| ▲ | Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop(github.com) |
| 112 points by samuell 5 days ago | 27 comments |
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| ▲ | logannyeMD 2 hours ago | parent | next [-] |
| 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 |
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| ▲ | p4ul 6 hours ago | parent | prev | next [-] |
| 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 |
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| ▲ | croemer 2 hours ago | parent | next [-] | | 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 | |
| ▲ | the__alchemist 3 hours ago | parent | prev | next [-] | | 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. | |
| ▲ | clmcleod 3 hours ago | parent | prev [-] | | Thanks for the shout out! |
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| ▲ | croemer 2 hours ago | parent | prev | next [-] |
| 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. |
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| ▲ | vatsachak 3 hours ago | parent | prev | next [-] |
| Looking at the commenting pattern, it seems like AI unfortunately |
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| ▲ | jghn 3 hours ago | parent [-] | | The OP? They're not AI, they've been active on X and bsky for years. | | |
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| ▲ | boron1006 4 hours ago | parent | prev | next [-] |
| Lots of bad smells in this repo. |
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| ▲ | the__alchemist 3 hours ago | parent [-] | | Do you have some examples to look at? I am curious. | | |
| ▲ | boron1006 3 hours ago | parent [-] | | 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. |
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| ▲ | semiinfinitely 4 hours ago | parent | prev | next [-] |
| bioinformaticians have been making these useless bioinformatic-toolkit-in-my-favorite-programming-language repos for years |
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| ▲ | maxall4 3 hours ago | parent | next [-] | | Well, what else are we going to do while waiting for the bench scientists to finish collecting data? | |
| ▲ | asdff 2 hours ago | parent | prev | next [-] | | Dissertationware is common in a lot of fields, honestly. | |
| ▲ | gilleain 4 hours ago | parent | prev [-] | | 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. |
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| ▲ | Rijanhastwoears 4 hours ago | parent | prev | next [-] |
| > A deterministic genomics engine with a compact memory footprint. Uhh... are there stochastic genomics pipelines? |
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| ▲ | shauniel 4 hours ago | parent | prev | next [-] |
| I would love to hear about what the sacrifices are, but this project really looks amazing. |
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| ▲ | bonsai_spool 4 hours ago | parent | prev | next [-] |
| Didn't see a publication or preprint for this - is there one? |
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| ▲ | peterfirefly 5 hours ago | parent | prev [-] |
| Should have called it Raymond. |
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| ▲ | flobosg 5 hours ago | parent [-] | | Or rather Margaret: https://en.wikipedia.org/wiki/Margaret_Oakley_Dayhoff | | |
| ▲ | cmpb 4 hours ago | parent [-] | | 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.org/wiki/Rosalind_Franklin | | |
| ▲ | philipallstar 2 hours ago | parent | next [-] | | 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 | | |
| ▲ | groby_b 27 minutes ago | parent [-] | | 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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| ▲ | flobosg 4 hours ago | parent | prev [-] | | > I'm not familiar with Margaret Oakley Dayhoff Then you’re one of today’s lucky 10,000. Any time! |
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