Viewing profile — totalperspectiv

Carp has been slowly inching forward and ticking those boxes

Per modular Twitter, the plan is still to open source the mojo compiler this year: https://x.com/Modular/status/2069787078032834635

I thought he stopped working on LuaJIT? Is it back in active development?

That's fair, I think I should have just said "comparable to Zig". The type'd ness is what I was thinking of, but having actually written some zig in the last few days to play with …

"requires" is a strong word, but I implemented an alignment kernel that can do alignments on the GPU. Overall I think there is going to be a lot of "old" gpu compute hanging around…

Me too! I've been using it for bioinformatics related work, and it is absolutely fantastic. I can't wait for it to hit fully open source status so it can be easily recommended.

Having written a lot of Mojo over the last two year, just for fun, it's a really cool language. Ownership model adjacent to Rust, comptime that is more powerful than Zig, Rich type…

The author works for Modular. He shared the write up on the Mojo Discord. I think Mojo users were the intended audience.

I've only tested this when writing my own parser where I could skip the record end checks, so idk if this improves perf on a existing parser. Excited to see what you find!

Removing the wrapping newline from the FASTA/FASTQ convention also dramatically improves parsing perf when you don't have to do as much lookahead to find record ends.

> a testament to the massive gap in perceived vs actual programming ability of the average bioinformatician. This is not really a fair statement. Literally all of software bears th…

Because I was originally writing some very CPU intensive SIMD stuff, which Mojo is also fantastic for. Once I got that working and running nicely I decided to try getting the same …

I can confirm, it’s quite nice.

They allow you to write a kernel for Nvidia, or AMD, that can take full advantage of the Hardware of either one, then throw a compile time if-statement in there to switch which ker…

I have used Mojo quite a bit. It’s fantastic and lives up to every claim it makes. When the compiler becomes open source I fully expect it to really start taking off for data scien…

I don’t follow your logic. Mojo can target multiple gpu vendors. What is the Modular specific lock in?

I can't speak to Gleam, but for Elixir I just used Burrito to create a single executable: https://github.com/burrito-elixir/burrito I think it works for just Erlang too.

I really wish Crystal had taken off a bit. I thought it had a chance in bfx with some good benchmarking and PR by lh3 in biofast.

I would rather write Groovy than YAML any day of the week. Why did you rule out Nextflow or Snakemake? I believe they both work with k8 clusters. Argo doesn’t look great from my st…

NF Tower / Seqera would be the selling points. They offer a nice UX for managing pipelines and abstract over AWS. Technically snakemake can do it all. But in practice NF seems to s…

Cool seeing a workflow language pop up on HN! Nextflow and Snakemake are the two most-used options in bioinformatics these days, with WDL trailing those two. I really wish Nextflow…

I think you hit the nail on the head with the mental model part. I really like this method of thinking about programming "Programming as Theory Building" https://gist.github.com/on…

ish is a CLI tool for searching records using alignment methods. It’s record-type aware and supports lines, FASTA, and FASTQ. I was really pleased with the dev experience using Moj…

ish is a CLI tool for searching records using alignment methods. It’s record-type aware and supports lines, FASTA, and FASTQ. I was really pleased with the dev experience using Moj…

Preprint can be found here: https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1 Code can be found here: https://github.com/BioRadOpenSource/ish