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docs/includes/abbreviations.md

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+*[sdRDM]: software-driven Research Data Management

docs/index.md

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+# Research Data Management in FOR5596
+
+![FOR5596 Logo](images/FOR5596.png "FOR5596 Logo"){{: style="height:159px;width:300px", align="left"}
+Within FOR5596 state-of-the-art research data management is developed and implemented for all research projects. The underlying goal is to create highly annotated, structured data sets that are in line with [FAIR principles](https://www.go-fair.org/fair-principles/). This includes the use of standardized data models as well as the development of new data standards. Ultimately, this leads to high-quality data assets that are re-analyzable and reusable for future research projects.

docs/installations/docker.md

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+---
+icon: simple/docker
+---
+
+Docker is a way to run software in a container. This means that the software is isolated from the rest of your system. This is useful because it means that you can run software without having to install it on your system. This is particularly useful for running software that has a lot of dependencies or that you only need to run occasionally. In this way, Docker is a bit like a virtual machine and enables running software without configuring the system to run it.
+
+To install Docker, follow the instructions for your operating system on the [Docker website](https://docs.docker.com/get-docker/).

docs/installations/jupyternotebook.md

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+---
+icon: simple/jupyter
+---
+
+Jupyter Notebook is a web-based interactive computing environment that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. It is a great tool for data analysis and visualization. In this Jupyter Notebook environment, sdRDM is already installed, allowing the usage of [RDM].
+  [RDM]: ../rdm/define.md#define-a-rdm
+
+1. Install [Docker]
+  [Docker]: docker.md#docker
+
+
+2. Run the FOR5596 Jupyter Lab Docker container from a command line
+
+    ```bash
+    docker run -it --rm -p 8888:8888 -v "${PWD}":/home/jovyan/work --name FOR5596-notebook for5596-notebook
+    ```
+
+3. Open the Docker Desktop application navigate to `Containers` and click on the running container named `FOR5596-notebook`
+
+4. within the `Logs` of the container, you will find a token, which is needed to access the Jupyter Notebook. 
+
+    ```bash
+    2024-02-25 17:44:54 [I 2024-02-25 16:44:54.937 ServerApp]     http://127.0.0.1:8888/lab token=a9a39e2f219edac28f66cf2c88a9954978f78626e58e03f6
+    2024-02-25 17:44:54 [I 2024-02-25 16:44:54.937 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
+    2024-02-25 17:44:54 [C 2024-02-25 16:44:54.939 ServerApp] 
+    2024-02-25 17:44:54     
+    2024-02-25 17:44:54     To access the server, open this file in a browser:
+    2024-02-25 17:44:54         file:///home/jovyan/.local/share/jupyter/runtime/jpserver-7-open.html
+    2024-02-25 17:44:54     Or copy and paste one of these URLs:
+    2024-02-25 17:44:54         http://e2376db8149d:8888/lab?token=a9a39e2f219edac28f66cf2c88a9954978f78626e58e03f6
+    2024-02-25 17:44:54         http://127.0.0.1:8888/lab?token=a9a39e2f219edac28f66cf2c88a9954978f78626e58e03f6
+    2024-02-25 17:44:55 [I 2024-02-25 16:44:55.984 ServerApp] Skipped non-installed server(s): bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-langserver, jedi-language-server, julia-language-server, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, yaml-language-server
+    ```
+
+    In the example above, the token is `a9a39e2f219edac28f66cf2c88a9954978f78626e58e03f6`.
+
+5. Click on the link `8888:8888` in the header of the container to open the Jupyter Notebook in your default web browser.
+
+    ![FOR5596-Notebook container](../images/docker_for_container.png "FOR5596-Notebook container")
+
+6. Enter the token from the logs in the field `Token` and click on `Log in`.
+
+7. You are now in the Jupyter Notebook environment your local files can be accessed via the `work` folder.

docs/installations/local_env.md

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+---
+icon: simple/anaconda
+---
+
+!!! Warning "🚧 Under Construction 🚧"
+    This page is currently under construction. Please check back later for updates.
+
+## Anaconda
+
+Anaconda is a distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. The distribution includes data science packages suitable for Windows, Linux, and macOS.
+
+## GitHub Desktop
+
+GitHub Desktop is a graphical user interface for GitHub, which allows you to manage your repositories, review pull requests, and more.
+
+## VS Code
+
+Visual Studio Code is a source-code editor developed for Windows, Linux, and macOS. It includes support for debugging, embedded Git control, syntax highlighting, intelligent code completion, snippets, and code refactoring.

docs/javascripts/mathjax.js

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+window.MathJax = {
+    tex: {
+        inlineMath: [["\\(", "\\)"]],
+        displayMath: [["\\[", "\\]"]],
+        processEscapes: true,
+        processEnvironments: true
+    },
+    options: {
+        ignoreHtmlClass: ".*|",
+        processHtmlClass: "arithmatex"
+    }
+};
+
+document$.subscribe(() => {
+    MathJax.startup.output.clearCache()
+    MathJax.typesetClear()
+    MathJax.texReset()
+    MathJax.typesetPromise()
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