First Steps with Python in Life Sciences

16-18.06.2026

Dre Wandrille Duchemin, SIB Bâle Dr Robin Engler, SIB Lausanne un assistant SIB Bâle

Overview

Have you ever struggled with a file format that didn't quite meet your needs, found yourself performing repetitive data manipulations, or faced challenges in efficiently managing and exploring your data? Python to the rescue!

Python is an open-source, general-purpose scripting language that runs on all major operating systems. It was designed with simplicity in mind-easy to read, easy to write-making it an excellent choice for beginners. Today, Python is widely used across disciplines and is one of the most popular languages in bioinformatics.

The Python community actively maintains a rich ecosystem of libraries and modules for everything from web development to machine learning. While other languages like R offer similar functionality, certain tasks are often more intuitive (and easier!) in Python.

In this course, participants will learn the fundamental concepts and data structures needed to tackle routine data manipulation tasks. We will also cover essential terminology, documentation practices, and approaches that will enable you to continue developing your Python skills independently. The ultimate goal: empower you to take control of your research questions with confidence.

Topics Covered

• Introduction to Python scripting and computing basics
• Creating, populating, and modifying data structures
• Working with files: reading and writing
• Installing and importing libraries/modules
• Writing functions
• Best practices in Python programming
• Debugging and documentation

Audience

This 3-day course is designed for beginners who want to learn how to write Python code for common tasks such as automated data parsing, basic statistical operations, and graphical representations.

If you are already proficient in programming, this course may feel slow-paced; we recommend checking our upcoming intermediate Python courses instead.

Learning Objectives

By the end of this course, you will be able to:

• Create, populate, and modify data structures
• Read from and write to files
• Install and import libraries and modules
• Write your own functions
• Apply best practices in Python programming
• Debug and document your code

You will also be prepared to advance to bioinformatics-specific applications in future courses.

Knowledge / Competencies

No prior Python experience is required. However, we recommend completing our First Steps with UNIX course or the UNIX Fundamentals tutorial. Basic algorithmic concepts are a plus.

Technical Requirements

Bring your own laptop.

We will use Python managed by Anaconda, a free, OS-agnostic platform for organizing Python libraries and environments. Anaconda includes Anaconda Navigator, a graphical interface that simplifies Python setup and usage.

Please download and install Anaconda for your operating system before the course. Any recent Python version (≥ 3.7) is fine. If disk space is limited, you may install Miniconda instead, but note that it lacks Anaconda Navigator and many pre-installed packages.

We will also use Jupyter Notebook for interactive coding. Please install Jupyter Notebook via conda.

UNIBAS

Reimbursements for CUSO Students: Train ticket, 2°class, half-fare from your institution to the place of the activity.

Reimbursement of your travel tickets can be asked online through your MyCUSO. See HERE for the procedure.

For any question concerning reimbursement please contact the CUSO Microbiology coordinator Sarah Miéville

Important informations :

• A waiting list will be prepared to ensure that there are no empty seats.
• For cancellations after the deadline of registration or no-show: 50 CHF administrative fee

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