97% of human history ran on legal slavery. We’ve had 3% without it, and even that’s generous: ~28 million people are in forced labor globally right now. It never actually ended. It just kept changing its name. My latest essay on Substack. #econsky #polisky #history #academicsky

We are excited to announce that the 2026 Great Lakes Annual Meeting of Evolutionary Genomics (GLAM-EvoGen) will take place on Saturday, August 15, 2026 at the University at Buffalo. More information is available on our website: gokcumenlab.org/glam2026/ @gokcumenlab.bsky.social

10 on-and-off months of learning#Golang later, I seem to have gotten my fork of the Lariat linked-read aligner, Arachne, working. If you got modern linked read data, I'd love for you to try it out and report back!#bioinformatics https://pdimens.github.io/arachne/

Well, AI slop finally became personal. A (presumably) well-meaning person outside of biology decided to reimplement all of the highly optimized and specialized packages in BioJulia into a single package using AI.

A be-floor and after of what I've been doing when I come home from work

Fifteen 2-year postdoc fellowships available at U. Toulouse 😍 through a MSCA-COFUND (AToUT tiris.univ-toulouse.fr/en/programs/...) Interested to apply for a postdoctoral research project focusing on the genomics of farm animals or pollinators? Let me know! Eligibility: <1 yr in 🇫🇷 in the last 3 yrs

Are you looking for a PhD position and want to spend your summers in the Rocky Mountains? My lab @cudenverclas.bsky.social is looking for 1 PhD student to work on a NSF-funded project to study elevational range shifts in Colorado! 🧪🌍🐙 Apply by Nov 1! Details here docs.google.com/document/d/1...

A 12-foot statue of Donald Trump and Jeffrey Epstein frolicking and holding hands appeared on the National Mall in Washington, DC on Tuesday, September 23. A plaque under the statue states that it has been erected “In Honor of Friendship Month."

I didn't love how monolithic Harpy was becoming with novel features. So, the file-modification things were split out into Djinn. So, use Djinn if you need to convert linked-read fastq/bams #bioinformatics github.com/pdimens/djin...

Band Name Idea; Blood Bath & Beyond Debut Album: Bath Salts

Hi, I’m Julie Cruse. I created AcademicAbuse.com – a dashboard of data, resources & tools to help survivors of academic abuse survive and safely speak out. (1/9 🧵) 🪜 🎓 📜 🍎 ♀️ 👩🏾🔬 👩🏼🔬 👩🏾🎓 #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #TimesUpHigherEd

Since finishing my PhD in 2022 I have: 1. Rediscovered my belly laugh 2. Cried at my first wedding Hard to describe how powerful it is to acknowledge healing.

My lil' baby turns 3.0 today! Most notable features: - autodetection of linked-read types (and not linked-read WGS too!) - more debuggin' and troubleshootin' options #bioinformatics #genomics #linkedreads

I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species yeamanlab.weebly.com/uploads/5/7/...

Today, that Go project *finally compiled*! It only took 7 complete project restructuring attempts. Now that it builds, the real work begins, and it's a good time to reveal I'm trying to revive Lariat, the linked-read aligner written by 10X Genomics. It's called Arachne 😁🕷️ github.com/pdimens/arac...

I'm trying to revive an abandoned #bioinformatics software written Go. I have no experience with Go (or similar langs), but doing my best. Does anyone here have even middling experience with Go that can lend some wisdom or time towards this effort?

There's a coffee tasting podcast and ya boi has a guest spot on it this week cupping Don't Be Alarmed by Coffeemania. Y'all should give their stuff a listen ☕ podcasts.apple.com/gb/podcast/q...

This morning, my sister told me that they're making The Mask 3 and I've been stressed ever since.

In the year of our lord 2025, I don't see why `scale_color_brewer()` is still case sensitive for the color palette

Out of necessity, I've recently got into reviving abandoned/dead linked-read bioinformatics software. Can be seen as software necromancy or adoption, depending on what you consider abandonware. I prefer calling it necromancy, tbh.

"How hard can it be?" he thought to himself before taking on another time-sucking project he is grossly unqualified to have even considered. Anyway, if this works, expect another linked read software with another monster/creature name 🐉

The Mimick logo has been updated to reflect its new #julialang codebase 👀🙌

If you've ever wondered how the sausage gets made over here in Harpy land, behold

Been writing in #Julialang again and BOY does it feel good. 😌

The world is crazy, still. Writing anything at all on social media feels stupid. But, I started learning to play Jake E. Lee's solo from Bark at the Moon and I guess I'm writing it here to 1. still somehow interact with the world and 2. foolishly hold myself accountable 🎸

Mimick now works with circular DNA, far all you microbial linked-read enthusiasts 🦠🧬 Go out and simulate you some data 💪 github.com/pdimens/mimick

According to Facebook, 8yrs ago today was the greatest day of my life

Oh hey, the Harpy paper is out. The software's been available, but it's nice to have something in writing! It also works with other linked read data and non-linked data (wgs, rad) 😁

Today was a really frustrating analytical/bioinformatics day and the entire time I had JLos catalog blasting in my headphones and it's 2am and I'm still reconciling the conflicting emotions about all of that.

Never in a million years did I think I’d be having regular conversations with my peers (most of them are other PRFB postdocs) about what we plan to do with our lives if we can’t be scientists anymore, i.e., if all the jobs continue disappearing. It’s all very bleak as an ECR right now.

leftists: that thing you teach us in school to be terrified of is happening historians: that thing is definitely happening star wars: here is a beat-for-beat breakdown of how the thing happens, but with pew pew lasers. we know you watched it news outlets: these protesters are out of control

7 months ago, in a mtg with Nina, she said I should absolutely not write a linked read simulator. And I didn't, I improved on an existing one. But then it became mine. And then I rewrote the entire thing 👀. So anyway, Mimick v2 is out. Simulate some linked reads, y'all. github.com/pdimens/mimick

Has anyone here been an editor for a sci journal and has wisdom to share about their experience?

Landlocked? Yes. Undeterred? Also yes.

There is still a few days to apply to this PhD offer! Come enjoy Paris and the "Jardin des Plantes" at the heart of it, while working on exciting science!

In Jan bought my first house and have been gradually learning about all the insane choices the previous owners made. Today, I learned that one of the floors is laminate over FOUR previous linoleum floors. Four. Which means it's a total of 5 floors. The top 2 lino floors were... THE SAME LINOLEUM 😶

I’m recruiting a PhD student in macrogenetics at Dalhousie University 🇨🇦! Focus will be on the biogeography of vertebrate genetic diversity or urban evolutionary ecology. Full ad: www.schmidt-biodiversity-lab.org/macrogenetic... If the ad is up, applications are still open. Please share widely! 🧬🧬

Anyone knows any QC pipeline for PacBio data as well as pipeline for de novo assembly? #consgen #popgen

It is with joy and exhaustion I'd like to announce the release of Harpy v2 🎆. What's different? Uh, almost everything. The changelog is so long that even I don't want to read it. BUT. IT WORKS WITH WGS DATA. AND MOST LINKED READ TECH. it just works 🙂 github.com/pdimens/harpy

i hate Liquid Death

The plan for NIH is in, source with full 64 page proposal for all of HHS is linked. Reported in WaPo. This is catastrophic. Reduction to 8 centers. 40% cut in budget. 15% IDC cap. This will decimate science across America open.substack.com/pub/insideme...

The simple solutions to my trickiest analysis problems always seem to appear when I'm walking my dog.

"The Story Behind Rebuilding the {tidyverse} in Julia" April 24, 2025 6:30 PM Irvine, CA www.meetup.com/socal-rug/ev... #julialang #rstats #tidyverse #pydata

Welp, the linked-read data simulator in Harpy will be moving to {drum roll}} Mimick! pdimens.github.io/mimick/#/ I'm quite grateful to David Bolognini for giving me stewardship over the XENIA module in VISOR (which is the basis for Mimick). It's *supercharged*!! #genetics #genomics #linkedreads

Me: so busy, everything is coo-coo bananas in the world, existential dread Also me: New software about to drop, and like Harpy, also named after a fictional monster that will absolutely try to murder you

TidierCourse is a free, work-in-progress set of materials for learning Julia and Tidier.jl. tidierorg.github.io/TidierCourse...

13 years ago, the recently appointed acting Undersecretary for NOAA and I were interns together at DISL. Not feeling great about this. In other news, I made a banana flambe-inspired pie to squash down those feelings.

If you think this can’t happen, remember that of the 125,000 Japanese Americans who were interned during WWII for years without charge or trial, two-thirds were U.S. citizens. Including me.

We have an open 4-year PhD position in the Slotte lab at Stockholm University, to investigate genomic signatures of selection associated with pollination mode shifts. Full ad: su.varbi.com/en/what:job/... Apply by April 22, 2025 via the University application portal (link). Please repost! 🧪