Overview

Git is an open source version control system for tracking changes in code and other types of text documents. First released in 2005, Git has become the de-facto standard for version control, and is
extensively used in both open source and commercial software development. Beyond software development, Git has also proven to be an essential tool in reproducible research - allowing to keep track of files such as data analysis scripts, pipelines, reports or more generally any text-based document. This 2-days course gives a comprehensive overview of Git and its most useful commands, as well as an introduction to collaborative workflows using GitHub through both theory and practical exercises.

Audience

This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who are interested in using a version control system for collaborative work, or simply to keep track of modifications in their scripts, files or code base. This includes people working on code development, but also scientists interested in improving the reproducibility of their data analyses by keeping track of their scripts using version control.

Learning objectives

At the end of the course, the participants should be able to:

• Recognize what version control systems are and how they work.
• Understand and practice basic Git concepts: commits, the HEAD pointer and the Git index.
• Comprehend how git branches work: introduction to branched workflows and collaborative workflow examples.
• Employ branch management: merge, rebase and cherry-pick.
• Experiment by retrieving data from the Git database: git checkout.
• Practice with remotes: share your work and collaborate.
• Recall basics of GitHub and GitLab.

Prerequisites

Knowledge/competencies:

The course is focused on using Git in command line mode (no graphical user interface). It is therefore necessary to have some basic knowledge of UNIX command line, e.g. how to change directory or how to edit a file in a command line editor such as vim/nano.

This course is part of the Data Management learning path. To get the most out of this course, you should meet the learning outcomes of the UNIX fundamentals e-learning.

Technical

You will need access to a computer with an Internet connection and a working microphone
Your computer must be installed with a recent version of Git. Git is available on all major platforms (https://git-scm.com/download).

Schedule

Day 1:

• Introduction to version control systems and Git.
• Git basics: creating a Git repository and making commits.
• Git concepts: commits, the HEAD pointer and the Git index.
• Git branches: introduction to branched workflows and collaborative workflow examples.
• Branch management: merge, rebase and cherry-pick.
• Retrieving data from the Git database: git checkout.
• Working with remotes: collaborating with Git and GitHub.

Day 2:

• Rewriting history: interactive rebase, git reset and commit amending.
• The detached HEAD state explained.
• The Git stash.
• Git tags: label important commits.
• GitHub: creating a new project, adding new users and collaborating wit them.

Application

Registration fees are 200 CHF for academics and 1000 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close on 21/10/2026 or as soon as the places will be filled up. Cancellation after 21/10/2026 will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 working days.

Venue and Time

This course will be take place at the University of Bern.

The course will start at 9:00 CET and end around 17:00 CET.

Precise information will be provided to the participants in due time.

Additional information

Coordination: Diana Marek, SIB Training Group.

A Certificate of Attendance will be sent provided you were present at the course, whereas a Certificate of Achievement recommending 0.5 ECTS will be sent provided you passed the exam.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact [email protected].