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

a basic introduction to Python and programming in general
to analyze, interpret and visualize scientific data to create publication ready plots
good programming practice, version control with GIT and virtual environments
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

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

Basics

Syntax, PEP8, Keyboard shortcuts, Introduction to Numpy and Matplotlib
Advanced Numpy, Pandas, File Input & Output, ChatGPT
Advanced Matplotlib, Inset Plots, Contour Plots, Interactive Plots
GIT, String Formatting, Video Creation, Notebook Structure

Specializations

Interpolation, Fitting, Complex Fitting, Filtering, Data analysis example
File creation, Generators, Parallelization, Sympy, Integration of Plots to Overleaf
Biopython, DNA sequencing, BLAST, Visualization of DNA
Image Analysis and Processing (Scikit Image)

Course overview

Module / Course	Python for Scientists	Python for Biologists	Python Basics
Introduction, Virtual Environments, Jupyter, Notebook extensions, Python Fundamentals	+	+	+
Syntax, PEP8, Keyboard Shortcuts, First examples in Numpy and Matplotlib	+	+	+
Advanced Numpy, File IO, Pandas, ChatGPT	+	+	+
Advanced Matplotlib, Plotting options, Inset Plots, Contour Plots, Interactive Plots	+	+	+
GIT, String Formatting, Video Creation, Notebook structure	+	+
Interpolation, Fitting, Complex Fitting, Filtering, Data analysis example	+	*
Creating Files, Generators, Parallelization, Sympy, Integration of Plots to Overleaf	+	*
Biopython, DNA sequencing, BLAST, Visualization of DNA		*
Image analysis and processing, Scikit Image		*

+ meaning the topics are both covered in the lecture and the tutorials
* meaning participants have access to the lecture materials but we will pick 1 or 2 topics to discuss in the tutorials

On-demand courses

Course licence	Description	Price
Python Basics course (4 modules)	This gives you access to the Python Basics (4 modules) lecture videos and materials	$149.00	Add to cart
Python course for Scientists & Engineers	This gives you access to the Python for Scientists & Engineers lecture videos and materials	$199.00	Add to cart
Python for Biologists	This gives you access to the Python for Biologists lecture videos and materials	$249.00	Add to cart