Mastering GitHub Pages (Jekyll and GitHub Pages)

One thing I'm increasingly conscious of is that I've a lot of demos and toy projects hanging around and the code for most of these isn't readily available. So, I plan to clean these up and put them in GitHub so others can explore the code, and reuse it if they see fit.First up is the code to create a HTML+Javascript clone of Nature's iPhone app, as described in an earlier post.There's a live version of the clone here here.

Bayesvl is R package for visually learning the graphical structures of Bayesian networks, and performing Hamiltonian Markov chain Monte Carlo (MCMC) with 'Stan'. ***** For more information, please visit: https://mindsponge.info/posts/14 *****

Quarto makes it very easy to publish a website via GitHub Pages: It is as simple as running quarto publish gh-pages. Here we explore a slightly different method that uses a GitHub Action to publish the website automatically every time it is updated. Classic GitHub Pages The classic way to publish a website via GitHub pages is to maintain a separate branch gh-pages.

I saw this Tweet a few days ago from Jeremy Leipzig counting the number of GitHub repositories that sequencing-related companies have on their organization page, but was immediately curious how many of these had an open-source license versus a restrictive or unknown license. I tried to one-shot this with GPT-5 given a screenshot of Jeremy's Tweet and a few instructions. It got me 90% of the way but I had to make a few tweaks here and there.

Set up ssh keys to make login to the HPC easy!

Donald Hobern drew my attention to nice the way iNaturalist displays taxonomic splits: In this example, observations identified as Rhipidura fuliginosa are being split into Rhipidura fuliginosa and Rhipidura albiscapa . This immediately reminds me of the idea which keeps circulating around, namely using version control tools to manage taxonomic classification.