Today begins the 30day clock until my funding runs out. I've been frantically applying to all sorts of jobs (all rejections 🫩). So if anyone here knows of someone hiring a molecular ecologist real good at field work and bioinformatics, please do let me know 🙏

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

The Slave Economy Never Ended. It Just Changed Its Labor Source.

What Rome's slave economy tells us about who should own the one we're building now, and the only version worth building.

open.substack.com

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/

Arachne linked-read aligner | Arachne

Arachne is a fork intended to be a revival and [hopefully] continuation of Lariat, the linked-read aware aligner created by 10X Genomics and bundled in their LongRanger pipeline.

pdimens.github.io

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...

2025 - Hypoxia PhD job ad

The Moore lab at the University of Colorado Denver is searching for 1 Ph.D. student to study the elevational limits of dragonflies in Colorado (http://moore-evo-eco.weebly.com). This position is fully...

docs.google.com

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...

GitHub - pdimens/djinn: Convert linked-read FASTQ/BAM files between formats, like magic.

Convert linked-read FASTQ/BAM files between formats, like magic. - pdimens/djinn

github.com

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...

Quit Yer Mouthbreathing–The open cup – Apple Podcasts

Podcast Episode · The open cup · 15/08/2025 · 21m

podcasts.apple.com

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

GitHub - pdimens/mimick: Linked-read sequence simulator

Linked-read sequence simulator. Contribute to pdimens/mimick development by creating an account on GitHub.

github.com

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) 😁

@bioinfoadv.bsky.social on Bluesky

🧬 Explore the latest from Bioinformatics Advances: “Harpy: A pipeline for processing haplotagging linked-read data”   Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133 Authors include: @pvdimens.bsky.social

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