Python for Biologists course

  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

  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)

FAQ (Frequently Asked Questions)

Prior experience isn’t necessary but beneficial. Planning extra time ensures Python for Biologists gets you from no experience to being confident in data handling.

Lecture videos run about 1 hour per module and are typically watched twice. Allocate 2-4 extra hours for exercises, and 2 more if opting for blended learning. Total: 5-8 hours per module.

Yes, during tutorials, we initially cover the lecture and exercise solutions. Then, there’s usually time to delve into topics beyond the module’s content. This often includes discussions about participants’ programming projects.

Active participation in tutorials and presenting exercise solutions qualifies you for a certificate upon course completion.

If you want to self study with the on-demand course and still get a certificate you can book a 1 on 1 Zoom call to test if you actually understood the concepts of the course. If you pass you will get the certificate.

Contact us if you are interested.

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

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Python for Biologists course
10/2024 Python for Biologists
Dates: | 17.10. | 24.10. | 31.10. | 21.11. | 28.11. | 5.12. |
Time: 9:00-11:00am German time
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Contact

Are you interested or have any questions about the Python course? Reach out any time!

email training scientists
call training scientists

contact@Training-Scientists.de

+49 15678 448154

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