Lecture workspace for the MSc Bioinformatics at Pwani University. Here is an outline of what we will learn in this course:

1. Introduction to Computing and Computational thinking: Lecture
2. A lecture on Open science and reproducible research
3. Introduction to Git and GitHub for version control: Hands-on session
4. Introduction to Linux on the command line:
   • Basic commands: Rik's page commands live coding
   • Dive deeper to Linux and scripting: lecture materials from IBT by Amel
   • Setting up a reproducible Bioinformatics project workspace
5. Python for Bioinformatics
   • Setting up and working with Python on IDLE console and the various text editors we can use
   • Setting up Jupyter Notebooks and the conda environment
   • Go through the materials on the Jupyter Notebooks starting from introduction all the way to Biopython but we do not cover the section on Object-Oriented programming

During this course, you will work on a python programming project, in which you will get to utilize the newfound skills, and learn even more by doing. I will use GitHub classroom for this part since you will be required to submit your work via GitHub.

The notebooks are infused with programming exercises on genomic data parsing and analysis.

We will use a lot of live coding in class, and very few lectures. I will, however, provide some reference text for a deeper grasp of the programming concepts. My focus will be to teach the thinking behind computing. How to turn a biological problem to a computational problem, and solve it using bash scripting or Python. The focus is on thinking.