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 four goals and teaches

1. a basic introduction to Python and programming in general
2. to analyze, interpret and visualize scientific data to create publication ready plots
3. good programming practice, version control with GIT and virtual environments
4. specialization in Biopython (DNA analysis), Image analysis, or more (see below)

There are different specialization modules which participants can choose from since biologists – even if working in the same workgroup – need different specializations depending on their research topic.

Target groups

The course is suited for people with previous experience in other programming languages and for people who already have experience with Python looking to improve their skills. A lot of previous participants have been self-taught and appreciated the structured introduction to Python. The course is also suitable for absolute beginners in programming, however, beginners should plan to invest additional time between tutorials to learn fundamentals from the additional resources.

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). The participants should plan to invest 6 hours per module or 36 hours in total.

Content

Installation

1. Introduction, Jupyter, Virtual Environments, Notebook extensions, Python fundamentals

Basics

1. Syntax, PEP8, Keyboard shortcuts, Introduction to Numpy and Matplotlib

2. Advanced Numpy, Pandas, File Input & Output, ChatGPT

3. Advanced Matplotlib, Inset Plots, Contour Plots, Interactive Plots

4. GIT, String Formatting, Video Creation, Notebook Structure

Specializations
Based on participant needs, we will do module 3 or 4 or both.

1. Interpolation, Fitting, Complex Fitting, Filtering, Data analysis example

2. File creation, Generators, Parallelization, Sympy, Integration of Plots to Overleaf

3. Biopython, DNA sequencing, BLAST, Visualization of DNA

4. Image Analysis and Processing (Scikit Image)

The times for the six online tutorials are as follows:

17.10| 24.10. | 31.10 | 21.11. | 28.11. | 5.12. - these are all Thursdays - from 9am - 10.30/11am

Before the first tutorial you should have watched the first lecture and set up your computer accordingly. Please plan 2-4 h for this.