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851-0623-00L 0.5 Credits DR D-GESS

Open Science Tools - Authoring and Publishing Workflows for Collaborative Scientific Writing

Lecturers & Examiners: Lars Schöbitz
While this course does not require experience in any programming language, learners that have previously been exposed to data science tools (R, RStudio IDE, Jupyter Notebooks, Python, VS Code) would benefit most from this course.
VVZ CR n/a

Last Updated: 2026-02-05 16:15:53

Abstract

As the expectations of researchers increase, publishing reproducible scientific articles becomes essential. However, choosing tools for these tasks can be difficult. This course aims to guide researchers through these challenges by introducing a workflow that utilizes Git, GitHub, and the Quarto scientific and technical publishing system for collaborative scientific writing.

Objective

This course has the following learning objectives: 1. Learn to use the Quarto file format and the RStudio IDE visual editing mode to produce scholarly documents with citations, footnotes, cross-references, figures, and tables. 2. Explain the differences between files written in markup languages like markdown (.md) and those in proprietary file formats like .docx. 3. Utilize an exported library from Zotero in Better BibTex Format to create an automated reference list in your scientific documents. 4. Interact with Git version control and GitHub through the RStudio IDE. 5. Collaborate with other researchers using the GitHub issue tracker and project management board to organize tasks and streamline communication. 6. Publish a public website using GitHub Pages to share research with a broader audience.

Content

This course offers researchers a hands-on opportunity to learn open source tools and platforms that are accessible beyond institutional employment. The participatory live coding teaching technique involves an instructor writing and narrating code as they teach, and inviting learners to write and execute the same code. Topics covered include: - Scientific communication. - Reproducible research (open research, version control, licensing). - Collaboration through Git and GitHub. During the course, participants will learn how to use the Quarto file format to prepare various scholarly documents, including slides, scientific articles, books, and websites. Additionally, we will demonstrate how GitHub can serve as both a project management tool and a publishing platform using GitHub Pages. While the course will introduce commonly used tools in software development, they will not be explained in great detail. Instead, the goal is to expose learners to the tools and concepts, requiring openness to new ideas.

Resources

Learning Materials (Links)

General Information

Language
English
Levels
DR

Examination

Type
ungraded semester performance
Successful participation in this course earns participants 0.5 ECTS, equivalent to 15 working hours. The course consists of two mandatory 4-hour modules, with the remaining 7 hours designated for participant preparation before the first module and between the two modules. Only students that participate in both modules will receive 0.5 ECTS.

Registration & Places

Max Places
16

Course Components

Type Title Time & Place Hours
seminar Open Science Tools - Authoring and Publishing Workflows for Collaborative Scientific Writing
Block course Time: 08:30 - 12:30
  • 17.10 Date 08:15-13:00 (HG F 33.5)
  • 24.10 Date 08:15-13:00 (HG F 33.5)
15 h semesterly

Offered In