Jos van Nijnatten

Jos van Nijnatten

Ph.D. candidate using bioinformatics to uncover the genetics and epigenetics of chronic obstructive pulmonary disease.

Blog posts

2024

SQL in iPython in VS Code

3 minute read

Published:

Yesterday, during working hours, I was studying for a data engineering certification, which I need to know in my new role. To practice anything in this course, I wanted to practice - however not on the company server. It is possible to set up a data engineering platform on cloud services such as Azure, however I do not have the money to invest in something like that, nor do I want to use the bulky Jupyter notebooks. So, I needed a solution to this problem. I needed to set a platform like databricks on my own computer. I wanted to use python in notebooks, but also be able to use SQL in the same notebook, without using Jupyter, Datalore, Collab, or other cloud or bulky software. This post describes that attempt on a MacBook.

2021

GPG signature of commits in GitHub

1 minute read

Published:

GitHub is a web-based version-control and collaboration platform for software developers. I use it all the time to version the source code of my PhD project. The GRIAC and RBMB bioinformatical groups both have a github page setup as well, even though we don’t use it very much. But if we were to work together even more, we should be able to trust the commits we make to our collaborative repositories. For that reason, GitHub had introduced signed commits. Below is a script to make a GPG signature and to add this to your local Git configuration to automatically sign your commits.