Rust-Bio VS Iron

Does anyone know of zig native libraries for bioinformatics (here is a Rust example https://rust-bio.github.io/ )? It seems as though one could pull in a lot of bioinformatics C libraries such as done with https://github.com/brentp/hts-zig.

e.g. Rust-Bio

I would start with the book and then rust-bio library. Rust is a pretty low level language compared to R/Python. It’s an especially good fit for writing efficient tools that make use of the kinds of algorithms / data structures that are implemented in rust-bio.

Absolutely! It already is, e.g., https://github.com/rust-bio/rust-bio. I'm moving from the academia/nonprofit world into industry bioinformatics, and I intend to use Rust as much as possible. I've already replaced as much of my Python as possible with Rust. I feel I'm able to create larger, more complex programs with Rust because I have the compiler to keep me from making common mistakes that are so easy to make in dynamically typed languages like Perl and Python. It might take longer to write a program initially, but I've started to create a library of functions I can paste together to do things like parse a positive integer, find a bunch of files with a certain file extension, search through data for a pattern, parse CSV files, etc. Writing my latest book has provided even more common patterns I keep finding I use over and over.

I think there is huge potential for Rust in bioinformatics, and there are already some great projects like https://rust-bio.github.io/. It seems industry is also hiring for these skills. This Nature article is a little old, but also covers why people in the field are looking for greater safety and performance. It's relatively easy to write a Python program to do bio stuff, but it's also very easy to get lots of things wrong or for the resulting program to be slow and/or impossible to extend and maintain. In the long run, I think it makes sense to write in Rust. Perl was king in biofx when I started, and I would not have predicted it being displaced by Python, so there's good reason to believe that Python may one day be eclipsed by Rust.

Well, someone mentioned https://rust-bio.github.io/

So generally stuff in this maths/numerical space. The term is a bit deceptive because it rarely means domain-specific science libraries like rust-bio even thought that might be what you think when you hear "scientific computing".

I've written many things using Iron and it's been fine. It's not particularly developed any more but I am not aware of any major outstanding issues.

I don't miss the time when we basically only had Iron

iron

There're many web framework in rust, such as SergioBenitez/Rocket , actix/actix-web ,poem-web/poem , iron/iron . How do I chiose, anyone suggestion？

I'm not sure which definition of backend you are thinking of here. In case you simply mean "server side", here are a couple of libraries that might be of use: iron - been a while since I used it, used it for a couple smaller projects rocket (nightly only) - no personal experience, but a lot of people seem to like it diesel - a bit complex to wrap your head around, but once you get the idea it's really nice. Definitely check out the examples.

it's taken by a web framework https://github.com/iron/iron

Your comment touches on a few misconceptions I see a lot.

Firstly, `reqwest` exposes both an async and a synchronous API, allowing the developer to choose which one to use. They are largely interchangeable code-wise. [1]

Secondarily, and more broadly, async is possible to opt out of. You must understand that most web and network related libraries will be async by default for performance, because people who write in Rust and people who write web servers typically care greatly about performance. This is the intersection of those two groups. That being said, there are options outside of that ecosystem. [2]

If you truly want to use an asynchronous library without migrating your application to run entirely on an async runtime like tokio, you can run it inside of a synchronous function without much trouble. I've put together a playground link for you. [3]

1. https://docs.rs/reqwest/0.11.2/reqwest/blocking/index.html

2. Iron: https://github.com/iron/iron

There are several web frameworks for Rust: Rocket, Actix, Warp, Iron - but only Actix has released a stable 1.0 release, and there has been considerable controversy over how it uses unsafe Rust.