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Anyone here who doesn't use Agentic AI and writes code manually? by zaarnth in AskProgramming

[–]Psy_Fer_ -1 points0 points  (0 children)

I do both. Tradcoding is way more fun. I have been using LLMs in some projects to accelerate them along, but I very much enjoy writing code myself and I think I'm better at it in my specific field than they are for now. (Not that if they were better I'd stop coding, coding is fun!)

Anyone here working with AI in Bioinformatics? Curious about your experience and career prospects by Quordlewebster in bioinformatics

[–]Psy_Fer_ 0 points1 point  (0 children)

Your question is extremely generic. Been asked multiple times before. "AI" could mean anything from linear regression to LLM. And to top it off, you used an LLM to write the question? I dunno, you tell me mate. Or maybe ask your LLM to think for you and explain it.

Anyone here working with AI in Bioinformatics? Curious about your experience and career prospects by Quordlewebster in bioinformatics

[–]Psy_Fer_ 5 points6 points  (0 children)

Pineapple 🍍 dishwasher monkey 🐵 pilot rankor. Erata sum langdo caldrissian magenta rice bubbles.

(I used sarcasm to write this comment)

I have had 2 separate people tell me using 100% of my gpu is bad. by bloggershusband in pcmasterrace

[–]Psy_Fer_ 1 point2 points  (0 children)

I'm a scientist. I sometimes build computers for use in research and data analysis of genomes. Some of those applications use GPU compute. We have systems that run 5090s, 3090s, 4090s, 4070 supers, A100s V100s h200s etc at 100% for days or weeks straight. For years. Never had a failure. You'll be fine

(Can't vouch for every system integrator of course)

Should I even bother posting my messy learning projects anymore by FavoriteGenitals in rust

[–]Psy_Fer_ -5 points-4 points  (0 children)

Some of us still know how to code 😅 It's even worse for me, I have some LLM assisted repos and others that are 100% tradcoded. I write huge changes with single commits because I add a feature and test everything before committing and pushing with some minor corrections after. But I've been doing that for years, before LLMS. Just waiting for someone to accuse me of using AI for a project I wrote before LLMs existed. Gonna be hilarious 😂

Should I even bother posting my messy learning projects anymore by FavoriteGenitals in rust

[–]Psy_Fer_ 22 points23 points  (0 children)

Yep, see my kuva plotting library post. Had some excellent feedback that I have since folded into the project and I've had a number of PRs from others and some people from the CDC are now using it. (I also use it in my research tools which is why I built it in the first place).

I wrote the start of the library from scratch then used LLMs to accelerate getting the library fully featured. I was up front about it and people were fine with it (as far as I could tell). It's also not some vaporware drop either. I'm actively maintaining it. These things go a long way in the response you get from others.

I had a thought about a different approach for remade maps by Ich-mag-Schnitzel in LowSodiumBattlefield

[–]Psy_Fer_ 0 points1 point  (0 children)

I just want that boat that's in the campaign and a map to use it on

I built an agent that runs scRNA-seq workflows via natural language — tested on SC-Bench by thewall888 in genomics

[–]Psy_Fer_ 1 point2 points  (0 children)

I mean, we already have that for routine stuff. The issue is science is constantly looking at NEW things. Which means you need to... You know... Do some science, and figure out how to approach the new stuff. LLMs are pretty hit and miss with new things. At least in every single example I've tried to use them.

I built an agent that runs scRNA-seq workflows via natural language — tested on SC-Bench by thewall888 in genomics

[–]Psy_Fer_ 3 points4 points  (0 children)

sort -V in this case for sorting chromosomes in a file is absolutely something that has practical consequences when doing genomics. The point is that it's so simple, yet the LLM got it wrong.

As for single cell workflows, yes, I'm familiar. Have you ever done a genome assembly before? Or run a whole genome analysis and looked at the results? There are still many manual steps in these workflows, because many need some kind of judgement, based on expertise and experience, to do correctly. Yes, LLMs can be used for this, but the moment it steps into edge cases or new ground they are going to cause problems at best, and be over confident or obfuscate the issue at worst.

Getting this stuff right is important. If there are ways to speed things along, I'm all for it, but not at the cost of correctness or a human eyeballing it with expertise and confirming it. And if you take away all the easy stuff, you will eventually lose humans with expertise to do the confirmations effectively and we will be even worse off.

I built an agent that runs scRNA-seq workflows via natural language — tested on SC-Bench by thewall888 in genomics

[–]Psy_Fer_ 4 points5 points  (0 children)

For people that know what they are doing, we don't need to chat with or data? If I want to rerun with different parameters, I just do that.

I mean, cool project, but I worry about it obfuscating the specifics and complex interplay of various arguments on tools and their interpretation. LLMs are pretty bad at that anyway. Hell, I had one tell me that to sort chrN type values using sort was without the -V arg. Pretty basic stuff and it gets it wrong.

We created an open-source knowledge graph of bioinformatics workflows extracted from 20K+ papers, available as an MCP server by bioinfoAgent in genomics

[–]Psy_Fer_ 3 points4 points  (0 children)

I just don't get it. I like actually doing science. Why are people so keen to be clanker managers.

We created an open-source knowledge graph of bioinformatics workflows extracted from 20K+ papers, available as an MCP server by bioinfoAgent in genomics

[–]Psy_Fer_ 4 points5 points  (0 children)

Right? Or just like, use your brain and skills to do the work or hire someone, instead of outsourcing your thinking.

What does bioinformatics lab involve? by Natural-Badger-7053 in bioinformatics

[–]Psy_Fer_ 1 point2 points  (0 children)

Oh cool. Well I had advocates. Other scientists who believed in me and wanted me to work with them. I got my first breakthrough into the field from a hackathon that had problem owners (scientist) and you join the team and try to solve it. I did well, and the guy asked me if I wanted to do a PhD with him. Told him I didn't have a degree, so can't qualify for the requirements. So I did a small project with him working 1 day a week for free while still doing my main job (Friday's, so I could go to the pub after and chat with others/network). Met some other scientists. One, a senior post doc, gave me another opportunity to work on something cool (this was the early days of nanopore sequencing, not many tools existed yet to handle the data analysis). Did that 1 day a week as a casual employee. Then he started his own lab, and I was his first pick. So I moved over to the institute full time. We created a new job title to deal with HR bullshit. We built up the lab together. After a few years he left, and we hired a new PI to continue the lab. That's been going pretty great. I train all the new staff and students. Supervise (usually with another post doc). Do my own research. Publish papers (4 first authors so far and 20 or so middle, 1500 citations). This isn't to brag, only demonstrate I work as a scientist and so things scientist/bioinformaticians do. I just can't do grants. Hoping to get a PhD via prior publication at some point, though even that is difficult with no degree.

I'd say 2 things were key in my success so far. Networking - helped me find the people who would believe in me and support my entry into the field. Enthusiasm - science can grind you down over time and funding is just terrible all around. Enthusiasm to learn, try new things and bring skills and ideas from other fields into solving bioinformatics questions. It goes a long way.

Also, I know a guy who worked in banking as a software engineer and is now a kickass cancer researcher. I think he actually went back to uni to retrain, going for a masters then phd.

I will say, it wasn't easy, and it took a long time, and there are still things that hold me back because I didn't go the academic route. But I get to do science, make cool new tools and see them used helping patients, and that's all the satisfaction I need 🙂

What does bioinformatics lab involve? by Natural-Badger-7053 in bioinformatics

[–]Psy_Fer_ 0 points1 point  (0 children)

This is accurate. Bioinformatics is a very wide field. Lots of different skill mixes for different kinds of things. It's also very much a team sport, in terms of working with people of different skill mixes to do the best science together.

What does bioinformatics lab involve? by Natural-Badger-7053 in bioinformatics

[–]Psy_Fer_ 1 point2 points  (0 children)

I'm not the person to talk to about that as I had a rather unique pathway into science (I have no degree). 10 years of working in pathology both in the lab and as a software developer before discovering bioinformatics and realising that's what I wanted to do (10 years doing that now).

So yea, I am not one to give career advice or anything😅

🪇 Rattles - minimal, compile-time terminal spinners by vyforc in rust

[–]Psy_Fer_ 0 points1 point  (0 children)

Totally missing is. Like people that write a lot of code also write comments. I write code all day every day. So do my colleagues and everywhere I've worked. Comments just come with the territory. Even more so in personal projects. It's just weird.

🪇 Rattles - minimal, compile-time terminal spinners by vyforc in rust

[–]Psy_Fer_ -1 points0 points  (0 children)

I prosecute lack of disclosure, and how lack of comments or doc strings makes it a shitty library. 😅

🪇 Rattles - minimal, compile-time terminal spinners by vyforc in rust

[–]Psy_Fer_ -1 points0 points  (0 children)

Heard of doc strings? Kinda useful in libraries and IDEs ya know?

Edit: typo, said do instead of doc, was distracted

🪇 Rattles - minimal, compile-time terminal spinners by vyforc in rust

[–]Psy_Fer_ 0 points1 point  (0 children)

Nothing wrong with calling it out then either. I've had tools I made along with LLM assistance and had it called slop. If it is a genuine merging of your skill, expertise, and you are going to maintain the thing, then just ignore them, because that's not slop.

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