There's a "fact" about COVID deaths that does the rounds, that suggests that deaths amongst Amish/Mennonites was no higher than pre-COVID times; the implication being that something else was causing the deaths. It's nonsense, of course...

Saved because it's of past interest to past me in a remote way.

Neat web-based sandbox of bioinformatics tutorials, providing a sandbox for some of the common tools.

Webinar covering information about Benchling's "Validated Cloud" offering.

The Genomics Boot Camp is a resource that helps you to start your journey in practical analysis of genomic data, with a focus on SNP data. The chapters follow the same structure all the time: provide background information and practical insight to the topic, and when appropriate exercises to reinforce the obtained knowledge. The Genomics Boot Camp as a whole was designed to cater to various learning preferences with written text, video demonstrations, and the possibility of hands-on exercises. There is a certain overlap between the book and the YouTube channel contents, but each has unique pieces of information as well. So for the full experience, I suggest checking out both.

Sequence alignment code, in Python, with a good explanation of the problem and the solution.

Paper about how a group selected a workflow management system. I'm not sure it's that worthy of a writeup, at least not as seen via the lens of a software developer, but it's a useful perspective to read it to get some insight into how others approach this.

Some good comments in here that explain some of the issues, and solutions, of acquiring a full sequence of a chromosome.

Many biomedical research graduate programs have been compelled to “go online” with little or no notice due to the COVID-19 pandemic. Since many professors are distinctly uncomfortable in front of a camera, students may not get exposure to some of the topics that they might have expected. Since my move to South Africa in 2015, I have tried to deposit video on YouTube (and PDFs of the slides to Google Drive) every time I have delivered a lecture for students. Since I teach a fairly broad range of coursework, the catalog of topics may be useful for students working from home or for departments that are trying to ensure their students get the training they need. This page indexes the series of lectures I have made available. I hope you enjoy watching them as much as I have enjoyed creating them!

Genbank data for SARS-CoV-2.

Interesting article that compares Seq to Julia, and in doing so results in speed improvements in a bioinformatics library for Julia.

Neat little twitter thread that outlines how the five bases (4 DNA and U for RNA) got their names.

A high-performance, Pythonic language for bioinformatics

Paper about a language, that is pretty much a twist on Python that's aimed at getting higher performance for bioinformatics applications.

Article that outlines the format of BED files.

The API rate limits for Benchling.

Description of palindromic sequences in DNA.

Documentation for the Benchling API.

An anatomical ontology that represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates

Rather silly but enjoyable twitter thread where someone makes fasta files of pasta.

Collection of bioinformatics tools for Julia.

Short introduction to pairwise alignment using BioPython.

Article that describes how DNA is turned into protein sequences.

Introduction to DNA nucleotides,strands, etc.

Handy background about DNA Sequencing and sequence assembly.

Useful introduction to transcription and translation.

Interesting DNA sequence visualisation library.

Handy list of IUPAC nucleotide code along with the complements.