Pavel Dimens
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
- Reposted by Pavel DimensFifteen 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
- Reposted by Pavel DimensAre 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...
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- 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
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- 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
- And the link, if you're into that sort of thing: github.com/pdimens/harpy
- Reposted by Pavel DimensI'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.
- Reposted by Pavel DimensNever 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.
- Reposted by Pavel Dimensleftists: 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.
- Reposted by Pavel DimensThere 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!
- 👋 Interested in working on the evolution of genetic architecture 🧬 of complex traits using linked-read sequencing of thousands of common lizards 🦎 from a wild population and common garden experiment? #evolution #genetics Well, I have a PhD offer for you 👇 devillemereuil.legtux.org/erc-funded-p...
- 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 😶
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- 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
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- The simple solutions to my trickiest analysis problems always seem to appear when I'm walking my dog.
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- 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
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- 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.
- Reposted by Pavel DimensIf 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.
- Reposted by Pavel DimensWe 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! 🧪
- Not-so-gentle reminder that GCRL at the U. of Southern Mississippi has some truly reprehensible PI's who you should be wary of and they keep being elevated into positions of power.
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- Harpy v2.0 is almost across the finish line, and I wrote a lil' post about what linked-read sequencing actually is and how we evaluate the data differently than standard short-read data. It's a quick and easy read (with pictures!), highly recommend 🤓 #PopGen pdimens.github.io/harpy/blog/l...
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- Reposted by Pavel DimensHi there, my student is making a survey about the use of R packages in Ecology, could you please spend two mins on filling it 🥹 Very appreciated! And if you could spread it further (RT), that would be just awesome. ❤️ docs.google.com/forms/d/e/1F...
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- Big Girls Don't Cry by Fergie was released in 2006, making it older than current freshmen undergrads.
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- Reposted by Pavel DimensJust a reminder that PMC is mirrored in Europe europepmc.org I honestly am having trouble believing it has come to this 🧪
- Reposted by Pavel DimensA reminder for these times.
