Octobox Untangle your GitHub Notifications

I still use octobox.io, more options than GitHub notifications (even tho they copied a lot of the good ones from octobox), and less chaotic than figuring out thru email

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens an...

Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.

www.biorxiv.org/content/10.1...

🏆 Conheça os premiados da Edição 2025 do Prêmio Dorneles Trémea / Jean Ferri ⭐ - 🏆 Adorilson Bezerra 📌 Ceará-Mirim - RN / Coimbra - Portugal • Organizador do Projeto Software Livre - Rio Grande do Norte • GruPy - RN • Professor do IFRN • Grupo de tradução da documentação do Python para PT-BR - 🏆 Rafahela Bazzanella 📌 Brasília - DF • Membra da comunidade Python desde 2004 • Co-fundadora da comunidade PloneGov - BR Organizadora/Co-organizadora de diversas conferências: Plone Conference de 2013 e 2024, Python Brasil de 2013 e Python Cerrado de 2024 e 2025 - 🏆 Thais Viana 📌 Rio de Janeiro - RJ • PyLadies Rio • Mestra em Inteligência Artificial (UFRJ) • Diretora de Tecnologia da APyB - 2020/2021 • Big Kahuna PyBR 2024 👏🏻 👏🏻 👏🏻 Parabéns às todas pessoas premiadas em 2025! A comunidade pythonista do Brasil agradece demais os seus esforços na disseminação do conhecimento! 💙 💛 🐍

🏆 Conheça os premiados da Edição 2025 do Prêmio Dorneles Trémea / Jean Ferri ⭐

- Adorilson Bezerra

📌 Ceará-Mirim - RN / Coimbra - Portugal

• Organizador do
Projeto Software Livre - Rio Grande do Norte
• GruPy - RN
• Professor do IFRN
• Grupo de tradução da documentação
do Python para PT-BR
+

Output of `sassy grep -p ACTGGCATGAGAACTGAG -k1 human-genome.fa`. Should fuzzy matches with up to one error, grouped by file, then by record. The matching part is highlighted with colours (green=match, orange=mismatch, red=delete, blue=insert), and the strandedness of each match, the location, and the cost are shown.

Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!

Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.

The official home of the Python Programming Language

TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵

The desperate need to accumulate more and more at the cost of everyone else’s wellbeing should be classified as a mental disorder, and I will absolutely die on this hill.

molho bechamel não é aquele negócio de duas mulheres conversando sem falar de homem

GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

O pampa é um dos nossos biomas mais ameaçados. Se entendi a imagem, toda árvore aí é monocultura de eucalipto. Tão matando um bioma plantando árvore. O pampa tem nem 10% de sua área protegida. Nele tem mais de 64 de plantas por metro quadrado… mas só é grama, né? Só floresta importa, né? 😤

That reminds me of an interactive BWT searching visualization I made here: (change 'algorithm' to BWT first)

curiouscoding.nl/posts/alg-viz/

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

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 ...

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...

Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...

The Great Genotyper: a graph-based method for population genotyping of small and structural variants Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...

A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."

O trabalho morto do processamento exige trabalho vivo do cientista para ser tornado útil.

Mas ninguém está nem aí pra utilidade, isso aqui é capitalismo. O objetivo é dinheiro.

Bem, 16 anos atrás, o capitalismo inventou uma forma 'exótica' de transformar processamento em dinheiro: criptomoedas.+

Existe uma história da escalada do processamento de dados global que é muito pouco contada.

Vai ser um fio longo, espero que interessem a vocês.

Em 1965, Gordon Moore, co-fundador da Intel, prevê que a capacidade de processamento /custo dobra a cada ano.

Ele previu que isso duraria 10 anos.+

E o nocivo e cretino empresariado brasileiro já se movimenta pra fuder o trabalhador por pura birra com a isenção de IR pra quem ganha até 5 mil.

Não há custo adicional algum - conforme a própria matéria destaca. É só ódio e nojo de pobre mesmo.

melhorrh.com.br/isencao-ir-5...

#RECOMB2026 is now accepting submissions and we'd love to see your best work!

📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025

📜 More info: recomb.org/recomb2026/call_for_papers.html

Normative framework of bigger tech

(aka, me trolling the tech audience)

GitHub - RagnarGrootKoerkamp/simd-sketch: Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. - RagnarGrootKoerkamp/simd-sketch

Looking for people to test the latest version of simd-sketch.

It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).

'cargo install simd-sketch' is right there under your fingertips ;)

github.com/RagnarGrootK...

the youtube vs yt-dlp arms race is hilarious, because of how lopsided it is.

on the one hand, you've got a company with the GDP of Denmark who has about a manhattan-project's worth of developers they can assign to this.

but on the other end, you've got every bored or annoyed javascript hacker.

Imagem de um cupcake, com o nome "Dragões de Garagem" e o balão volumétrico que é símbolo do grupo estampado na parte de baixo do cupcake, onde seria o papel da forma, com um topo de creme branco, salpicado de bolinhas marrons, como se fossem pequenos pedaços de chocolate, e uma vela acesa no topo. O fundo da imagem é num tom de verde vibrante. Tem algumas estrelas ao redor da imagem do cupcake. E está escrito do lado esquerdo da imagem "13 anos".

Hoje o podcast Dragões de Garagem completa 13 anos no ar! Ao longo desses anos a mídia podcast teve vários momentos, mas acreditamos que a essência permanece: trazer conteúdos sobre ciência de forma responsável. +

Imagem sintética mostrando os 3 volumes do Python Fluente, 2ª edição.

«Python Fluente» à venda no Catarse agora!

www.catarse.me/pythonfluente

Volume 1 por R$ 99+frete, ou os 3 volumes, em 2 opções de acabamento (brochura P&B, espiral cor).

Também: kits com xilogravura do calango da capa, assinada e numerada pelo artista Thiago Castor.

👉 Nas lojas será mais caro!

a cultura paulistana é anúncio publicitário, ir visitar o café-anúncio, a exposição-anúncio, assistir o filme-anúncio, ir no teatro-anúncio, pagar pra ir no parque-anúncio, tirar foto na frente do anúncio