Python for Biologists course

  Python for Biologists


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:

  1. to analyze, interpret and visualize scientific data to create publication ready plots
  2. 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 BiopythonHTSeq 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. It can be taken on-demand or as a blended learning course. The on-demand modules each contain

  • a 60-90 minute video lecture that participants can watch when it suits them
  • exercises for the participants to apply what they have learned
The blended learning modules each additionally contain a live Zoom tutorial to answer questions (90-120min).
In total, the participants should plan to invest 20 to 35 hours.


  1. Installation, Anaconda, Jupyter, GIT, Notebook extensions
  2. Syntax, PEP8, keyboard shortcuts, Notebook structure
  3. Numpy, Data analysis, Pandas, File IO: Ascii, HDF5, Excel
  4. Matplotlib, Visualization, Advanced Plotting, String Formatting
  5. Video creation, Symbolic Calculation with Sympy, Biopython
  6. HTSeq, Pysam, Data Analysis example

See preview

Course overview

Module / Course​ Python for Scientists​ Python for Biologists Python Basics (3/4 modules) Good Programming Practice ​ Advanced Plotting HPC Image Analysis
Good programming practice, Notebook structure, Extensions, shortcuts +++ in 4 module course +++
Intro, Installation, Syntax, PEP8, First Examples +++ +++ +++
Data analysis, Big Data, Numpy, Pandas +++ +++ +++
Interpolation, Fitting, Filtering, Data Analysis Example +++
Visualization, Advanced Plotting, Matplotlib, String Formatting +++ +++ +++
Interactive Plots, widgets, 3D Visualizations, LaTeX integration +++
GIT, File Creation, Generators, Dask Parallelization +++ only GIT
Video Creation, Symbolic Calculation, Virtual Environments, Complex Fitting +++ without fitting
Biopython, HTSeq, Pysam +++
Performance optimization and profiling for Single- and multi core applications +++
Image analysis and processing, Scikit Image +++

On-demand courses

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Python Basics (4 module) logo
This gives you access to the Python Basics (4 modules) lecture videos and materials
Python for Biologists course
This gives you access to the Python for Biologists lecture videos and materials
Training Scientists Logo
This gives you access to all the course videos and materials of: Python for Scientists & Engineers, Python for Biologists, Good Programming Practice, Advanced Plotting in Python, Image Processing in Python

Upcoming Live Courses

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Python Basics (4 module) logo
Dates: | 7.11. | 9.11. | 14.11. | 16.11. |
Time: 9:00-11:00am German time
Python for Biologists course
Dates: | 23.10. | 30.10. | 6.11. | 13.11. | 20.11. | 27.11. |
Time: 9:00-11:00am German time


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