Bioinformatics with Rust

Antibody, noun: A body’s personal security guard. They patrol the bloodstream. Their job: to spot and stop harmful intruders like viruses…

Vector, noun: A reformed rogue of the microscopic world, once specialising in chaos and disease, now intriguingly repurposed as a genetic…

Discrete cell states represent the distinct functional stages that cells can assume, reflecting their diverse roles in biological…

Homology modelling, also known as comparative modelling, is a computational technique used in bioinformatics to predict the…

Pathway analysis is a method used in biology to understand how different molecules in a cell interact and work together to carry out…

Rust functions that return Simpson’s Diversity Index and Shannon-Weiner Index based on count of species and count of individuals within a…

This work is a simplified version of an article published in Nature called how to build a virtual embryo.

A Rust struct for solving Punnett Square problems

I am just starting to learn the jargon biologists use. So looking at a genome browser is intimidating. But UCSC (University of California…

Bash scripting is a useful skill for computational biologists. Since writing all algorithms from scratch in Rust is not our goal, there are…

A Rust function that returns a vector of string slices that match a regex pattern

The Stardoc series by S. L. Viehl is addictive. If you like imagining yourself as a kickass doctor who gets to learn and treat alien life…

The order represents how beginner-friendly these resources are. ONE being highest, and THREE being lowest.

A Rust struct for processing a DNA sequence: check for valid bases, transcribe, find the reverse complement, calculate length and GC…

Python is an important tool in any bioinformatician’s toolkit. My goal is to help you add Rust in this toolkit rather than replace Python…

Rust has a crate called ndarray. It’s like numpy in Python. These exercises are designed to help you get familiar with ndarray, so you can…

Let’s say we want to generate sequences with point mutations at random locations based on a wild type sequence. We decide to store this…

Generated with AI

This is going to be a super short article. After installing Rust and Jupyter Lab, you just need to run the following commands one-by-one.

A Rust function that returns a HashMap containing sequence IDs or headers as keys and DNA sequences as values extracted from a FASTA file

A Rust function that returns count of point mutations (hamming distance)

This is an example of how to use AI to understand someone else's code for calculating GC content.

A Rust function that returns counts for A, C, G, and T in a DNA sequence