Python for Biologists
Summary
The Python for Biologists course is the next evolution of the Python for Scientists & Engineers course tailored specifically to Biologists by including libraries like Biopython.
Biologists need programming skills in Python to analyze their data but have rarely had any programming education during their Bachelor’s and Master’s degrees. Hence, this course has two distinct goals and teaches:
- to analyze, interpret and visualize scientific data to create publication ready plots
- good programming practice, version control with GIT and virtual environments
Target groups
Beginners get a well structured introduction to Python, covering a wide range of topics including libraries like Biopython, HTSeq and Pysam.
Experienced programmers get to improve their understanding of data analysis and visualization, while good programming practice helps to save time.
Python for Biologists can be taken as a standalone course or it can be coupled together with the specialization courses.
Course structure
The course is held in English and currently consists of 6 modules. Every module contains
- a 60-90 minute video lecture on moodle.training-scientists.de that the participants can watch when it suits them
- exercises for the participants to apply what they have learned
- a live Zoom tutorial to answer questions (90-120min)
Content
- Installation, Anaconda, Jupyter, GIT, Notebook extensions
- Syntax, PEP8, keyboard shortcuts, Notebook structure
- Numpy, Data analysis, Pandas, File IO: Ascii, HDF5, Excel
- Matplotlib, Visualization, Advanced Plotting, String Formatting
- Video creation, Symbolic Calculation with Sympy, Biopython
- HTSeq, Pysam, Data Analysis example
