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

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

#22

Post by croemer »

Those are all the tests for alignment. They don't even check the alignment is correct. Just that there are no errors. This is a joke: https://github.com/logannye/rosalind/blob/main/tests/alignme...

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.

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

#23

Post by philipallstar »

cmpb wrote: post #6
flobosg wrote: post #5

Earlier quoted context omitted.

Or rather Margaret: https://en.wikipedia.org/wiki/Margaret_Oakley_Dayhoff

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 [1] https://en.wikipedia.o…

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.

[0] https://en.wikipedia.org/wiki/Photo_51

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

#24

Post by croemer »

p4ul wrote: post #2

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. [1] https://github.com/stjude-rust-labs

We rewrote Nextclade in Rust and are very happy. Works nicely both for CLI and client side browser with wasm.

https://github.com/nextstrain/nextclade

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

#27

Post by logannyeMD »

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

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

#29

Post by croemer »

logannyeMD wrote: post #27

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 ed…

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.

LinkedIn link on your website points to: https://linkedin.com/in/logannye

Website bio: https://www.logannye.io/about

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

#30

Post by groby_b »

philipallstar wrote: post #23
cmpb wrote: post #6

Earlier quoted context omitted.

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 [1] https://en.wikipedia.o…

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. [0] https://en.wikipedia.org/wiki/Photo_51

It's not quite that clear-cut. Franklin was pretty clear on the helical structure in both research notes and papers, but she didn't quite nail the overall structure (2 strands with opposing winding, complementing bases).

Fundamentally, she suffered the curse of the experimental scientist - waiting for actual data before being willing to build a model. Watson & Crick postulated ahead based on partial data.

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