How the use of AI by colleagues to generate citations or overviews, even if we avoid these “tools” ourselves, may put new pressures on scientific publishing: brianomeara.info/posts/ai_opt... #AcademicSky

Another good bird! A ruff, at Barn Island WMA, Stonington, CT.

Grasshopper sparrow in Old Lyme, CT this morning.

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

to me, a non-ai expert, this gets at one of the most curious things about the hype. it kinda feels like doing ever increasing numbers of matrix multiplications on every text ever written is probably barking up the wrong tree for creating "intelligence".

Join us Nov 18–20 for a Virtual Genome Annotation Workshop! Learn Linux, genome assembly, evidence-based annotation, & evaluation. No experience needed! 📅 10 AM – 2 PM ET 💻 MS Teams + recording 💰 $500 ($400 UConn) Register: bioinformatics.uconn.edu/cbc-workshops/ #GenomeAnnotation #Bioinformatics

per the blog post, many of the ideas that inspired this live on in other projects, but still, this site shutting down feels like an emblem of the gap between what everyone thought the internet could be in the 1990s and what it has become.

Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry. But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out! doi.org/10.1126/scie... 🧵1/6

Tebibytes/Gibibytes/Mebibytes etc are cursed. Maybe I'm just a computational rube, but WTF. I get that computers are working in base 2 so nothing will ever be clean if you count storage in base 10, but the solution is to essentially to MIX base 2 and base 10 in a way that is endlessly confusing?

I did my PhD at LSU and this makes my blood boil. www.espn.com/college-foot...

Proud of the latest edition of my free intro biostats book. gitrepo: github.com/ybrandvain/b... book: ybrandvain.github.io/biostats/ Not complete but at a good point to take a break, and I think its quite usable dm me with comments , ideas etc

It's a Miyazaki Clouds kind of day.

This workshop is right around the corner. See the link for the rest of our upcoming workshop schedule.

Maybe time to rewatch The Wire

look, I don't want people going to jail for weed, but is there some compromise position that makes it so I don't have to smell weed 100% of the time in any populated part of the country?

The number one thing I miss about being 20 is the ability to sleep like the dead for 12 straight hours.

we started using Starfish to look at data on our HPC. it's pretty amazing. getting a high level view of storage and being able to immediately see problems like, say, 60TB of old nextflow work directories floating around is fantastic.

Reminds me of 2020, with then 4yo: S: we got you a present for your birthday, daddy! Me: great! I can't wait to see what it is. S: I'm never going to tell you what it is. Me: very good. Keep it a surprise.

My worst trait as an instructor of online courses is my tendency to start demo videos with "this will be a short video about X" and then the demonstration is absolutely not short. I console myself with the fact that students can see the progress bar and know that I am lying.

Can someone explain to me what is happening here

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

RE NCBI and the shutdown: I was able to grab some SRA data I needed last night. Is there any reason to think that NCBI databases might become inaccessible?

Okay this one is actually good.

UConn's CBC is offering a virtual workshop on ChIP and ATAC seq at the end of October.

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

I wanted to get a video of this ghost crab but every time I got close to their hole they scuttled back in, so I tried getting clever with it. I made a little sandcastle and shoved my phone into it, hit record, and walked away. Crab was VERY suspicious of this addition to their environment.

real basic bioinfo q: bioawk has a function `meanqual` that takes the arithmetic mean of phred-scaled base qualities. this is the geometric mean of the actual base error probabilities. why would anyone actually want that vs the arithmetic mean which can be interpreted as expected # errors?

I'm not a big boycotter, but we canceled Hulu/Disney+ over the Kimmel thing. This is straightforward authoritarianism.

In my fantasy world, the late night hosts are planning to get together on one of their shows and just do an hour long MAGA themed "aristocrats" riff.

I watched like 20 people sit in a patch of poison ivy this weekend. I tried to tell them, but it had been mowed and was all mangled and didn't much look like poison ivy anymore. Everyone I told was like "nah, I don't believe you" and stayed where they were.

What is the longest anything has ever sat in your brain's "I should look that up on the internet" queue? In like 2006 my MS advisor showed me this book, and ever since I have periodically been like "what was the name of that book again? I should figure that out and get a copy"

Pundits beefing on social media is usually tedious and depressing to me, but, "when I want my thoughts to be widely read, I post them in the New York times" is probably the greatest own I have ever read.

Loved this book so much as a kid. Carried it to and from school in second grade for weeks.

My department (ecology and evolution) is hiring a core bioinformatics/comp bio person (not TT but the last person retired after 25+ years). It's a great place to work!: stonybrooku.taleo.net/careersectio...

We're running a virtual genome assembly workshop next week. Online, but live instruction on a real HPC. Code and session recordings distributed to participants.

I am curious about why right-wingers use the term "racialism".

Just discovered >200 users have access to an undocumented QoS on our cluster that has no resource limits. Apparently only two of them knew it existed.

In the earliest stages of adaptive introgression, beneficial immigration can drive genome-wide changes. In a new preprint www.biorxiv.org/content/10.1... colleagues & I document exceptionally rapid genomic introgression in a lake population of stickleback.

A relative who lives in the boston area (watertown) has found two obviously unwell mammals in the last week (an opossum and a gray squirrel) stumbling in circles on the sidewalk where she lives. this is an indicator someone nearby is putting out rat poison, right?

Our latest preprint on the evolution of the primate amylase locus is now on biorxiv! I hope to share a brief thread soon about our main findings.

We Need To Take Trump’s Rhetoric Seriously, But Not Literally vs. Have That Guy Killed theonion.com/we-need-to-t...

Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.

Our review on the last decade+ of hybrid incompatibility research is now out! www.sciencedirect.com/science/arti... Original thread here: bsky.app/profile/moll...

TIL about Value-Supressing Uncertainty Palettes. This really has really started the wheels turning! medium.com/@uwdata/valu...

New paper out on the dangers of using patterns across spatial climate gradients to predict what will happen with changing climate. That includes species distribution modeling. Space-for-time substitution can be misleading in sign, not just the magnitude of effects. www.nature.com/articles/s41...

Every time I get back from a long bike ride on dirt roads and my seat tube is covered in tire sealant I think tubeless tires, while kind of a pain in the ass sometimes, are pretty damn cool.

Mind the lag: understanding genetic extinction debt for conservation www.sciencedirect.com/science/arti...

So actually potato comes from tomato! 🤯🤯 A cross between a Solanum and a tuberosum derived in the actual potatoes! (Another) Incredible work by the lab of Sanwen Huang and colaborators www.cell.com/cell/fulltex...