pgx VS Rust-Bio

It uses pgx (https://github.com/tcdi/pgx) which is our more generalized framework for developing Postgres extensions with Rust.

It's a great question, considering I've been using Rust for a number of years now, and I generally advocate its use for its rich ecosystem, safety and tooling. I actively contribute to pgx, a library for building Postgres extensions in Rust. Yet, Omnigres appears to be all done in C.

Our release today is a framework which extends this functionality to other databases/systems. If you’re familiar with Multicorn[1] or Steampipe[2], then it’s very similar. The framework is written in Rust, using the excellent pgx[3].

We have developed FDWs for Stripe, Firebase, BigQuery, Clickhouse, and Airtable (all in various “pre-release” states). The plan is to focus on the tools we’re using internally while we stabalize the framework.

There’s a lot in the blog post into our goals for this release. It’s early, but one of the things I’m most excited about.

[0] Postgres FDW: [https://www.postgresql.org/docs/current/sql-createforeigndat...

[1] Multicorn: https://multicorn.org/

[2] Steampipe: https://steampipe.io/

[2] pgx: [https://github.com/tcdi/pgx](https://github.com/tcdi/pgx)

BTW one nice easter egg is that with pgx there is actually no reason that we can't build even better search solutions inside the database itself.

> That thread led me to a project/product idea where you take an existing Postgres instance used for normal products or whatever, replicate it to various read only clusters with a custom search extension loaded and some orchestrator sitting on top (I’ve written most of one in rust that uses 0mq to communicate with it’s nodes) and create drop in search from existing databases with a nice guided web gui for automatic tuning suitable for most business use cases.

Very interesting idea -- just want to add one thing, write it in rust (with pgx?[0]) :)

[0]: https://github.com/tcdi/pgx

Hey HN,

It turns out choosing a good database-optimized UUID (and deciding whether to use serial, etc) isn't quite so simple, and I finally got a chance to do some exploration, write about it[0].

One of the reasons Postgres is the best open source database out there is it's extensibility -- so I hacked up a small extension for generating some of the more exotic (but crucially, lexicograhically sortable) UUID generation mechanisms:

https://github.com/t3hmrman/pg_idkit

This idea has been bumbling around my head for a while, but I finally got a chance to build it while working with Supabase on a post about IDs[0]!

Most of the heavy lifting is done by pgx[1] which is an amazing framework for building Postgres extensions in Rust. I think we are very early to the trend of amazing postgres extensions built in Rust, and it's yet another reason that it's an exciting time to be all-in on Postgres.

[0]: https://supabase.com/blog/choosing-a-postgres-primary-key

[1]: https://github.com/tcdi/pgx

[0]: https://supabase.com/blog/choosing-a-postgres-primary-key

The extension is still WIP but for those of ya'll that like Rust it's built on pgx which has excellent DX. The rust involved isn't complicated -- I'm basically laundering the functionality from other crates that are listed in the README.md.

Seems to be using this: https://github.com/tcdi/pgx

- https://github.com/furstenheim/is_jsonb_valid

pgx[0] is going to be pretty revolutionary for the postgres ecosystem I think -- there is so much functionality that can be utilized at the database level and I can't think of a language I want to do it with more than Rust.

[0]: https://github.com/tcdi/pgx

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".