SPROuT - Science Powered through Reproducibility, Openness, and Teamwork - MB120C26

• Title: SPROuT - Science Powered through Reproducibility, Openness, and Teamwork
• Czech title: SPROuT - Společně Pro Rozvoj Otevřené vědy a Týmové práce
• Guaranteed by: Department of Botany (31-120)
• Faculty: Faculty of Science
• Actual: from 2024
• Semester: winter
• E-Credits: 3
• Examination process: winter s.:
• Hours per week, examination: winter s.:0/4, C [DS]
• Capacity: 15
• Min. number of students: 5
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment
• Guarantor: Mgr. Ondřej Mottl, Ph.D.

Annotation

In today's dynamic landscape of scientific research, mastering the art of reproducibility, openness, and teamwork
isn't just advantageous—it's essential. "SPROuT" offers a light-hearted yet meticulous four-day workshop tailored
for master and PhD students, transcending traditional research methodologies. This workshop promises a
compelling exploration of the scientific research world in the digital era, emphasizing efficient data and project
organization (say goodbye to lost files forever!), and facilitating effortless and effective project collaboration.

Expected Learning Outcomes
- Reproducibility in science and the principles of Open Science: Learn how to make your research fully reproducible, manage complex analyses, share data and code openly, and apply Open Science principles to enhance transparency and collaboration.
- Version control with Git and GitHub: Master the use of Git and GitHub for tracking changes in code and datasets, enabling smooth project collaboration, and ensuring a complete history of your work to avoid data loss or version conflicts.
- Project, time, and task management techniques: Explore practical tools like GitHub Projects, Milestones, and Issues to efficiently organise tasks, meet deadlines, and manage large, collaborative research projects.
- Tools and strategies for effective teamwork and collaboration: Learn how to streamline teamwork in research settings, using tools like GitHub for code review and real-time data analysis in RStudio, while fostering clear communication and productive collaboration.

Participants will engage in group-based practical sessions using RStudio that highlight the core of Open Science,
the fundamentals of Science Reproducibility, and the application of Version Control using Git and GitHub
integrated in the R environment. "SPROuT" is dedicated to dismantling the obstacles to collaboration, simplifying
the process of working together on scientific endeavours, or even just seeking project assistance. The course is
designed to nurture a culture of collaborative and transparent research practices among the next generation of
scientists, equipping them to navigate the complexities of modern science with confidence and ease.

The course will be held during November. The course is designed as a practical exercise over several days. Based on the participants’ preferences and room availability, the course will take part:
05.11. 14:45 - 19:30
07.11. 14:45 - 19:30
13.11. 14:00 - 19:30
14.11. 14:45 - 19:30
19.11. 14:45 - 19:30

For those interested, additional courses can be explored here: https://bit.ly/mottl_teaching.

Last update: Mottl Ondřej, Mgr., Ph.D. (05.11.2024)

Syllabus

English

• Day 1: Introduction to Open Science and Reproducibility

• - Overview of the Course: Structure, requirements, and material locations.

• - Preparation of Tools: Setting up machines, accounts, RStudio, and linking necessary platforms.

• - Open Science Fundamentals: Understanding the importance and implications of open scientific research.

• Day 2: Version Control with Git/GitHub (with R)

• - Introduction to Reproducibility: Exploring the significance of reproducibility in the scientific method.

• - Basics of Git/GitHub: Setting up, managing, and utilizing Git and GitHub.

• - Repository Management: Initiating a new GitHub repository, committing code, and managing changes.

• - Advanced Git Operations: Branching, pull requests, merge conflicts, forking, and merging.

• Day 3: Collaboration and Project Management on GitHub (with R)

• - Collaborative Tools Overview: Identifying tools and practices for effective collaboration.

• - Issue Management on GitHub: Creating, assigning, linking PRs to issues, and closing issues.

• - Milestones, Teams, and Projects: Creating and managing milestones, teams, and projects on GitHub for streamlined collaboration.

• Day 4: Ensuring Project Reproducibility

• - Coding Etiquette: The importance and utility of coding style and project hygiene.

• - Project Structure and Management: Best practices for project setup and maintenance.

• - Version Control for R Packages: Strategies for handling R package versions.

• - Documentation and Reporting: Introduction to various R packages for reproducibility.

Last update: Štefánek Michal, Mgr. (15.05.2024)