BIO-3027 Scientific Programming with Python in the life sciences

Course content
The first week introduces the participants to basic computation in Python. It includes all the basics necessary to get started writing working Python code. Programming concepts and techniques in Python are introduced with plentiful exercises gleaned, as far as possible, from the scientific praxis. After the first week the participants will have a good understanding of general computation in Python. They will have also completed some simpler projects. The second week then further introduces students to the most common aspects and tasks of scientific coding. Participants learn to use many of Python’s scientific packages in realistic settings. Exercises again will mostly be taken from the life sciences. Lastly, students shortly learn about the most important good coding practices. These include needs for documentation and maintainability, as well as techniques for quality assurance.

The more detailed sections of the course are:

• Introduction to computing and Python
• The command line, Interactive shell, Scripts
• Basics, variables, string handling
• Functions & control flow
• Object-Oriented Programming
• File in- and output
• Error handling
• Libraries and foreign code
• Commonly used packages
• Jupyter Notebooks
• Data handling with Pandas and SciPy
• Plotting with Matplotlib and Seaborn
  • Sequence analysis with Biopython
  • Text search with Regular Expressions
  • Generally useful packages
• Using Blast with own code
• Best practices: effective and efficient coding
• Maintainable coding, testing, and debugging
• Resources for Python programmers

Language of instruction and examination

English

Teaching methods
The course consist of 2 weeks active participation and ~ 3 week full-time (120 hours) working on the project. Course includes ca. 40 hours of lectures and ca. 40 hours computer practical and 20 hours of course preparation.