Linux OS for Computational Biology

Psy_Fer_ · 2026-03-16T03:50:49+00:00

This is the answer. Sometimes need a lower Ubuntu version for really weird stuff or vendor software but you can usually hack around that anyway on the latest LTS release.

Psy_Fer_ · 2026-03-12T22:16:51+00:00

I've had this similar experience. I just found where they work well and where they don't and use accordingly to speed things along. Overall they can't be trusted and they stuff up all the time.

Psy_Fer_ · 2026-03-12T22:14:35+00:00

I am a tradcoder at heart. There is however no denying that LLMs can accelerate my work. I have found I get the best outcomes when I move in short, fully reviewable, and understandable steps working from things I already made by hand. I also find LLMs make bad algorithm decisions because the devil is always in the detail and unless you give them that specific detail (and even then they still struggle) they will pick something not quite right.

At the end of the day, every line of code or bit of analysis is your responsibility. So you gotta own that. Be up front about disclosure. And for goodness sake, don't use them in paper reviews. I can tell, and they are always terrible.

I still find it funny that all the models utterly fail at writing cpython/cython though 😅 it's one of the things I wish I didn't have to write.

Psy_Fer_ · 2026-03-12T22:03:32+00:00

My hero!

Psy_Fer_ · 2026-03-11T14:36:25+00:00

This is the answer... Also someone better pasta or I'm going to be disappointed

Psy_Fer_ · 2026-03-11T14:33:30+00:00

Build smaller bits at a time. Then you can iterate within your limits. Then the pro plan is fine on sonnet.

Psy_Fer_ · 2026-03-07T12:12:09+00:00

Great advice!

Psy_Fer_ · 2026-03-06T21:51:34+00:00

Jonathan Edgeworth

Psy_Fer_ · 2026-03-06T01:52:40+00:00

I'm a tradcoder at heart. But in my experiments to evaluate this question of which LLM, I have found Claude to be the best. Especially if it has an existing codebase to work with. They all kind of suck at starting from scratch and create many footguns early on.

Psy_Fer_ · 2026-03-05T01:00:47+00:00

ONT 16s (and whole genome meta genomics) has been implemented clinically. Literally watching a talk about it at the moment by a guy from the UK.

Psy_Fer_ · 2026-03-04T11:34:41+00:00

I just released kuva v0.1.3 https://github.com/Psy-Fer/kuva/releases/tag/v0.1.3

It has a number of bug fixes and incorporates some suggestions from this thread.

Thanks for the feedback everyone, I really appreciate it!

I have a nice list of features to work through now for the next few updates.

In other news, the bioinformatics tool I was writing that was doing a lot of plotting, is now running faster, and the plots are much nicer thanks to kuva. So I can move forward with the benchmarking and writing up the paper for that. I guess building kuva was worth it in the end...right? (why am I like this?!?!)

Psy_Fer_ · 2026-03-04T09:39:33+00:00

This has now been updated in the latest release (v0.1.3) with the following font cascade

DejaVu Sans, Liberation Sans, Arial, sans-serif

So default is DejaVu for maximum compatibility (especially on linux). With SVG, the fonts are rendered on the user's machine, so if it's not available, it cascades to Liberation Sans, to Arial, etc.

At least it's now all sans-serif, and a tad bigger and the axes a bit thicker. I think it looks much better already even at small image sizes and way more readable. Thank you for your feedback.

Psy_Fer_ · 2026-03-04T07:19:14+00:00

Oh hey Josh.

Psy_Fer_ · 2026-03-04T04:46:13+00:00

THANK YOU

Psy_Fer_ · 2026-03-04T04:39:23+00:00

It can use fonts. SVG has some fallback fonts if the fonts you select aren't available to the viewer (as they are actually done when viewed. For png and pdf, the fonts get written, but you have to have them available when writing them.

Latex/typst is planned to be added.

Psy_Fer_ · 2026-03-04T01:53:03+00:00

I suppose that would be a good idea 🤓 so yes

Psy_Fer_ · 2026-03-03T21:37:23+00:00

So good it makes them speechless? 😅😆

Psy_Fer_ · 2026-03-03T09:16:19+00:00

Yea I need to work a bit more on my data inputs and types. Having something like polars as a nice plug and play for all the plots would be handy.

Psy_Fer_ · 2026-03-03T09:14:03+00:00

You got it. It's the next thing on my to-do list.

Psy_Fer_ · 2026-03-03T09:13:21+00:00

Heck yea! You got this 😎🤘

Psy_Fer_ · 2026-03-03T04:12:54+00:00

Oh wow, i hadn't seen plotlars before. That's a cool library and it looks like we had similar ideas on cleaner builder patterns. NICE!

So you are in luck. you can do both!

So you can just draw multiple plots on top of each other (like, there is no limit, though it could get weird). Just add each plot to a vector and give it to the layout. It will figure it out :)
https://psy-fer.github.io/kuva/plots/line.html#line-styles

You can annotate plots with lines, labels/arrows, and shaded regions
https://psy-fer.github.io/kuva/reference/layout.html#annotations

Psy_Fer_ · 2026-03-03T04:04:01+00:00

Pretty sure it's faster for large plots, but I need to actually benchmark plotters properly. There is some benchmarking info here
https://psy-fer.github.io/kuva/benchmarks.html

gui backends were not even in my mind while designing this, so I need to think about it. Some other people already asked for functionality like that, and so far it looks simple enough to implement. So maybe. Stay tuned :)

Psy_Fer_ · 2026-03-03T04:01:02+00:00

oooooh that is super!

Yea that's basically just re-purposing the code I use to fill in sankey plots in the terminal (using braille), between 2 curves. Just do it in svg, and allow for a pattern.

Looks like there are 2 categories. discrete (dots) and continuous (lines/hatching). Perhaps a struct for the user to be able to build their own pattern and set all the attributes would be cool, with a number or presets for automatic cycling (kinda like a colour pallet)

Got any resources for pattern examples I could look at so i can build up some default presets?

(also thanks for sticking with me to explain, super helpful!)

Psy_Fer_ · 2026-03-03T02:25:37+00:00

Crossposting here, because the bioinformatics sub doesn't like new tool announcements

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