1 02-PlatformTools

1.1 Audio-recording

1.2 What is a data-oriented “lab”?

in bio-informatics or computational-biology
…or a lab in any field of -informatics or computational-

My personal experience felt about like this:

1.3 How to explore data?

1.4 What is a data-oriented “lab notebook”?

in bio-informatics or computational-biology
…or a lab in any field of -informatics or computational-
* Lab notebooks are a real thing, and scientists actually keep them!
* They are used for documentation, which feeds into publication.

1.5 Consistency and publication!

The classic paper model:
How to increase consistency, transparency, and computability in scientific publishing?

1.5.1 How to publish experimental data exploration code?

Goal: A communicative, transparent, easy-to-read, and actually executable publication.

1.5.2 Tools

A variety of data-focused documentation and publication tools. Jupyter

* System repos:
* There are multiple packages, named differently across distribution, so search:
* $ sudo dnf/apt/zypper search jupyter
* For example, install some, or all, of the results of the previous search:
* $ sudo dnf/apt/zypper install jupyter-* Jupytext

pip3 install –upgrade –force jupyter jupyterlab notebook jupytext –user
jupyter serverextension enable jupytext –user
jupyter nbextension install –py jupytext –user
jupyter nbextension enable –py jupytext –user
``` Quarto Jupyter-book Pandoc Sagemath

1.5.3 Where to archive working versions of code, and publish?

1.5.4 How to bundle code, data, and environment?

Often, you want the entire experiment to be reproducible, by another lab or person!
Hiding your own data or code is counter to the scientific process! Virtual machines (VM) and VM-snapshots Online virtualization of shared code, data, and environment

* Is this as future-proof and standalone reproducible as a VM?
* Is it as easy as a VM?
* Is it as likely to be reproduced?