Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression
Our webapp for root-to-tip regression Clockor2 (clockor2.github.io) has just been published in Systematic Biology . Clockor2 is a webapp for performing root...
Posts by Category
blog
Using BEAST 2.7 with Snakemake
BEAST 2.7 is out and promises to be better than ever. However, it’s not available on conda yet. This post will show you how to use BEAST 2.7 with Snakemake t...
The Fall of Reason: Navigating an AI-Dominated World of Thought
The ruliad is everything that is computationally possible. It is the limit of following all possible paths of computation in all possible ways. The idea of a...
Your Virologist Friend
Here are a few post I’ve made about the ongoing pandemic. 24th of January 2020 - In the beginning I thought I should say something about the current corona...
Integrating qsub with RStudio
In a previous post, I explained how to run RStudio on the compute nodes of the HPC. I am going to continue on this theme and explore some of the interesting ...
Containerised applications on the HPC (RStan example)
Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible...
RStudio on the HPC
This post details how to get RStudio server running on the compute nodes of the HPC. This is achieved though a combination of singularity and ssh commands. ...
Vectorising chisq.test()
Writing fast code is actually about writing efficient code. Writing code in R doesn’t magically make electrons slower. The perceived slowness of higher-level...
Using VScode to access the HPC
One of the biggest hurdles to using a high performance computer (HPC) is the user interface. Researchers have to ssh into the HPC via the command line. This ...
Interactive diagnostic test statistics
I’ve been watching a lot of coding train, and it has got me keen to do something with the javascipt library P5.js. My housemate has been learning about diagn...
init blog
Hi! This is the first post on my blog. Hopefully more to follow :)
project
Auto-Scope: An open source whole slide scanner
I’m feeling nostalgic for the time my Python friend Eike and I built a whole slide scanner from scratch. It was a fun project that combined my interests in p...
🐙🐁 BEASTIARY 🐁🐙
Introducing Beastiary, a package designed for visualising and analysing MCMC trace files generated from Bayesian phylogenetic analyses.
monitauR 🐮
Introducing MonitauR, a package to easily and remotely monitor the progress of your R scripts.
pyoinformatics 🐍
Introducing pyoinformatics, a simple bioinformatics package. pip install pyoinformatics I’m working on the bioinformatics problems on rosalind.info. Some o...
Interactive diagnostic test statistics
I’ve been watching a lot of coding train, and it has got me keen to do something with the javascipt library P5.js. My housemate has been learning about diagn...
Blog
Run RStudio on Unimelb Spartan HPC
I’ve written a few different posts and tutorials about how to run RStudio on an HPC using RStudio Server. In this post, I’ll detail the process specifically ...
52 Apps in 2025
In 2025 I set my self the challenge of building 52 apps