HN user

samuell

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Fascinated by Living Systems | Clin Microbio Bioinfo @ Karolinska | PhD http://pharmb.io | Reproducibility, #SciWorkflows | Curious: Genomic Algos, TEs etc

R&D: https://livesys.se Thinking: https://livingsystems.substack.com

Married. Dad. Sinner saved by grace.

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livingsystems.substack.com 12d ago

AI progress should upgrade our view of the human brain – not devalue it

samuell
2pts0
github.com 2mo ago

Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

samuell
185pts57
twitter.com 2mo ago

Flux Matching – Generalizing diffusion models to non-scoring func vector fields

samuell
2pts0
livingsystems.substack.com 2mo ago

Playing freely – and not limiting innovation to what is already best practice

samuell
1pts0
github.com 2mo ago

Epiq: Distributed Git-backed CLI native issue tracker TUI

samuell
4pts1
www.heise.de 7mo ago

Nvidia aquires SchedMD – developer of Slurm HPC scheduling software

samuell
4pts1
www.koi.ai 8mo ago

GlassWorm: Self-propagating Worm Using Invisible Code Hits OpenVSX Marketplace

samuell
2pts1
www.bleepingcomputer.com 11mo ago

Pro-Russian hackers blamed for water dam sabotage in Norway

samuell
8pts1
docs.carbon-lang.dev 11mo ago

Carbon Language: An experimental successor to C++

samuell
155pts193
www.hackster.io 12mo ago

Embedded computing startup launches chip based on dataflow, saving tons of power

samuell
1pts0
github.com 1y ago

GROS: Implementation of Rust in Go

samuell
1pts0
news.ycombinator.com 1y ago

Ask HN: AI tool to convert videostream of slideshow into original slide quality?

samuell
1pts0
watermill.io 1y ago

Watermill – Building event-driven applications the easy way in Go

samuell
3pts0
news.ycombinator.com 1y ago

Ask HN: How do you use AI/LLMs to accelerate your own learning?

samuell
6pts3
www.cogentcore.org 1y ago

Cogent Core: A New Cross-platform GUI Framework for Go

samuell
4pts1
thenewstack.io 2y ago

MoonBit: WASM-Optimized Language Creates Less Code Than Rust

samuell
2pts0
nanoporetech.com 2y ago

Improving DNA Basecalling with Transformers

samuell
1pts0
bionics.it 2y ago

Why didn't Go get a breakthrough in Bioinformatics?

samuell
2pts0
friction.graphics 2y ago

Friction – An Open Source 2D Animation Software

samuell
2pts1
twitter.com 2y ago

Heng Li recommends Rust (author of some of most used bioinformatics software)

samuell
2pts1
news.ycombinator.com 2y ago

Give some new links a chance

samuell
71pts23
bionics.it 2y ago

Matrix transformation as model for declarative atomic dataflow operations (2015)

samuell
1pts0
lh3.github.io 2y ago

What high-performance language to learn [for bioinformatics]?

samuell
5pts3
news.ycombinator.com 2y ago

Ask HN: Easiest way to create a CRUD web app in 2024?

samuell
34pts33
www.modular.com 2y ago

Mojo vs. Rust: is Mojo faster than Rust?

samuell
54pts31
github.com 2y ago

Flashcards in 40 Lines of Bash

samuell
2pts1
twitter.com 2y ago

Nvidia CEO: Digital Biology will be the next revolution - one of biggest ever

samuell
2pts0
www.biorxiv.org 2y ago

Movi: A fast and cache-efficient full-text pangenome index

samuell
1pts2
news.ycombinator.com 2y ago

Ask HN: What makes SRE great compared to "plain" DevOps?

samuell
10pts17
www.businessinsider.com 2y ago

Andrew Ng: Big Tech inflating fears about AI risks to dominate the market

samuell
5pts3
Back to Kagi 9 hours ago

I'll second the rec for Brave search. Been a happy user for at least 1-2 years now. Its AI summaries are great and, I have the feeling it works a little better than DuckDuckGo for some reason.

Well, I was referring to "value" here in a very pragmatic sense, in terms of the ability to come with "novel" thoughts and ideas.

And I argue that the notion of AI models having overtaken the human mind in practically all areas, is vastly inaccurate.

I could back it up with a number of references of course, but I think this is already quite well known and accepted by most people with some insight into the field.

While I understand this is a PR talk for a startup, I think the text itself contains a number of interesting observations.

Regarding the idea of distributed models communicating with each other, I have also been thinking (and writing [1]) along those lines, where I see that the data amounts needed to fully digitalize ourselves and our society requires far too much storage if just serialized (limited by bandwidth if nothing else), while smart, updateable models are actually a much better storage medium for such information, as it can communicate only the important bits (any new information) on a higher level, with each other.

The other observation here that rings bells for me is how I think lessons from trying to develop intelligent systems should upvalue the human mind rather than devalue it, as we start to treat it less like an ad-hoc thing, and more like the finely tuned machine it is, which also benefits greatly from optimizing what data we feed it with, the architecture of solution strategies etc. All of which is an area where humans and machines can do wonders together [2].

[1] https://livingsystems.substack.com/p/the-future-of-data-less...

[2] https://livingsystems.substack.com/p/ai-progress-should-upgr...

Quite thought-provoking, and connecting it to a related field it seems the (relative) success of LLMs and the likes are indications that enough data can at least learn you something without always needing to interfere with the world first(?)

As someone who has spent some time in sub-saharan Africa, I can tell you that there is lots that can be done if just seeing the possibilities.

Not everyone everywhere are "engineering oriented", and having people with the skills and eye for practical solutions based on available materials, can help tons, and also open up people's imagination for what can be done.

In fact, this goes for northern Europe too, just that more people can manage without home-built solutions and can "buy away the problem" here.

Also, people where immensely thankful e.g. when my quite clever and crafty father managed to repair a water tank tower that'd been broken for months and years, by sourcing some local material, coming up with a repair design, and having local welders create it, etc etc.

No, this was pure speculation based on what seems like a popular view on where Mojo ended up, where the initial Python-focus don't seem to help it that much anymore.

Maybe Chris was a little unhappy about where Mojo ended up, and sees this as an opportunity to start anew on a properly designed language from scratch :D

I'm actually mostly worried about the future of Mojo at this time.

Though hopefully it will be fully released open source still, but I feel there are question marks around whether it will be a priority to continue to develop by Qualcomm, or if they are mainly interested in the AI compute stack?

Time will tell I guess, but a lot feels to be up in the air.

DaVinci Resolve 21 2 months ago

I'll second looking at KdenLive.

You might want to stay away from very recent major versions for stability, but it is a very capable editor that is also much more robust and performant than openshot.

I haven't compared with Blender VSE though.

DaVinci Resolve 21 2 months ago

Stability sounds interesting. While KdenLive has worked OKish for me, certain versions have broken my projects, and there are some long-standing bugs, like subtitles disappearing if I do a specific operation in the wrong moment. While the latter is fixed by a simple Ctrl+Z it is giving me second thoughts about using this for really large projects.

DaVinci Resolve 21 2 months ago

For people using Resolve, would you recommend someone already quite well-versed in KDenLive to switch, for some non-profit work on cutting together educational content with some animations, some talks etc?

Will it allow me to drastically improve my workflow (save time for some tedious tasks), increase quality of the outputs etc?

I grew up in a christian home, so got my initial belief from there.

Had a kind of pivot moment when I moved out from home though, where I immediately realized my parents will not be there forever, and the inner me needs to reach for my ultimate parent. This got me into a much closer relation with the Lord. I had (and have) many somewhat spectacular answers to prayer, and basically learned to have a really trustful relationship with him.

I know many people's faith is challenged when going to the university and learning about biology as I did (studying biotech and bioinformatics).

I had came into contact with some great apologetics material, especially around evolution etc, in Swedish, which I found super interesting.

Still, I must say my faith was even more reinforced when we started to study macro-molecular machines, and I realized that biology is a whole world of extremely advanced nano-machines, working in an extremely intricate network of interlocking interdependencies.

I've been involved in quite a bit of debates regarding evolutionism and creationism over the years, and one thing I have noticed is that scientific creationism is much closer to modern evolutionary theory than most people realize. Recent secular paradigms such as "The third way of evolution" [1] pretty much perfectly recapitulates what many creationists have said for years; Biology is shock-full of pre-programmed ability to adapt, according to pre-existing modules and adjustable parameters, in an extremely dynamic software system, with tons of generative algorithms for how animals and plants are built up through embryogenesis, which allows for powerful adjustments of a lot of parameters with often surprisingly little change in the genomic "source code".

For people interested in an introduction to what secular science has to say here, I often recommend "The Plausability of Life", by Gerhart and Kirschner [2]. Other great titles are "Evolution: A View from the 21st century" by James Shapiro [3], and a few more (the third way website lists a lot of great books).

In my view, the Genesis story in the Bible matches these findings perfectly, disagreeing mainly in the expected age of things. But these biological mechanisms actually mean that "evolution" can happen extremely fast, without even actual genomic changes just by turning on and off or regulating features, via mechanisms like Epigenetics.

Eventually I've became involved in trying to figure out the more detailed view of how the Biblical narrative could explain the bleeding edge of biology, which led me to co-organize a seminar in Sweden in 2024 with European researchers (mostly), which resulted in both a video series and a book, which is available from this web store among others (not affiliated).

This work, especially the chapters on 1) Mendelian genetics 2) Epigenetics and 3) Transposable elements (think Endogenous Retroviruses, Jumping Genes etc), together in my mind creates an extremely interesting explanatory framework for how life was pre-programmed to be extremely efficient - and fast - mind you - at adapting to varying environments.

Whether you want to call that "evolution" or "pre-programmed adaptive creation" is in my mind very much a question of definitions, and TBF, the term evolution hasn't had a very strict definition for as long as I remember.

Anyways, today I'm more fascinated than ever the more I learn about the extremely complex and ingenuous solutions out there in nature to vastly different problem areas like chemistry, metabolism, mechanics, information processing and general cognition. It fills me with awe and respect for the creator that must be there behind all this.

[1] https://www.thethirdwayofevolution.com/

[2] https://yalebooks.yale.edu/book/9780300119770/the-plausibili...

[3] https://www.goodreads.com/book/show/11004717-evolution

[4] https://www.youtube.com/playlist?list=PLNkVOx7YbWiDABv5nB3Ih...

[5] https://store.answersingenesis.co.uk/product/a-creation-scie...

Optimizing for local-first checking is 100% the way to go, and should be used much more widely I think.

I have done a similar thing using simple makefiles though, collecting more complex chains of tasks into a "meta rule" in Make and just calling that from whatever CI config we're using.

I shared this since it seems to address a somewhat similar niche that I have had hopes to one day develop, based on FlowBase [1]; A library of streaming processing components based on basic operations, that can be easily stitched together into larger pipelines in a compiled language that can run on smaller hardware too.

FlowBase or I didn't have much of ideas about how to keep data structures compact, as the linked library does, and I was mostly aiming to make it really easy to build streaming pipelines.

I haven't yet got my head around how the composability story is in rosalind though, so would be interested in any pointers or examples on how this would be done using it.

[1] https://github.com/flowbase/flowbase

Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community.

Nature even wrote a feature article about it a couple years ago:

Why scientists are turning to Rust

https://www.nature.com/articles/d41586-020-03382-2

They mention the Rust-Bio [1] project by well known Snakemake author Johannes Köster & co, and there are some other widely used libraries like needletail [2] and noodles [3].

A cool smaller tool developed by performance wiz Ragnar Groot Koerkamp which was just published is Sassy [4] [5]. He has also been involved in developing some high performance SIMD based stuff (minimizers) [6].

[1] https://github.com/rust-bio/rust-bio

[2] https://github.com/onecodex/needletail

[3] https://github.com/zaeleus/noodles

[4] https://github.com/RagnarGrootKoerkamp/sassy

[5] https://academic.oup.com/bioinformatics/article/42/5/btag244...

[6] https://github.com/rust-seq/simd-minimizers

Mojo 1.0 Beta 2 months ago

I'm really quite divided about Rust vs Mojo for bioinformatics in the future.

The syntax i Mojo really seems to shine a lot ... though I still wonder if the train has already left now that so much bioinfo work is already done in Rust.