The crank doesn't actually do anything, but it makes the humans happy. COMIC ◆ www.smbc-comics.com/comic/crank PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com
Davide CIttaro
@daweonline.bsky.social
Coordinator of λ-lab @ Center for Omics Sciences, Milan | Assistant professor of bioinformatics @unisr.bsky.social
These are numbers for a 2M cells dataset (lung HCA). I’ll update schist ASAP to support newest graph-tool.
Davide CIttaro@daweonline.bsky.social · 3w agoIt’s 2282447 nodes and 51427121 edges. Took 7082.49s with simple init and 29069.77s with default init
😱😱😱😱
Tiago Peixoto@tiago.skewed.de · 4w agoGood news everyone! 🎉 The new version 3.0 of graph-tool is just out with major improvements! See below. graph-tool.skewed.de graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
Perhaps one way to help combat unapproved AI use in technical courses is to pose all homework problems as questions about biology and cybersecurity? combine-lab.github.io/blog/2026/07...
COMBINE-lab - Fable is not a useful model
COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.
combine-lab.github.io
So it seems from my discussions with others in the field, that @anthropic.com's #Fable5 is ENTIRELY AND COMPLETELY unusable for any bioinformatics or computational biology. It rejects every prompt, not matter how benign or innocuous. It may as well not exist for our field ☹️.
Across >1,000 human samples, we identified numerous abundant proteins whose amino acid sequences differ from those predicted by the genetic code. 🔗 Links: Nature Article: nature.com/articles/s41... OA version: biorxiv.org/content/10.1... Science highlight: science.org/content/blog...
Alternate RNA decoding results in stable and abundant proteins in mammals - Nature
Alternate RNA decoding, an understudied process, leads to peptide sequence modifications that can have substantial functional effects on protein stability, tissue-specific proteomes and dise...
nature.com
Efficient sampling of reads (with replacement). www.biorxiv.org/content/10.6...
fastQpick: scalable bootstrap and subsampling of FASTQ reads
fastQpick is a command-line tool and Python library for sampling FASTQ reads with replacement. Sampling with replacement turns a single FASTQ file into an arbitrary number of bootstrap replicates, whi...
biorxiv.org
Atera World tour comes to Milan. Everybody looks excited but I can only see an impressionist portrait of Pinocchio wearing Red Riding Hood’s cape.
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
I’ve been in the field for enough time to witness many hype waves, the sad part is that funding is shifting to hypes because an increasing amount of private entities are betting their money on this. open.substack.com/pub/evgenyki...
A cell is not a spreadsheet- why “Virtual Cells” are still mostly hype
Every few years, biology gets a new phrase that sounds inevitable.
open.substack.com
One of the good things about the AI co-scientist brouhaha is that it makes us discuss what science *is*, and how to measure its value, impact, quality. — Questions that have been there all along, but many preferred to gloss over.
It seems I’m the only person with many problems
Randall Munroe@xkcd.com · 3mo agoResults Age xkcd.com/3245/
![Comic. [Person 1 sitting at desk typing on laptop while Person 2 with shoulder-length hair stands behind.] PERSON 1: Aw man, speedrun.com removed my world record just because I listened to lateralus and ænima to get in the flow. PERSON 2: Oh, a copyright thing? PERSON 1: No, they don’t allow tool-assisted speedruns.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreiar3wsjy5rdmexkvbkh322xd77jkkihi55attsje5jknacobnmjti)
Is it possible to have anchors and hyperlinks in online papers that link results to relevant sections in methods?
Sneak peek of the next greatest device for spatial transcriptomics!
Something similar happens to biologists as well, and to physicists studying biology
Randall Munroe@xkcd.com · 3mo agoSoniferous Aether xkcd.com/3238/
![Comic. [Person and second person with ponytail on stage. Person 1 gestures behind at a display of different wavelengths while Person 2 addresses people off-panel.] PERSON 2: We all know the speed of light is constant for all observers. But our experiments show that the speed of sound *changes* based on the observer's motion. Thus, we posit the existence of the *soniferous aether*, a medium that fills the space between us and carries sound waves. [caption] Sometimes physicists forget that air exists and rediscover it from first principles.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreihw3odqgiz2qkryc3oav6r53wwxyod7537cy5qmhdhzqbui4cennq)
The what?
Pujuan Poppy Deng@poppy-pujuan-deng.bsky.social · 4mo agoI am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...
Whenever there’s a hopeless case, I’m the designated collaborator. One day I will write a book about all the failed experiments (lost causes) I had to analyze.
'Despite (...) attempts to limit the emphasis of the ‘publish-or-perish’ mindset, it will take time for the culture to change. As such, journal publishers still yield a lot of power – & they make a lot of money from that power. Some of the big publishing houses have profit margins approaching 40%'
Why we won’t be funding open access publishing any more - Cancer Research UK - Cancer News
The open access movement was bold and promising, but ultimately disappointing. Now is the time to stop and call for a new way to make publishing work…
news.cancerresearchuk.org
The alternative was artisanal soap biiiiiitch. COMIC ◆ www.smbc-comics.com/comic/learn-2 PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com
On the last Socrates joke, like a dozen people told me I should've called his nutritional supplements Himlock, and it just kills me that I didn't. COMIC ◆ www.smbc-comics.com/comic/athenian PATREON ◆ www.patreon.com/ZachWeinersm... STORE ◆ smbc-store.myshopify.com
A bit frustrating when a PI presents data and results but doesn’t go into details because “I’m not a bioinformatician”. You may not be able to do the same calculations, but I expect you to be able to understand and present data.
The 978 genes in L1000 assay can be used to infer the expression of many other genes, and yet don’t make a commercial panel in any assay (that I’m aware of). Why?
The "publish or perish" culture must perish. Scientists need time to think. We just published our Slow Science Manifesto, where we argue that huge changes are needed in the way we fund, publish, and evaluate science. Read more and sign here: www.slow-science.com
Every time I need to test an R package I spend hours compiling, resolving dependencies, fix inconsistencies. I used to work with FreeBSD and Gentoo Linux, I swear I never spent so much time in compiling and complaining like with R
I wanted to share today’s experience with AI writing code for me. Interesting (ish). I had to process some large fastq files to count specific sequences (barcode/guide, CRISPR library), I had a Python script that works but is slow (~200 items/s). [1/n]