Building PDF output in a Python Sphinx project
A tutorial on creating a Python Sphinx project and generating PDF output using LaTeX on Linux.
My note-taking setup
An overview of my current note-taking set up using QOwnNotes and Nextcloud. I also discuss programs I have used in the past like Zim, org-mode and Joplin.
Convert Markdown to HTML using a custom Pandoc template
A tutorial on using Pandoc to convert Markdown to HTML using a CSS stylesheet and a custom template.
Introducing Python programming to a general audience
This was my attempt at introducing Python to a general audience at Tech me out at home — an online event organised by Pint of Science, Ireland.
BioVM 18.04.1
Summary of changes in BioVM 18.04.1 — a Linux virtual machine based on Ubuntu for teaching and learning Bioinformatics.
Learn Python With Me
An online Python course for beginners in programming
Get lineage of an organism from NCBI taxonomy data
A Python script to obtain the complete taxonomic lineage of an organism from NCBI taxonomy data.
BioVM 18.04
A new release of BioVM with updated software, Galaxy configuration, documentation and includes recommendations for installing new software.
Running Galaxy project on Ubuntu 16.04 LTS
This is a step-by-step tutorial on running an instance of the Galaxy platform (v17.09) for biomedical research on Ubuntu 16.04 LTS.
Docker images for Bioinformatics software
How to run containers of VIGA, QIIME, PyFBA, Cutadapt and DADA2 and a helpful wrapper script for non-root users.
An unofficial VirtualBox image for QIIME 1
This is a VirtualBox VM I made for QIIME 1.9 based on the current version Ubuntu MATE LTS (16.04.3) with some additional improvements.
A Python script to update NCBI BLAST databases
Updating BLAST databases can can be done using the update_blastdb command but this script only updates databases if they are not being used.
Creating an online course using free and open source software
This post is about the free and open source software I used for creating an online course.