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The most shocking thing about this exercise wasn't how nice the Click library is for creating CLI tools, or how nice Simon Willison's cookiecutter template was for getting started. It was how much caffeine remains in circulation at bedtime after a large midmorning coffee.

“We’re very excited to see what people do with this” AlphaFold3 is open at last go.nature.com/4fHAfio

AncestryGrapher toolkit: visualize global- and local- ancestry inferences academic.oup.com/bioinformatics… 🧬🖥️ github.com/alisi1989/RFmi…

🚨🛠 Service Update: We are aware that some species are missing from Ensembl 113 BioMart. Thank you for your patience as we work to restore these as soon as possible. More information on our blog (ensembl.info/2024/11/13/tem…).

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes academic.oup.com/nar/advance-ar…

Whoa. This looks like an amazing project. Scholars at UMichigan have recently collected a massive dataset of over 1.1M podcast transcripts that is largely comprehensive of all English language podcasts. Using this data, they conduct an investigation into the content,

While browsing Simon Willison's newsletter I found an open-source web app that will turn any webpage into markdown for LLM-friendly input. Works with PDFs too. I made a bookmarklet that'll do it for you. blog.stephenturner.us/p/turn-any-web…

Visualize genomic data with ease using gggenomes, an R package that extends ggplot2 to handle and display genomic information intuitively. Whether you’re comparing genomes, analyzing features, or showcasing synteny, gggenomes provides the tools you need to turn complex genomic

Sunday hack: an experimental VCF extension for duckdb. No support for genotypes yet, but it rocks for summarizing data in the INFO column. Here are some simple examples of processing a VCF of chr22 CADD scores.

YMMV. I did this so I could learn how to create a custom GPT. This is just a waypoint until I figure out how to build an actual RAG app, self-hosted using llama3.3 via open-webui. Give it a try if you're interested. chatgpt.com/g/g-677277d002… 🧬🖥️🧪

Noam is doing incredible work here in the bioinformatics Rust space!

A unified analysis of atlas single-cell data genome.cshlp.org/content/early/… 🧬🖥️🧪 github.com/chenhcs/GIANT

Excited to launch DataMap – a portable, browser-based tool for generating heatmaps and PCA & tSNE plots. No installs. No servers. Your data never leaves your device. ✔️ Interactive heatmaps, PCA, and t-SNE ✔️ Transform & normalize data on the fly ✔️ Upload CSV, TSV, Excel +

nf-core modules are amazing but it’s often useful to navigate your pipeline code logically vs having to jump through module directories. The VSCode extension is a neat solution to this

This is huge! This fixes the universal problem with conversational agents: hallucinations! Every company that builds customer-facing agents struggles to align them with business rules and make them consistent. If you solve this, you'll become a hero overnight. Check out

🚨 Two undergrads with almost no AI background just built a speech model called "Dia" that rivals Google’s NotebookLM and ElevenLabs. And it's open-source. Here's how they pulled it off and why it matters:

How Good is AlphaFold3 at Ranking Drug Binding Affinities? １．This work explores a compelling question: Can AlphaFold3-like models not only predict structures, but also accurately rank ligand binding affinities? The authors show the answer is yes — with a method that comes

The high-quality telomere-to-telomere genome assembly of the earthworm (Amynthas aspergillum). #EarthwormGenome #ChromosomeLevelAssembly #Genomics Scientific Data nature.com/articles/s4159…

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata microbiologyresearch.org/content/journa… 🧬🖥️ Nextflow code: github.com/ag-computation…

AbDesign: Database of point mutants of antibodies with associated structures reveals poor generalization of binding predictions from machine learning models １．The AbDesign database introduces 672 antibody-antigen binding measurements, doubling the number of available