Phyletica bio photo


Exploring biodiversification.

Email Twitter Github Youtube Interweb Auburn AU Biology AU Museum

Scripting for Biologists


This course is designed to help biology graduate students learn computational skills that will allow them to approach biological questions in new ways.


Topic 1: Getting set up

Topic 2: Intro to Bash

Topic 3: Intro to Git

Topic 4: Intro to Python

Topic 5: Scripting best practices

Topic 6: Regular expressions

Topic 7: Reading and writing files

Topic 8: Debugging

Topic 9: Using external packages to manipulate, analyze, and plot data

Topic 10: A simple demo of argparse for parsing command-line args

Topic 11: Classes in Python


Extra Topic 1: SSH Keys


This work was made possible by funding provided to Jamie Oaks from the National Science Foundation (DEB 1656004).