Hey guys, this is my github repo. Glad it's received some interest - I figured HN might be the culprit when it suddenly jumped ~100 stars despite not working on the code base since last year. I prototyped this out of personal curiosity last year and moved on abruptly so there's a lot of gaps I still need to close and knobs that need to be optimized. But if people genuinely find "deterministic genomics workloads on edge devices" proposal useful, I'll begin refining the code tonight and try to make it as useful as possible. If you have any particular bioinformatics tasks or use cases that you want to be feasible on edge devices, lmk and I'll work on integrating new capabilities. Always happy to be helpful
Your website bio and LinkedIn don't match at all. Is the LinkedIn link on your website wrong? Update: yes it is. This is the correct one: https://www.linkedin.com/in/logan-nye
You're doing too much vibe coding and not enough checking/testing.
This is interesting; thanks for sharing! I have been curious about the adoption of Rust in computational biology. I know that the folks at Saint Jude's [1] are also using Rust for their 'omics research.
I'm building a structural bio crate system in rust (na_seq, bio_files, bio_apis, dynamics and some more specialized). No one is using it AFAIK other than myself. I am using it to build a GUI multi-purpose structural bio GUI program called Molchanica.
Note that this doesn't have much overlap with the traditional bioinformatics workflows like the OP (Rosland), or the one you linked to seem to be focused on.
Well the √t stuff looks like nonsense or way overblown, existing tools already do similar things, there’s pretty much a single commit with no follow up commits etc etc.
Hate to agree, but it is true. For a while, I think, the main sequencing framework was in perl (Bioperl). Not sure what was best for structures - possibly Biojava?
It is very tempting, though - 'just' make a nice, clean API in your favourite language (eg Haskell, Ruby, ...) and everyone will flock to use it! Maybe.
I'm not familiar with Margaret Oakley Dayhoff, but I am aware that Rosalind Franklin [1] was extremely important for our understanding of DNA, comparable to Watson/Crick, with whom she co-discovered the structure of DNA. So it seems "Rosalind" is at least very appropriate as a name for a genomics tool such as this.
Not to say the other names mentioned aren't also deserving of similar honors
Rosalind Franklin was the team lead of the research team that photographed DNA.
The actual team member that took the key photo[0] was Raymond Gosling.
That team didn't interpret the double helix structure of DNA that the photograph had captured - that was Watson and Crick working it out from the photograph.
You're doing too much vibe coding and not enough checking/testing.
LinkedIn link on your website points to: https://linkedin.com/in/logannye
Website bio: https://www.logannye.io/about
[1] https://github.com/stjude-rust-labs
https://github.com/nextstrain/nextclade
Note that this doesn't have much overlap with the traditional bioinformatics workflows like the OP (Rosland), or the one you linked to seem to be focused on.
Looks like total slop to me. All code in one commit, then a bunch of commits polishing the Readme.
No release, no updates in half a year.
Uhh... are there stochastic genomics pipelines?
It is very tempting, though - 'just' make a nice, clean API in your favourite language (eg Haskell, Ruby, ...) and everyone will flock to use it! Maybe.
Not to say the other names mentioned aren't also deserving of similar honors
[1] https://en.wikipedia.org/wiki/Rosalind_Franklin
The actual team member that took the key photo[0] was Raymond Gosling.
That team didn't interpret the double helix structure of DNA that the photograph had captured - that was Watson and Crick working it out from the photograph.
[0] https://en.wikipedia.org/wiki/Photo_51
Then you’re one of today’s lucky 10,000. Any time!