, sir, and a most jocund welcome to the sink. I am your electronic valet and household central processor. May I be of service, sir?"

A view of the Central Intelligence Unit in Fallout New Vegas: Old World Blues.

Found ChatGPT in Fallout New Vegas:

"Are you some kind of AI?"
"Regrettably not, sir. All modules in this habitat are synthetic personalities atop a mundane operating system. There is no intelligence here, sir."

www.youtube.com/watch?v=4XJw...

💡 Tip: You can set your website as your username on Bluesky!

This is one form of self-verification, and we especially encourage official organizations and brands to do this! Examples include @npr.org @react.dev @duolingobrasil.com.br.

Here's our guide for how to do this:

“Liberal democracy,” he says, “offers moral constraints without problem-solving” — a lot of rules, not a lot of change — while “populism offers problem-solving without moral constraints.”

Opinion | This Is the Dark, Unspoken Promise of Trump’s Return Liberal democracy offers moral constraints without problem-solving. Populism offers problem-solving without moral constraints.

This piece that includes a conversation with a professor of autocracy who’s an Hungarian exile has some strong points in my opinion (gift article)

www.nytimes.com/2024/11/15/o...

Every time I watch a HBO doc on a cult (The Vow, Love Has Won, Breath of Fire, Synanon, …), I’m taking notes 📝

Tagging for 🧬🖥️

It took me nearly a week to figure out why the BAM generated by a coworker gave different results than one that I generated myself 😱

To prevent this, we manually specified the fragment length mean with BWA's -I flag in future analyses.

If a downstream task filters improperly paired alignments (which is pretty common), it might filter accurate alignments that just happened to be in a batch with few other reads that aligned.