bioinformaticians have been making these useless bioinformatic-toolkit-in-my-favorite-programming-language repos for years
Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
11–20 of 63 posts
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#12> A deterministic genomics engine with a compact memory footprint.
Uhh... are there stochastic genomics pipelines?
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#13bioinformaticians have been making these useless bioinformatic-toolkit-in-my-favorite-programming-language repos for years
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.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#14bioinformaticians have been making these useless bioinformatic-toolkit-in-my-favorite-programming-language repos for years
Well, what else are we going to do while waiting for the bench scientists to finish collecting data?
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#15This 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
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.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#16Lots of bad smells in this repo.
Do you have some examples to look at? I am curious.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#17Looking at the commenting pattern, it seems like AI unfortunately
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#18Looking at the commenting pattern, it seems like AI unfortunately
The OP? They're not AI, they've been active on X and bsky for years.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#19This 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
Thanks for the shout out!