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First Steps with Python in Life Sciences

3 days, Spring 2024, TBD

Venue

University of Berne, Room TBD

Instructor:

Dr. Wandrille Duchemin, SIB Basel

Dr. Robin Engler, SIB Lausanne

 

Description

Have you ever been stuck with a file format that doesn't precisely conform to your needs, found yourself doing annoyingly repetitive data manipulations, or struggled to efficiently manage and explore your data? Python to the rescue!

Python is an open-source and general-purpose scripting language which runs on all major operating systems. It was designed to be easily read and written with comparatively simple syntax, and is thus a good choice for beginners in programming. Python is applied in many disciplines and is one of the most common languages for bioinformatics. The Python community enthusiastically maintains a rich collection of libraries/modules for everything from web development to machine learning. Other programming languages such as R have comparable functionality to Python, however some tasks are more natural (and easier!) in Python.

In this course, participants will learn the basic concepts and data structures necessary to solve routine data manipulation tasks. Importantly, we will cover the concepts, terminology, and approach to documentation required to further develop skills in Python programming independently. The goal is to take control of your research questions in an independent manner.

Topics include: A basic introduction to Python scripting and computing in general; Creating, populating, and modifying data structures; Working with files: reading / writing; Installing / Importing libraries/modules; Writing functions; Best practices in Python programming & Debugging and documentation. Learning objectives By the end of this course, you will not only be prepared to learn more advanced bioinformatics-specific applications in forthcoming courses, but also be able to: Create, populate, and modify data structures; Work with files: read and write files; Install and import libraries and modules; Write functions; Apply best practices in Python programming & Debug and document your own code.

 

Learning objectives

By the end of this course, you will not only be prepared to learn more advanced bioinformatics-specific applications in forthcoming courses, but also be able to:

  • Create, populate, and modify data structures
  • Work with files: read and write files
  • Install and import libraries and modules
  • Write functions
  • Apply best practices in Python programming
  • Debug and document your own code

 

For more details: https://www.sib.swiss/training/course/20240925_FSWP

Program

The course starts at 9:15 and ends around 17:15. A social apero might be organised at the end of the first day (TBC).

Precise information will be provided to the participants in due time

 

Prerequisites

This course is designed for beginners; there is no requirement for previous training in Python

Registration

Registration through SIB  here

Application / cancellation deadline: 15 September 2024

 

Free for DSLS students

Reimbursement of Train ticket, 2°class, half-fare from your institution to the place of the activity.

 

Credits

Credits: 1.5

Category: Research tools (R)