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naturepoker @binomicalabs.org · 29/09/2026

Autumn rain's finally let up a bit. #nyc

naturepoker @binomicalabs.org · 19/09/2026

Setting up #guile within #android #termux environment. Guile 3.0.11 is in termux pkg, and guile-colorized install via cloning the repo, running: mkdir -p "$(guile -c '(display (car %load-path))')/ice-9" Then make install. Add necessary lines to .guile & we have first class repl on arm android

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naturepoker @binomicalabs.org · 14/09/2026

The demo AA sequence folds on my 11 year old P50 with quadro M2000M & 4gb vram, which is probably worse gpu than the one in my phone (1.45 TFLOPs on the quadro, 1.68 TFLOPS on Mali-G715). Wow, tech's come a long way.

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naturepoker @binomicalabs.org · 14/09/2026

Something from 🦣. Looks like #linux #Zoom client calls home with captured system x11 clipboard content. If you have api keys or passwords on clipboard, this could be a big problem. Apparently Slack client does it too? It can be turned off in config.

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naturepoker @binomicalabs.org · 11/09/2026

That's good to know - but built in syntax highlighting in 1.13 update isn't behaving like how I'd expect. For example, in 1.12 OhMyREPL typing exit() would highlight 'exit' and '()' appropriately. But in 1.13, they're just regular texts. Do you know if 1.13 highlight requires additional config?

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naturepoker @binomicalabs.org · 29/08/2026

Alright. Time to set up an extra 26TB of storage in an independent sequencing and microbiology lab run by warehouse and construction job money. I'm thinking wiping everything and running Debian. About time too, I had to halt a bunch of work in the background due to the storage ceiling.

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naturepoker @binomicalabs.org · 28/08/2026

A local store started carrying these for a very nice ~1.50 a bottle. I really enjoyed yebisu when I worked in Osaka for a bit, but those are close to impossible to come by in the US. It's perfect for when I have a ton of stuff to do in the lab & can't imagine dragging myself there after work.

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naturepoker @binomicalabs.org · 24/08/2026

Still wrangling extracting colored kmer table out of genomes using in-line, piped #Julialang one liner. I added canonicalization to account for reverse complements, and filtering for ambiguous bases. Still a pretty reasonable 10 short pipe blocks or so. It's all just tuples and dictionaries.

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naturepoker @binomicalabs.org · 23/08/2026

Quite a pour this morning in #nyc just in time for commute for most people too. It's oddly refreshing though.

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naturepoker @binomicalabs.org · 17/08/2026

What is this blade runner scene today morning in the city lol. Half expecting some radio chatter from a street corner.

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naturepoker @binomicalabs.org · 17/08/2026

Rainy morning in #nyc. Early morning skies are slipping back into the dark, summer is almost gone.

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naturepoker @binomicalabs.org · 11/08/2026

Makeshift lab desk setup to fit in a new 37in curved monitor sent in from a new contract job. So... Futuristic. I can fit so much on one screen it's a bit overwhelming.

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naturepoker @binomicalabs.org · 05/08/2026

#rustlang has an official LLM policy. Pretty sensible - everything boils down to "you can't copy paste LLM output without any work and call it a contribution". QC requirements are higher for LLM generated code, also common sense. blog.rust-lang.org/inside-rust/... Also this part cracked me up:

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naturepoker @binomicalabs.org · 04/08/2026

Picked up a refurbished Keychron Q2 on the cheap... And going into it without high expectations, wow this is genuinely different from the generic cooler master I've been using. Brown switches are not as noisy as I expected too. This thing also weighs a ton despite the size.

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naturepoker @binomicalabs.org · 03/08/2026

It's raining even more than earlier in the morning. Enjoying the view but not looking forward to wading through all this soon. #nyc

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naturepoker @binomicalabs.org · 28/07/2026

This is not at all a good way to use the tool, but I love it nonetheless. Feeding linux shell output directly to #julialang -e module env for inline plots without repl. 2 seconds to plot because of module compilation, but maybe I can keep a precompiled env just for inline figs 😆

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naturepoker @binomicalabs.org · 26/07/2026

Quick film photography snap from my trip to Washington DC National Gallery. It was a welcome relief from everything outside those walls.

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naturepoker @binomicalabs.org · 18/07/2026

아아 동심의 이솝 밥상뒤집기 이야기

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naturepoker @binomicalabs.org · 18/07/2026

Wildfire smokes haven't cleared up yet. Looking forward to the supposedly pretty big thunderstorm later this morning. #nyc

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naturepoker @binomicalabs.org · 16/07/2026

I think @martinsteinegger.bsky.social lab has some of the best lab sticker designs I've seen. Definitely going on my nanopore. Thanks for the chat!

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naturepoker @binomicalabs.org · 13/07/2026

There's pre-canned jack daniels and coke? I'm disturbed yet curious.

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naturepoker @binomicalabs.org · 12/07/2026

Also spent some quality time at the Smithsonian museum of American Indian. The exhibit on Native American art 1900s onward was extremely compelling. And the exhibit on the history of treaties between Indian nations and the USA... Man that cut deep.

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naturepoker @binomicalabs.org · 12/07/2026

In DC again for ISMB/BOSC. DC metro is certainly something else. Some of the entryways basically look like bunker entrances. Also, the platform's air conditioned. Something NYC will never have for many reasons har har.

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naturepoker @binomicalabs.org · 08/07/2026

Got it. Yeah we just sent some of the genome extracts to an Illumina vendor for comparison data, spent some time on asm to asm synteny and alignment stat script too (fig). Looking forward to analyzing properly soon. Thanks for responding & all the write-ups you do! They're great learning materials

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naturepoker @binomicalabs.org · 26/06/2026

Close to wrapping up reciprocal best hits & minimap2 alignment based assembly comparison tool in #Julialang. It's an offshoot of a Julia based synteny study project started a year ago... It took almost a darn year of learning Julia to reliably write RBH+paf parser and plotting script T_T

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naturepoker @binomicalabs.org · 22/06/2026

For #bbm2026 folks - come check out my poster on 3FL, #21! It's part of the data going out on my soon-to-be published preprint, some aspects can definitely use feedback. 🧫🦠

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naturepoker @binomicalabs.org · 11/06/2026

And here's an animation of a demo set - sequencing quality for this run was... Not good

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naturepoker @binomicalabs.org · 11/06/2026

Mad 4AM dash to wrap up a #Julialang tool for #archaea lab collaboration. Pure terminal UnicodePlots pipe for assessing & plotting raw BAM reads quality then generating length x quality plot animation in mp4. The whole thing takes seconds even for pretty large BAMs - great for bulk analysis! 💻🧬🧫🦠

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naturepoker @binomicalabs.org · 08/06/2026

IMHO we need to resist the natural urge to make associations when viewing these paintings. They're not supposed to resemble anything, and pattern recognition is a barrier to taking them in entirely. Interesting in light of our LLM world and cultural push to associate pattern matching with humanity.

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naturepoker @binomicalabs.org · 08/06/2026

Got some much anticipated quality time with the Rothko rotation at the Washington DC NGA. The rotating collection (from 1000+ works!) is located at E615, best way to get there is an elevator to the rooftop and then walking in via the glass doors.

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naturepoker @binomicalabs.org · 08/06/2026

My good friend Gustave, you're there wherever I go, and life is better for it. La Grotte de la Loue

A person stands at the entrance of a great dark cave, water current flowing out of it toward the world. This is the origin of a river.

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naturepoker @binomicalabs.org · 08/06/2026

I couldn't pass up the opportunity to stop by the DC National Gallery of Art! Really looking forward to the Rothkos.

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naturepoker @binomicalabs.org · 04/06/2026

Leaving for DC on Amtrak - #ASMicrobe2026 woot! If anyone around here wants to chat about #archaea, #sequencing, or independent research please feel free to drop a note or come say hi!

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naturepoker @binomicalabs.org · 01/06/2026

Trying out one of those newfangled low/non alcoholic beer the young people love so much. Hey it's not too bad? #beer

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naturepoker @binomicalabs.org · 25/05/2026

I've been deep into ONT basecalling model land as part of my recent archaea study, trying to see if it's worth it in the first place. Here's read to phred map plot per hour of sequencing time- ONT SUP model on the left, and archaea tuned custom model on the right. Interesting! #archaeasky 💻🧬

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naturepoker @binomicalabs.org · 24/05/2026

Almost done rewriting BAM score to length plotting script by @jpelbers.bsky.social! Can't believe this was a month's worth of digging :P New version is based off CairoMakie, thinking about playing with 3D WGL output using topographic map. Also, this was a half decent sequencing run! #julialang

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naturepoker @binomicalabs.org · 23/05/2026

Found a dog-eared copy of Flower Wreath Hill. Lost my own a while ago and had to bring it home. Fun fact. When I got here as an 11 year old I didn't know English. A local college lit student took a shine to me and this is one of the passages we went over night after night. Good memories.

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naturepoker @binomicalabs.org · 21/05/2026

Picked up a used copy of The Penguin Book of the Prose Poem at a used bookstore while coming back from work. So happy it didn't get drenched in the sudden rainstorm. I've been really enjoying Rilke's Dinggedicht pieces recently - curious to see if there's a prose poem match for the practice.

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naturepoker @binomicalabs.org · 19/05/2026

I've been wondering about role of reference assembly contiguity when training/tuning an ONT basecaller model. Stumbled into implementing a crude forward pass in #Julia with tuned weights, contig level genome ref vs complete genome ref. Model behaves very differently on same POD5 signal input! 💻🧬

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naturepoker @binomicalabs.org · 11/05/2026

Korean painting of a cat from the 1800's, artist unknown. I don't know why but older Korean works from the era tend to veer on the humorous side.

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naturepoker @binomicalabs.org · 11/05/2026

Put together a #Julialang monitoring script to keep an eye on gradient norm spikes in ONT basecalling model training. Need to figure out if I can afford another epoch and if learning rate needs to decrease. All done on my phone while on a warehouse shift coffee break! What a world.

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naturepoker @binomicalabs.org · 03/05/2026

Found during a morning shift - maybe I'm just uninitiated but this part absolutely blew my weariness away. For those who don't know I've been digging into extra chromosomal rrns in Archaea for about two years now - preprint coming this summer! #archaeasky 🧫🦠 journals.plos.org/plosbiology/...

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naturepoker @binomicalabs.org · 01/05/2026

Spring night in #nyc Queens. It was nice to feel a bit at ease, if just for a moment.

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naturepoker @binomicalabs.org · 29/04/2026

Done disassembling shelves, moving in a new height adjustable desk and unpacking the new #Opentrons and Bamboo A1 at the lab. Six whole hours of work. This is prep to work with local community college kids, surveying and sequencing local superfund waterways late this summer!

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naturepoker @binomicalabs.org · 26/04/2026

AMD-gigabyte MB combo still wonky on linux after nearly 6 years. I'm pretty sure none of my workstation component's running at -55C lol.

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naturepoker @binomicalabs.org · 24/04/2026

This is probably one of the better shots of the city I took on film. TriX developed in caffenol, from upper floors of our warehouse-lab. #nyc

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naturepoker @binomicalabs.org · 12/04/2026

Savoring little moments of calm in between shifts. Spring comes to early morning colors.

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naturepoker @binomicalabs.org · 02/04/2026

Happy to have made a small contribution for @gbouras13.bsky.social's study. Hope this is just one of many examples in independent researcher collaboration with academic scientists! #archaeasky folks, this pipeline rules for global baseline annotation for archaea doi.org/10.64898/202... 💻🧬🧫🦠

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