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anotherpaul

132 karma · joined May 3, 2024

bioinformatician

Python, NGS, ML

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anotherpaul··on CUDA Ontology
Yes, this is the actual lived reality. Thank you for outlining it so well.
anotherpaul··on Niri – A scrollable-tiling Wayland compositor
+1 Fullscreen Mac os but not the "Mac full screen" but normal full screen.
anotherpaul··on Myocardial infarction may be an infectious disease
"The most unique finding in our study was that viridans streptococci seemed to colonize the lipid core and wall of an atheroma as a biofilm and that this biofilm was not recognized by cells of the innate immune system. "

This is a pretty cool finding. Biofilms are also beyond reach of antibacterials usually. And seing a commensal become a problem due to "location, location, location" is also cool.

Nice article. Cool leads

anotherpaul··on Vibe coding as a VC
No major bugs maybe for you as a user, but I would bet there are some very serious security issues in multiple components. So I hope none of that code is reachable from the outside. Which ofc is already not true as you are processing data from the outside with llms.
anotherpaul··on Scientists No Longer Find X Professionally Useful, and Have Switched to Bluesky
Yes, same experience. I only read posts from people I follow, which solves this problem.

But of course this is a slow way to grow my network. But I like the slow linearity of the timeline this way.

anotherpaul··on Should you take creatine?
I can recommend the science vs Podcast. They did an episode on it.

https://podcasts.apple.com/us/podcast/creatine-a-hack-to-get...

As per usual: supplements are not that marvelous as the influencers say.

anotherpaul··on Claude Code is all you need
Yeah the old one was much worse. They have really stepped up their game recently. Thats why I am wondering how large the gap still is. I only ever see people compare cursor and Claude code. Never GitHub copilot. So I assume there is either a blind spot or it's much worse
anotherpaul··on Claude Code is all you need
I feel like Claude code is great but how is it so much different from the agent of GitHub copilot? They both can use the same model (Claude 4) and the agent behaves very similar. For 10 bucks I think GitHub copilot is very reasonably priced as well. But ofc usage limits are maybe where they differ a lot. Am I missing out?
anotherpaul··on Abogen – Generate audiobooks from EPUBs, PDFs and text
Does it turn it into spoken word or an audiobook? Because good audiobooks often have voice actors that read the characters with different emphasis and dialects. I imagine tools like chatgpt could do this for a few sentences but what about an 8-20 hour audiobook?

I think there are still basic hurdles to take before we can go epub to audiobook in a quality that can compete with current state of the art.

Or am I missing something?

anotherpaul··on I watched Gemini CLI hallucinate and delete my files
Yes, I was also stumped by the use of windows and then even the use of windows shell. Seems like asking for trouble.

But I am glad they tested this, clearly it should work. In the end many more people use windows than I like to think about. And by far not all of them have WSL.

But yeah, seems like agents are even worse when they are outside of the Linux-bubble comfortzone.

anotherpaul··on Show HN: iPantry – Track food inventory and reduce waste
Apps like this I can never believe that anyone really has the time or energy to keep the app and reality in sync. I am not saying it's not possible or useful. I am doubtful I would care enough to really dedicate time to it. Wouldove to hear from someone who actually has been tracking their pantry for longer than a week.
anotherpaul··on Mercury: Ultra-fast language models based on diffusion
Well diffusion models have long already made the jump to biology at least. Esm3 and alphafold 3 both are diffusion based.
anotherpaul··on Remote MCP Support in Claude Code
If I understand correctly MCP is the interface to connect any API to LLMs.

Now a lot of people use it to add context to their model. And also tool calls?

I am using continue.dev not Claude but I imagine this tech stack will be ported everywhere.

As a python Dev I don't quite yet understand though how and what service I should be running. Or be using. Tbh. Can anyone ELI5?

anotherpaul··on David Attenborough at 99: 'I will not see how the story ends'
On mobile Firefox with blocking I still see - cookie consent - some self add for subscription - an altert that I have to login

Can't read it

anotherpaul··on Student discovers fungus predicted by Albert Hoffman
It's great for the student. And it shows that the lab she worked in and the university are able to do this type of science.

Sequencing a new fungus is not that rare. It's done all the time these past years. People discover new species all the time.

What is cool is that they already know a bit about where this fungus lives and what it might do.

The hard biology will be go actually culture it, test it's abilities and see what else it can do.

I mean the article is very short so this is me speculating, but if it is of interest they might figure out what the symbiosis really means to the plant and the fungus.

Also discovering the gene clusters that produce the active compounds will be cool and interesting.

Edit: just so it's clear, its amazing that the student was involved and had the trive to do this. It's easy to not be curious but she was and also she was in an environment where her curiosity was taken serious. That's a great feat of the superiviser or whoever else was involved

anotherpaul··on Self-Host and Tech Independence: The Joy of Building Your Own
Glad I am not alone in this. Old laptops are much better than Raspberry pies and often free and power efficient.
anotherpaul··on FLUX.1 Kontext
Well it's a "generative flow matching model"

That's not the same as a diffusion model.

Here is a post about the difference that seems right at first glance: https://diffusionflow.github.io/

anotherpaul··on MicroPython v1.25.0
Thank you for explaining and giving context.
anotherpaul··on Show HN: VectorVFS, your filesystem as a vector database
Great idea indeed. The documentation needs a bit more information to be useful. What GPU backends are supported for example? How do I delete the embedding information after I decide to uninstall it? Will give it a try though.
anotherpaul··on Everyone knows your location, Part 2: try it yourself and share the results
I haven't gone through setting it up (yet) but I imagine there should be differences between EU and US versions of the apps. Is that something you expect to and if so, are you recording that info in your survey? Or am I just naive here?
anotherpaul··on Matrix.org Will Migrate to MAS
For me the issue was contact names tbh. Is that solved? It used to be that the contact name was set by the contact and not by me/my address book.
anotherpaul··on I can smell when people have cancer
I saw this too, not Shure if a reddit post is HN worthy. Regardless, I think there are studies in dogs, but I have not heard of human smelling cancer.and there are multiple people (?) claiming it in the comments.
anotherpaul··on Crawlers impact the operations of the Wikimedia projects
Seems like a serious issue many sites have nowadays. I really don't want this solved by Captchas everywhere.
anotherpaul··on Show HN: Duolingo-style exercises but with real-world content like the news
Nice, tried it. Looks cool. On the phone the drag and drop is a bit tricky. Dropped a wrong word and it got score emediatly as wrong, even though I was going to fix it. I expected scoring to happen after I click "submit". But maybe that's the same in Duolingo, no idea.
anotherpaul··on Natural occurring molecule rivals Ozempic in weight loss, sidesteps side effects
Very nice, thank you. This indeed answers my question.
anotherpaul··on Natural occurring molecule rivals Ozempic in weight loss, sidesteps side effects
https://www.nature.com/articles/s41586-025-08683-y

This seems to be the paper, but its behind a paywall.

Anyone with access can tell me if they publish the 12mer amino acid sequence? Is there more to it (post translational modifications)

Or is it just the peptide?

anotherpaul··on NIH.gov DNS servers down, making PubMed, BLAST, etc. unreachable
Thank you for writing this down. Might become relevant if they don't solve that before Monday.

One can only hope this is not intentional.

anotherpaul··on Restaurant Menu Tricks (2020)
This article is interesting, but the author seems more excited about tricking people into spending more money. You could easily use endpoints that are more in the direction of satisfaction and happiness than always using money as the goalpost.

I understand that the people he interviewed are likely in the business of profit making but as a journalist for the BBC I would have hoped for a more honest take.

"Put the most expensive item first so that the others seem more reasonable"

That's just messed up and not something to be celebrated IMHO

anotherpaul··on Scientists Clone Two Black-Footed Ferrets from Frozen Tissues
I could not find the answer for you, but I speculate not many: the frozen dna was only stored for 35 years. Cloning also does not need to introduce additional mutations into the dna afaik. So I'd expect very few if any mutations from the material they froze.

And to the reconstruction: I don't think it does in this case. As they talk about working with frozen cells and we are not in the realm of frozen Mammuts who's genomes has degraded and needs to be reconstructed. In that case yes, we would talk about smaller pieces.

anotherpaul··on Sci-fi books that you may never have heard of, but definitely should read
I really like the shepherd.com way of curating the recommendation. Browsing trough books and picking something to read has become much easier this way.

One scifi book that was very impactful to me is the black cloud by Fred Hoyle. It's such a well thought out story and has held up remarkably well for a 50 year old novel.

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