Build dsci-lab_ws2025

Build dsci-lab_ws2025#

Linux Mint 22.04.5, WS 2025

This file:

  • Build of dsci-lab_ws2025, 2025-09-15

  • Basis: Linux Mint 22.1 “Xia”, Xfce Edition, source: https://linuxmint.com/edition.php?id=320

  • GPT-5: “Linux Mint 22.1 “Xia” is a long-term-support (LTS) release based on Ubuntu 22.04 LTS (Jammy Jellyfish) … Linux kernel 5.15 (Ubuntu 22.04 default)”

previous versions:

Important: You are not requested to build the dsci-lab by yourself. Instead you are advised to download the fully configured dsci-lab as a ready-to-use virtual machine, see Download the dsci-lab OVA file.

However, if you are a lecturer or a interested student you might want to learn how we set up the dsci-lab. Here are the steps.

Install VM Virtual Box 7.1#

Download ISO image#

https://linuxmint-installation-guide.readthedocs.io/en/latest/

Create the virtual XUbuntu machine#

Start Oracle VM Virtual Box Manager 7.1

Name und Betriebssystem:

  • Maschine > Neu > Name: e.g. dsci-lab_ws2025

  • Ort: z.B. /home/jb/VirtualBox VMs

  • ISO Abbild: /home/jb/VirtualBox VMs/dsci-lab_ws2025/linuxmint-22.1-xfce-64bit.iso

  • Typ: Linux

  • Subtyp: Ubuntu

  • Version: Ubuntu 22.04

  • Button unbeaufsichtigte Installation: ÜBERSPRINGEN!

unbeaufsichtigte Installation:

  • verwenden wir nicht

Hardware

  • Hauptspeicher: minimal 4096 MB, besser z.B. 16000 MB ;-) )

  • Prozessoren: 1

Festplatte

  • jetzt eine Festplatte erstellen: /home/jb/VirtualBox VMs/dsci-lab_ws2025/dsci-lab_ws2025.vdi

  • Dateityp und Variante der Festplatte: VDI;

  • Größe: hier mindestens 100 GB angeben

  • Virtualbox 7.1: Volle Größe im Voraus allozieren: NEIN

    • (vormals Virtualbox 6: Art der Speicherung: dynamisch alloziert)

Press FERTIGSTELLEN; Start machine dsci-lab_ws2025.

  • Start Linux Mint

  • Install Linux Mint

  • Select language: “Deutsch”

  • Tastaturbelegung: German > German

  • Multimadia-Codecs installieren: JA

  • Aktualisierungen herunterladen: Ja

  • Installationsart: Festplatte löschen und installieren (this will clean only your newly allocated virtual hard disc, NOT the disk of your host system;-) ); JA > Jetzt installieren

    • Änderungen auf die Festplatte schreiben? ja, weiter

  • Wo befinden Sie sich? > Berlin

  • “Who are You?”:

    • Name: Data Scientist

    • Name des Rechners: dsci-lab-ws2025

    • Benutzername: dsci

    • password: dscidsci

A basic version of xubuntu will be installed.

“Die Installation ist abgeschlossen. Sie müssen jetzt den Rechner neu starten, um das System zu benutzen”

  • “Jetzt neu starten”

  • “Please remove instalation medium”: nothing to do, press ENTER

Your freshly installed Linux Mint Linux starts. Login:

  • user: dsci

  • password: dscidsci

It starts a guided tour: “Willkommen”

Update Basic System: MUST!#

System auf den neuestes Stand bringen:

  • “Willkommen”-Tour > Erste Schritte > Aktualisierungsverwaltung

  • OR Startmenue > System > Aktualisierungsverwaltung:

OR as an alternative to using “Aktualisierungsverwaltung” you can keep the system current with apt:

sudo apt update; sudo apt upgrade

Try it! Your system already should be up to date.

Restart the machine afterwards. Login again.

We will use the command line hereafter where possible. Get a new terminal by typing Strg-Alt-t.

NEU 2025-09-15, HOST: Copy the basic updated installation

jb@jb-ThinkPad-T16-Gen-2:~/VirtualBox VMs/dsci-lab_ws2025$ cp -rp dsci-lab_ws2025/ dsci-lab_ws2025_Grundinstallation_2025-09-15T1100

Start firefox:



## VirtualBox Guest Extensions


Oracle Virtual Box > Geräte > Gasterweiterungen einlegen: A window pops up, showing the directory `/media/data/VBox_GAs_7.1.12/` > rightclick on background, "Open Terminal here",  a new terminal opens. Type in:

```sh
sudo ./VBoxLinuxAdditions.run

Some new kernel modules will be built. To replace the running kernel modules with the new ones you have to reboot the VM:

2024-09-19: Machine says “VirtualBox Guest Additions: reloading kernel modules and services”: The mouse cannot be used any more. However, CTRL-T works. We shut down the machine manually:

sudo reboot

Login again. You now should be able to resize the VM window. Try it!

Activate bidirectional Copy & Paste from Windows-Host to VB etc.

Geräte > Gemeinsame Zwischenablage > bidirektional

After updating virtualbox on the host you might want to update the guest extensions on the guest. Simply repeat the steps above. Donn’t forget to reboot your guest engine.

Firefox Privacy#

Start firefox. Hit the “ALT”-button to show the menu.

Edit > Settings (Bearbeiten > Einstellungen):

  • Home > New Windows and Tabs (Startseite und neue Fenster): point default to https://www.startpage.com/

    • Inhalte des Firefox-Startbildschirms: privacy! … but do not deactivate these widges (don’t close your eyes), but go to

  • Datenschutz und Sicherheit > Benuzerdefiniert > Cookies und Website-Daten

    • Cookies und Website-Daten beim Beenden von Firefox löschen: Check!

    • Hauptpasswort verwenden: Enter a save password!

    • Chronik: Firefox wird eine Chronik > nach benutzerdefinierten Einstellungen anlegen

      • “Die Chronik löschen, wenn Firefox geschlossen wird”: Check!

    • Datenerhebung durch Firefox und deren Verwendung

      • (de-)select whatever you want

Extras > Add-Ons und Themes > Erweiterungen

  • Ghostery – datenschutzorientierter Werbeblocker

    • optionally configure Ghostery: “ausführen in privaten Fenstern erlauben”

document this installation properly#

To document subsequent personal installations of your VM you might wish to update this very file you are reading currently.

  • In Firefox push the .md-Button in the upper right corner of the page and save the file to Downloads/build.md.

  • Alternatively you might want to download the markdown-source of this file locally:

cd ~/Downloads
wget http://jbusse.de/dsci-lab/_sources/build.md
cd

Edit the file build.md e.g. with Mousepad. Alternatively you want to use your favourite programming editor.

vim, emacs, vscode#

Only if you are over 50 years old ;-) you still want to stick to vim or emacs:

sudo apt install vim emacs

If you are a normal young student we recommend to dive eventually into Microsoft Visual Studio Code (aka VS Code) https://code.visualstudio.com/docs/python/python-tutorial:

snap install code --classic

From File > Preferences > Settings, search for telemetry, and set the Telemetry: Telemetry Level setting to off. This will silence all telemetry events including crash reporting from VS Code. You will need to restart VS Code for the setting change to take effect. https://code.visualstudio.com/docs/supporting/FAQ#_how-to-disable-crash-reporting

Optionally also get MyST-Marksown Syntax extension for VS Code: https://marketplace.visualstudio.com/items?itemName=ExecutableBookProject.myst-highlight

More basic Packages#

At this stage you have a clean, brand new virtual XUbuntu machine, with VirtualBox Guest extensions enabled.

To get our dsci-lab version you have to install some more packages. You can do so by simply copying the following commands into a terminal (open a new terminal e.g. by typing Strg-Alt-t):

freeplane incl. Java#

Mindmap (incl. Java):

sudo apt install freeplane

GitHub Desktop TBD#

GitHub Desktop - The Linux Fork: shiftkey/desktop

wget -qO - https://apt.packages.shiftkey.dev/gpg.key | gpg --dearmor | sudo tee /usr/share/keyrings/shiftkey-packages.gpg > /dev/null
sudo sh -c 'echo "deb [arch=amd64 signed-by=/usr/share/keyrings/shiftkey-packages.gpg] https://apt.packages.shiftkey.dev/ubuntu/ any main" > /etc/apt/sources.list.d/shiftkey-packages.list'
sudo apt update && sudo apt install github-desktop

ca 300 MB (!)

LaTeX#

https://jupyterbook.org/en/stable/advanced/pdf.html recommends using the texlive distribution.

We have found that in combination with jupyterbook (see below) the following packes are actually required, with a total size about 2 GB (!):

sudo apt install imagemagick\
     	 	 texlive-latex-recommended texlive-latex-extra \
                 texlive-fonts-recommended texlive-fonts-extra \
                 texlive-xetex latexmk texlive-lang-german\
		 xindy biber texlive-science

(Mini-)Conda#

Important: *DO NOT install Conda with sudo. Install Miniconda with the role of a normal user instead. Every user and every virtual conda environment are completely independent from each other. There is no system-wide installation.

Installing on Linux:

cd
cd Downloads
chmod +x

Miniconda Installer: https://docs.conda.io/projects/miniconda/en/latest/ > Quick command line install:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash

==> For changes to take effect, close and re-open your current shell. <==

Why close and re-open? Conda puts an extra virtual environment layer over the standard Python installation, so we can work with multiple Python configurations in parallel. To learn more about virtual environments:

Your termial command line now should start with (base), which is the name of your current virtual environment:

(base) dsci@dsci-lab-ss24:~$

Keep conda current:

conda update --all

(Note:Instead of installing miniconda you instead want to install anaconda (https://www.anaconda.com/products/individual). Anaconda is much more complete than miniconda, but IMHO fo “fat”. In our dsci-lab we prefer a lightweight system. This allows you to look more easily “under the hood”, to understand what’s going on, and to maintain the whole system - the dependencies in our setup are complex enough anyhow.)

Install pandas, jupyter notebook, jupyterbook#

As said: Conda is minimalistic. Tus we have to install some modules by ourselfes.

Some important ones are:

pip install pandas numpy matplotlib scikit-learn seaborn \
   rdflib owlrl markdownify lxml markdown python-slugify \
   jupyter jupyter-book jupytext

Note: We do install these packages into the virtual conda environment base. If we decide to create another virtual conda environment, it will be empty again, and we have to populate it with libraries again. This is the reason (a) why we prefer lightweight environments, and (b) why we want to learn how to install libraries by ourselfes.

Test the jupyterbook installation: Build the book according to https://jupyterbook.org/start/build.html

mkdir -p ~/c
cd ~/c
jb create jupyterbook-test

build html:

jb build jupyterbook-test
firefox jupyterbook-test/_build/html/index.html &

build pdf via LaTeX:

jb build jupyterbook-test --builder pdflatex
atril jupyterbook-test/_build/latex/book.pdf &

Start Jupyter. Jupyter will launch firefox. Stop Jupyter again:

jupyter notebook &
jupyter notebook stop

System login screen image TBD: CHANGE TO MINT LINUX#

Download desired image to /Downloads.

cp this image with sudo rights into folder /usr/share/xfce4/backdrops/:

cd  /usr/share/xfce4/backdrops/
sudo mv /tmp/IMG_2247.JPG .
sudo chmod 655 IMG_2247.JPG

“Bildschirmhintergrund des Nutzers verwenden, falls verfügbar”: NO

Open Whisker-Menue > Settings > LightDM GTK+ Greeter

  • select image in folder backdrops

  • enter install password

  • select background image

customize user install background image#

copy private background image into folder Documents.

right click on background > desktop settings > folder Documents > select image

Zotero#

https://www.jbusse.de/dsci-lab/h_zotero.html

Export OVA#

Maschine aktualisieren, Gasterweiterungen installieren, Shared Folder deaktivieren, Medium auswerfen, Maschine ‘runterfahren, USB auf 1.0 umstellen, dann Export OVA:

  • /home/jb/v/dsci-lab_ws2025.ova

  • “alle Netzwerkadressen mit einbeziehen”

  • Hersteller-URL: jbusse.de/dsci-lab

SHA und Größe der Datei feststellen:

ls -ls v/dsci-lab_ws2025.ova
# 11558000 -rw------- 1 jb jb 11835387904 Sep 30 09:20 v/dsci-lab_ws2025.ova

sha256sum v/dsci-lab_ws2025.ova
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  v/dsci-lab_ws2025.ova

Auf den Server hochladen, auch dort sha256sum berechnen, kontrollieren, erst dann in Download the dsci-lab OVA file eintragen.

Admin#

Aktualisieren:

sudo apt update; sudo apt upgrade

next steps#

http://jbusse.de/dsci-lab/h_shared-folders.html

http://jbusse.de/dsci-lab/h_customizing.html

Contents