Module 1.3 Getting started with python (outline)
Theme 1: Getting started with bioinformatics
Getting started with python
Time | Activity description | ILOs |
9.00-9.30 | Lecture: “Python introduction” (Leandro Escobar-Herrera, Gitte Aasbjerg) | · Be able to write a simple python script · Be familiar with the Spyder interface · Name some of the major programmering languages, and explain why there are so many · Describe what a Conda environment is, and know how to use it · Understand the overall purpose and opportunigies with BioPython · Be able to write a simple script using BioPython |
9.30-10.15 | Practical: “Python introduction” (Leandro Escobar-Herrera, Gitte Aasbjerg) | |
10.30-10.50 | Lecture: “Python as a bioinformatical tool” (Leandro Escobar-Herrera, Gitte Aasbjerg) | |
10.50-12.00 | Practical: “Getting started with python” (Leandro Escobar-Herrera, Gitte Aasbjerg) |
Details
Currently, Python stands out as one of the most extensively utilized programming languages in bioinformatics. Consequently, in this module, participants will employ Python to create small scripts where they will acquaint themselves with fundamental Python commands, learning how to construct simple scripts that execute these commands. Participants will navigate typical interfaces of integrated development environments (IDEs), as well as packages in both conda and Python, with a special emphasis on Biopython. Biopython, a collection of freely available tools for biological computations, simplifies tasks such as parsing a variety of bioinformatics files. Throughout the course, participants will encounter different file types, anticipating exposure to many more as they progress in their bioinformatics careers. Recognizing that Biopython may appear daunting initially, the first module will focus on maintaining simplicity.