Presentations about the full-semester course on “Version control of code and data using Git and DataLad”
Welcome! This website hosts slides and other resources for presentations about the full-semester course on “Version control of code and data using Git and DataLad”. You can find the GitHub repository with all the source code here. All contents are licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) license (for details, see here and here), except where noted otherwise. If you notice any issues or have suggestions for improvement, we would be glad to hear from you! Please open an issue on GitHub or get in touch via email. Thanks!
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TURN 2024
Title: FAIR and reproducible development of open educational resources using Quarto and Git
Abstract
University staff spend much time and effort developing educational materials that are rarely shared or easily reusable. Adopting the FAIR principles (Findability, Accessibility, Interoperability, Reusability), known for improving research data management, can similarly enhance educational resources, but practical implementations of these principles are few. In addition, a technical framework for transparent and collaborative development of teaching materials is needed.
We propose an approach using the open-source tools Quarto and Git, which facilitate the FAIR and reproducible development of educational content. Quarto is a publishing system that supports diverse outputs like articles, websites, and presentations from sources such as Jupyter notebooks or Markdown documents. It integrates narrative and code from languages like Python, R, and Julia, ideal for dynamic educational materials such as course websites and online textbooks. Git, a widely-used version control system, tracks file changes, helping users manage revisions and maintain a history of modifications. Online platforms like GitHub and GitLab allow educators to share materials for extension or reuse and foster effective collaboration.
We exemplify this approach in a full-semester MSc Psychology course at the University of Hamburg, using Quarto and Git to develop and manage a course website, an online textbook, as well as interactive exercises and surveys. This example demonstrates how these tools can produce transparent and reproducible educational content adhering to FAIR principles that are readily adaptable and reusable. Major releases of the materials are tagged, annotated with metadata, and archived in repositories like Zenodo, ensuring long-term accessibility. Together, this approach opens new avenues for participatory and adaptable teaching methods.
Description
University staff often develop educational materials that are not widely shared or reusable. Adopting the FAIR principles (Findability, Accessibility, Interoperability, Reusability) and a framework for collaborative development could improve this situation, but practical implementations are few.
We propose using the open-source tools Quarto and Git for creating and managing educational content following FAIR standards. Quarto allows publication of various formats such as articles, websites and presentations, integrating text and code from multiple programming languages. Git tracks changes and maintains history, facilitating revisions. Platforms like GitHub and GitLab enable sharing and collaborative development.
In a semester-long MSc Psychology course at the University of Hamburg, we used these tools to develop a course website, an online textbook, and interactive materials. This practical application demonstrates that such tools can produce transparent and reproducible educational resources. Major releases are archived in established repositories like Zenodo, promoting long-term availability.
Keywords
Open Educational Resources, FAIR, Reproducibility, Version Control, Open Science
Psychologie und Gehirn (PuG) 2024
49th Annual Conference “Psychology and Brain” at University of Hamburg, Germany
Bürgerhaus Wilhelmsburg, Hamburg, Germany
2024-05-31
Poster
Dr. Lennart Wittkuhn & Konrad Pagenstedt
Abstract
In this age of computational and data-driven science, systematic tracking of the evolution of digital objects like code and data is essential for reproducible research and effective collaboration, crucially addressing the reproducibility crisis prevalent in many research fields, including Psychology. Still, chaotic workflows are pervasive in science, reflecting a lack of training in tools and practices from software engineering and scientific computing that provide established solutions for collaborative digital work. Addressing these challenges, we introduced the full-semester course “Version Control of Code and Data: An introduction to Git and DataLad for psychological research”, in the Psychology M.Sc. program at University of Hamburg. At the heart of this course is the “Version Control Book”, a dynamic online learning resource that covers essential concepts of version control in scientific settings. Complementing this resource, we created quizzes and exercises, and shared all materials on GitHub as extendable, open educational resources. In the first iteration of the course, M.Sc. and Ph.D. students effectively used the online book and successfully engaged in the hands-on exercises and quizzes. Feedback from students was overwhelmingly positive, resulting in four nominations for the university’s teaching award, underscoring an enriching learning experience. As a result, the course is scheduled to be repeated in future semesters and adapted to other learning formats. Finally, we are committed to continually improving our online resources as open-source projects. Together, our open educational resources contribute to training researchers essential skills in tracking, organizing and sharing their work, thereby promoting more open, reproducible and effective science.
Poster
Justification for IGOR Prize
The Interest Group Open and Reproducible Science in the Biological Psychology Section of the German Psychological Society (IGOR) awards the annual Open and Reproducible Science Prize.
Papers (poster and symposium presentations) presented at PuG 2024 that exemplify the application of open and reproducible science practices or represent metascience on open and reproducible science topics are eligible. The abstract should include statements on the open and reproducible science aspects of the published or unpublished work (this includes, but is not limited to, pre-registration, open data and materials, reproducible analyses, and metascience work).
When submitting an entry, it must be stated that it is to be considered for the IGOR Prize. Applicants will then be contacted separately by email and asked to write a short letter of justification (approx. 100 words).
Based on this information (abstract, justification), the jury will select the most promising entries. Two jury members will look at each shortlisted presentation and evaluate it according to various aspects related to the promotion of openness and reproducibility.
The contribution that best meets the objectives of IGOR will be honoured at PuG 2024 with a certificate and a cash prize of €500.
Addressing the reproducibility crisis, scientists benefit from adopting tools that enable professional digital workflows. Git, a standard tool in software engineering, enables traceable collaborative development of research outputs, like code and data, but (aspiring) scientists are still not widely trained to use it. To change this, we created a curriculum on Git, including a 200-page online guide, websites with slides, exercises, and quizzes. 30 MSc/PhD Psychology students were successfully trained already. All materials, openly developed on GitHub, are freely available for reuse and extension, thereby also showcasing an approach to the FAIR and reproducible development of open educational resources.
IGOR Quiz Question
Why are Git and GitHub great tools for educators, when they want to develop FAIR and reproducible teaching materials?
- They let them sell their teaching materials online (fast).
- They keep their teaching materials completely private.
- They allow transparent and collaborative development of teaching materials.
- They limit access to teaching materials to certain student.
Digital and Data Literacy in Teaching Lab (DDLitLab)
Event: Closing event of the second funding round of the Digital and Data Literacy in Teaching Lab (DDLitLab) program (presented in person in Hamburg, Germany)
Venue: DDLitLab at University of Hamburg
Date: 2024-03-06
Presenters: Dr. Lennart Wittkuhn & Konrad Pagenstedt
Poster
One Minute Pitch
- Wir kennen vermutlich alle das “Final”.doc Problem
- Und haben erlebt, wie leicht es zu Chaos führen kann
- Texte, Code und Daten auf unseren Computern verändern sich ständig, oft in Zusammenarbeit mit anderen
- Was brauchen wir also?
- Wir wollen wissen, wer, wie was, wieso weshalb warum und wann in einer Datei über die Zeit verändert hat
- Wir wollen an parallelen Versionen arbeiten und flexibel miteinander integrieren
- Und wir wollen das ganze kollaborativ, transparent und reproduzierbar gestalten
- Wir brauchen also ein Versionskontrollsystem.
- In unserem Lehrprojekt haben wir Studierenden Git beigebracht, das wohl bekannteste Versionskontrollsystem und ein Standardtool in der Softwareentwicklung
- Wer mehr erfahren will, wie wir das gemacht haben und dabei u.a. ein 180-seitigen Online-Guide geschrieben haben, kommt zu unserem blauen Poster da drüben
MPRG NeuroCode
Event: Hybrid lab meeting of the Max Planck Research Group “NeuroCode” and the Research Group “Mechanisms of Learning and Change” at University of Hamburg (presented online)
Venue: Max Planck Research Group “NeuroCode” at the Max Planck Institute for Human Development Berlin & Research Group “Mechanisms of Learning and Change” at University of Hamburg
Date: 2023-08-29
Presenters: Dr. Lennart Wittkuhn & Konrad Pagenstedt
QUEST Center
Event: Hybrid symposium on “Reproducible Research: Education and Teaching Formats Reports From the Reproducibility Networks” (presented in person in Berlin)
Venue: QUEST Center of the Berlin Institute of Health at Charité (BIH)
Date: 2023-05-11
Presenter: Dr. Lennart Wittkuhn
