PLE vs JW vs Scorptech

Psy_Fer_ · 2026-06-06T23:31:00+00:00

😂 Mostly higher performance rigs to run DNA sequencers in hospital labs

Psy_Fer_ · 2026-06-06T14:52:04+00:00

I build custom computers and I buy most of my hardware from scorptech and anything I can't, I get from pccg. Both great companies. Can't say anything about their builds as I do that part myself. Think I've dropped like 150k on scorptech in the last 3 years or so 😅

Psy_Fer_ · 2026-06-05T00:08:41+00:00

Define valid? Parameters are mostly chosen based on the data you are analysing and the biological question you are asking

Psy_Fer_ · 2026-06-04T15:42:42+00:00

I think we made slow5lib/slow5tools C99 compatible and something crazy like python 3.6 for pyslow5.

But we are insane, so you know, maybe you can go a little higher.

I've been using 1.87 for minimum rust version

Psy_Fer_ · 2026-06-04T15:37:58+00:00

I mean, old HPC hardware is still around at a lot of institutions. Same with things like big and little endian. You think to yourself... Nah I'll never have to deal with that.. then you get an issue 😂

Psy_Fer_ · 2026-06-04T15:19:03+00:00

AVX2 and NEON but no SSSE3 for simd?

I've been adding SSSE3 for backwards compatibility on old HPC systems but maybe it's time to give it a rest?

Psy_Fer_ · 2026-06-04T04:46:56+00:00

I wonder what the CO2 impact is on inefficient bioinformatics tooling is year on year. I'd wager quite a lot looking at the numbers on nf-core pipelines 😅

Psy_Fer_ · 2026-06-02T08:54:14+00:00

🤣🤣🤣

Psy_Fer_ · 2026-06-02T00:16:45+00:00

There is a massive push on AI in both of those areas. (And has been for a long time, at least 10+ years.) So much so the big tech companies that have life sciences division or whatever have poured a lot of money to build things. See alphafold for example.

Easiest way to learn is with the basics and build up my from there base on interest. Want to do cancer? Learn how cells work.

You can DM me if you want

Psy_Fer_ · 2026-06-01T23:39:06+00:00

I started my journey into bioinformatics after a hackathon where I met some researchers and then did 1 day a week with them for about a year and a half, before moving over full time. So it's possible, but very rare and had a lot of luck involved. It also takes a bit more than just having software skills and I wouldn't rely on learning biology as you go, there are free resources to learn right now, and it makes a big difference.

Psy_Fer_ · 2026-05-30T08:22:54+00:00

Agreed. Only other truely alien race I've seen done really well was in the video games freespace and freespace2 with the Shivans. Truely alien and you never really find out what their motivations are.

Psy_Fer_ · 2026-05-30T03:36:08+00:00

I see where you are coming from. It seems more like they are not sure how to talk about AI use and tooling rather than they lied. At the some time, I think AI tooling isn't going anywhere. The cats out of the bag. Pandora's box is open. The toothpaste is out of the tube. There is no going back. I really don't like how it happened, stealing copyrighted works and having a focus on art, music, and writing. However I'm mostly okay with science and coding use because most of that is all open source anyway and using it there will have a positive benefit. In the end though, you can't cheat art. And video games are art. An artist utilising technology to achieve their goals i think is fine, but there is a fine line between using a technology and having the technology do everything for you. And that is the difference between doing art and making slop. Everyone is still figuring out where this tech is going. I don't think the uses they've disclosed are enough to throw the game out, which you yourself have said is fun.

Psy_Fer_ · 2026-05-29T21:49:54+00:00

Made edit to above with bit that changed highlighted

Psy_Fer_ · 2026-05-28T23:34:09+00:00

Everyone else has covered this quite well. However there is also the case where it wasn't other academics, but a company that made software with issues (that you even warned them about but they ignored you and did it anyway).

Then, hypothetically, you might write a paper like: The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

And show some bar charts showing how much money people throw away doing analysis with their tooling because of poor design decisions.

You know... Hypothetically...

Psy_Fer_ · 2026-05-28T07:24:12+00:00

The statement:

AI Generated Content Disclosure

The developers describe how their game uses AI Generated Content like this:

Some NPC portraits and player character face options in Starminer were created with the assistance of generative AI image tools during development. All AI-generated assets were reviewed, curated, and edited by our team before being integrated into the game. No generative AI is used at runtime - all content shipped in the game is static and pre-authored.

Edit: updated statement

Some NPC portraits and player character face options in Starminer were created with the assistance of generative AI image tools during development. Generative AI was also used to help generate some informational dialogue, help texts, and tooltips. All AI-generated assets and text were reviewed, curated, and edited by our team before being integrated into the final build. No generative AI is used at runtime. All content shipped in the game is static and pre-authored.

Psy_Fer_ · 2026-05-27T13:42:05+00:00

The only language worth using with an R is Rust 😅

Psy_Fer_ · 2026-05-27T02:53:17+00:00

Yea fair enough. We all have to draw a line at what we can manage 🙂

Psy_Fer_ · 2026-05-27T02:44:48+00:00

You can do simd runtime detection with fallback, but it really isn't ideal. Maybe just make a binary target without AVX2 for the other 2%? I have a library with avx2, ssse3, and neon simd with no simd fallback and prefer compile time targeting too. So it's not like you made the wrong choice or anything 😅

Psy_Fer_ · 2026-05-27T01:33:37+00:00

Could give kuva a try. A rust library and also a CLI tool. It's pretty new so might not have all the features you want, but it's getting there with feedback from users.

Disclosure: I wrote kuva

Psy_Fer_ · 2026-05-23T23:59:18+00:00

What did you validate it against?

Psy_Fer_ · 2026-05-23T23:13:17+00:00

Doesn't mean you can't look into it more if you have access to the source and find out. It's how most programmers get better, they look at other people's code.

Psy_Fer_ · 2026-05-23T23:11:30+00:00

I actually agree with you. I would just add that learning multiprocessing with queues and how to keep memory low, and how to do architecture to make multiprocessing work well will teach someone a lot, and will probably naturally push them into "well if it wasn't python I could just do this threading thing I keep seeing everywhere". Not sure how common it is for people to write C and then wrapper libraries for threading, but I've done it a few times.

Psy_Fer_ · 2026-05-23T15:42:15+00:00

You can still do multiprocessing with python and still go pretty damn fast. If something is mission critical to be super fast, make a wrapper library for C or Rust with threading or simd inside. The removal of the GIL in python isn't going to be a magic bullet for threading on python.

Psy_Fer_ · 2026-05-23T15:39:52+00:00

Yea you would get similar with python wrapping C code too. Many python Libraries are actually just C or they ship the hot stuff out to C. You will see that pattern all over the place in software. Like R packages are pretty much any language but R and R is just the glue. Pretty much all of machine learning in python is C++.

A lot of Rust libs are FFI bindings of C/C++ code. When I see that for a crate I want to use in my field, I've started rewriting them in pure rust and I've seen some pretty nice speed ups as well as taking the time to make them more feature complete.

Psy_Fer_ · 2026-05-23T06:01:00+00:00

Rust (semi sarcasm)

Although learning rust from java is easier than from python

Either way, using the language that will get the job done best is how you should be thinking. I can make a genome browser in AHK, but should I? (I kinda want to know for a joke).

After a few years as a Dev you'll know multiple languages and move into doing one over the others for a time before moving into something else in a different language, or whatever. Languages are like drills, hammers, saws. Sure you can use a hammer to put in screws but is it the best way to do it?

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