Rust-Bio
scryer-prolog
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Rust-Bio | scryer-prolog | |
---|---|---|
9 | 42 | |
1,494 | 1,891 | |
2.3% | - | |
6.7 | 9.7 | |
16 days ago | 13 days ago | |
Rust | Rust | |
MIT License | BSD 3-clause "New" or "Revised" License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Rust-Bio
- Bioinformatics Data Structures in Rust
- Bioinformatics with Rust
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bioinformatic libraries and zig?
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.
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Proteomics search engine written in Rust
e.g. Rust-Bio
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What are your top 3-5 programming languages and why?
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.
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I have to admit. The free code camp course is a bit more sparing than I would have preferred. How did everyone learn Rust?
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.
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Is learning Rust and systems programming through the books Rust in Action and Crafting Interpreters a good idea?
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.
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Whats your favourite open source Rust project that needs more recognition?
Well, someone mentioned https://rust-bio.github.io/
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How can one make Rust excel in the Sciences
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".
scryer-prolog
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The Shen Programming Language
thank you! the scryer community deserves much of the credit too. everyone is welcome and encouraged to join us at https://github.com/mthom/scryer-prolog! some exciting plans in the pipe
- Appreciating Clpz_t/2
- Advent of Code 2023 is nigh
- Scryer Prolog version 0.9.3 is out
- Announcing Basic WebAssembly support in Scryer Prolog
- Basic WebAssembly Support in Scryer Prolog
- Scryer-Prolog 0.9.2
- Release v1.1.0 of PostgreSQL-Prolog
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Djot is a light markup syntax
Djot is the markup syntax that is used for the documentation of Scryer Prolog, using a parser written in Prolog:
https://github.com/aarroyoc/djota
It works well so far. One of the few limitations I noticed so far pertains to the formatting of tables. For instance, consider the table used in library(format) to describe control sequences:
https://github.com/mthom/scryer-prolog/blob/b0566e41503a6c8d...
It contains several entries that span multiple lines, yet are meant to denote only a single row of the table, such as:
% | `~Nr` | where N is an integer between 2 and 36: format the |
- The First Annual Scryer Prolog Meetup
What are some alternatives?
dash - Data Apps & Dashboards for Python. No JavaScript Required.
swipl-devel - SWI-Prolog Main development repository
kanidm - Kanidm: A simple, secure and fast identity management platform
logica - Logica is a logic programming language that compiles to SQL. It runs on Google BigQuery, PostgreSQL and SQLite.
clickhouse-rs - Asynchronous ClickHouse client library for Rust programming language.
differential-datalog - DDlog is a programming language for incremental computation. It is well suited for writing programs that continuously update their output in response to input changes. A DDlog programmer does not write incremental algorithms; instead they specify the desired input-output mapping in a declarative manner.
GeoRust - Geospatial primitives and algorithms for Rust
materialize - The data warehouse for operational workloads.
Rhai - Rhai - An embedded scripting language for Rust.
tau-prolog - An open source Prolog interpreter in JavaScript
cycle - Modern and safe symbolic mathematics
prolog - The only reasonable scripting engine for Go.