The Living Thing / Notebooks :

Containerized apps for the vexed

Note

These are rapidly evolving standards. Check the timestamps on any advice.

The other, lighter, hipper alternative to virtual machines, which, AFAICT, attempts to make VM provisioning more like installing an app than building a computer, because it aims to containerise apps rather than OSes, which emphasis leads to less dicking around.

The apps must, AFAICT be linux-ish, but the host can be anything.

Docker

The most common way of doing this.

Do you get the following error?

Error response from daemon: Get https://registry-1.docker.io/v2/: net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)

According to thaJeztah, the solution is to use google DNS for docker. You can set this by providing a JSON configuration in the preference panel (under daemon -> advanced), e.g

{ "dns" : [ "8.8.8.8", "8.8.4.4" ]}

Building a container to do some reproducible research thing

Docker may not be the ultimate answer for reproducibility but it is a start. (TODO: fact-check the linked article.)

…How do you get your data in?

Tiffany Timbers gives a brisk run-through for academics.

Jon Zelner goes in-depth with R in a series culminating in continuous integration for science.

Handling passwords is a bit fiddly - see secrets.