Pavel Dimens
@pvdimens.bsky.social
A PhD in population genetics of marine fishes, Julia package dev, linked-read aficionado, guitar player, rock climber, and once described as endearingly mediocre.
A be-floor and after of what I've been doing when I come home from work
November 3, 2025 at 10:09 PM
A be-floor and after of what I've been doing when I come home from work
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
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
August 28, 2025 at 7:14 PM
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
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
Real betrayal with how that PNG was rendered. Here's the actual logo
August 20, 2025 at 6:55 PM
Real betrayal with how that PNG was rendered. Here's the actual logo
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...
August 20, 2025 at 6:53 PM
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...
The Mimick logo has been updated to reflect its new #julialang codebase 👀🙌
July 21, 2025 at 2:23 PM
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
July 17, 2025 at 8:45 PM
If you've ever wondered how the sausage gets made over here in Harpy land, behold
b/c accountability
7hrs to get these 20sec mostly up to speed. Helluva conversion ratio.
7hrs to get these 20sec mostly up to speed. Helluva conversion ratio.
July 8, 2025 at 2:57 AM
b/c accountability
7hrs to get these 20sec mostly up to speed. Helluva conversion ratio.
7hrs to get these 20sec mostly up to speed. Helluva conversion ratio.
According to Facebook, 8yrs ago today was the greatest day of my life
June 19, 2025 at 2:12 PM
According to Facebook, 8yrs ago today was the greatest day of my life
Landlocked? Yes. Undeterred? Also yes.
May 7, 2025 at 12:47 PM
Landlocked? Yes. Undeterred? Also yes.
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
Also me:
New software about to drop, and like Harpy, also named after a fictional monster that will absolutely try to murder you
April 10, 2025 at 10:38 PM
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
Also me:
New software about to drop, and like Harpy, also named after a fictional monster that will absolutely try to murder you
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.
April 5, 2025 at 12:37 PM
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.
And, you can use Jupyter from VScode (like I do, see screenshot) if you don't want to bother with the native browser-based UIs. It's amazing. My mental overhead is so much less for organization. It looks NICE. It's TRANSPARENT. It's REPRODUCIBLE.
February 26, 2025 at 3:32 PM
And, you can use Jupyter from VScode (like I do, see screenshot) if you don't want to bother with the native browser-based UIs. It's amazing. My mental overhead is so much less for organization. It looks NICE. It's TRANSPARENT. It's REPRODUCIBLE.
Some wonderful colleagues are hosting this-- consider attending!
November 20, 2024 at 12:09 AM
Some wonderful colleagues are hosting this-- consider attending!
Catch me at AFS 2024 in Honolulu next week! Say hi-- let's grab a meal and chat or ask me for some stickers. There's still time to sign up for the workshop Meg Oshima and I are co-hosting (see below). Looking forward to seeing you there 😀
September 10, 2024 at 2:21 PM
Catch me at AFS 2024 in Honolulu next week! Say hi-- let's grab a meal and chat or ask me for some stickers. There's still time to sign up for the workshop Meg Oshima and I are co-hosting (see below). Looking forward to seeing you there 😀
After several failed attempts to hide the snakemake output in favor of progress bars, a very fortuitous accident finally made it possible! The next release of Harpy won't vomit out snakemake output any more!
August 13, 2024 at 3:06 PM
After several failed attempts to hide the snakemake output in favor of progress bars, a very fortuitous accident finally made it possible! The next release of Harpy won't vomit out snakemake output any more!
Folks at #Evol2024, I've a fresh batch of pride stickers with some fun new variants this year. New Harpy stickers too (the software I work on)! Stop me in the halls (or DM) and I'll happily give you some! 🙂
July 28, 2024 at 1:26 PM
Folks at #Evol2024, I've a fresh batch of pride stickers with some fun new variants this year. New Harpy stickers too (the software I work on)! Stop me in the halls (or DM) and I'll happily give you some! 🙂
For anyone attending AFS2024 in Honolulu, Meg and I are hosting a 2-day workshop to get you much, much better at visualizing data and putting together showstopping Powerpoint presentations. I highly recommend you consider signing up b/c we know what we're talking about and are fun as heck 😁
July 18, 2024 at 7:40 PM
For anyone attending AFS2024 in Honolulu, Meg and I are hosting a 2-day workshop to get you much, much better at visualizing data and putting together showstopping Powerpoint presentations. I highly recommend you consider signing up b/c we know what we're talking about and are fun as heck 😁
Hosted an emo-themed karaoke, despite never having an emo phase. I'm second from the left-- you gotta commit to the bit.
April 13, 2024 at 4:45 AM
Hosted an emo-themed karaoke, despite never having an emo phase. I'm second from the left-- you gotta commit to the bit.
As Harpy nears v0.7, error messages became SUPERCHARGED, 10X data is accepted, infinite and arbitrary input files/folders, workflows much more reproducible, and I finally figured out github actions and bioconda enough to be dangerous.🦅⚡
github.com/pdimens/HARPY
github.com/pdimens/HARPY
February 26, 2024 at 3:37 PM
As Harpy nears v0.7, error messages became SUPERCHARGED, 10X data is accepted, infinite and arbitrary input files/folders, workflows much more reproducible, and I finally figured out github actions and bioconda enough to be dangerous.🦅⚡
github.com/pdimens/HARPY
github.com/pdimens/HARPY
In 2014, my lab in TX, brand new at the time, asked me to make them a logo and I loved it. 9 years later, they asked me to revamp it and I had so much fun taking a second stab at it with way more experience. It's so preeeeetty 😍
October 30, 2023 at 3:19 PM
In 2014, my lab in TX, brand new at the time, asked me to make them a logo and I loved it. 9 years later, they asked me to revamp it and I had so much fun taking a second stab at it with way more experience. It's so preeeeetty 😍
A bit of a spoiler but too excited not to share. This handsome synteny plot took only* 40min to render.
(*sarcasm)
(*sarcasm)
October 24, 2023 at 3:05 PM
A bit of a spoiler but too excited not to share. This handsome synteny plot took only* 40min to render.
(*sarcasm)
(*sarcasm)
I had unhealthy work habits during my PhD and I'm making a real effort to be better with the post doc.
1. Every day at 12pm is an event on my calendar to take a break. It's called PAUSE THE FUCK UP. All caps.
2. At 5pm, I leave a #TODO in my code and legit forget about it until the next day.
1. Every day at 12pm is an event on my calendar to take a break. It's called PAUSE THE FUCK UP. All caps.
2. At 5pm, I leave a #TODO in my code and legit forget about it until the next day.
October 21, 2023 at 8:16 PM
I had unhealthy work habits during my PhD and I'm making a real effort to be better with the post doc.
1. Every day at 12pm is an event on my calendar to take a break. It's called PAUSE THE FUCK UP. All caps.
2. At 5pm, I leave a #TODO in my code and legit forget about it until the next day.
1. Every day at 12pm is an event on my calendar to take a break. It's called PAUSE THE FUCK UP. All caps.
2. At 5pm, I leave a #TODO in my code and legit forget about it until the next day.
Hi! I'm Pavel and I'm a postdoc at Cornell looking into eco-evo fish things, mainly movement and gene flow over evolutionary time. I also play guitar, rock climb, do a ton of bioinformatics while preaching about the Julia programming language, and constantly try to excise toxicity from academia.
October 19, 2023 at 11:36 AM
Hi! I'm Pavel and I'm a postdoc at Cornell looking into eco-evo fish things, mainly movement and gene flow over evolutionary time. I also play guitar, rock climb, do a ton of bioinformatics while preaching about the Julia programming language, and constantly try to excise toxicity from academia.