Scripting for Biologists

Contents

• Topics
  • 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
• Extras
  • Extra Topic 1: SSH Keys
• Acknowledgments

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

Topics

Topic 1: Getting set up

Topic 2: Intro to Bash

• Slides
• Video:

Topic 3: Intro to Git

• Slides
• Videos:

• Exercise

Topic 4: Intro to Python

• Slides
• Exercise:
  • Exercise 1 of Python translation project

Topic 5: Scripting best practices

• Exercise

Topic 6: Regular expressions

• Resources:
  • See Canvas for Randy’s notes
  • Jamie’s regex notes
  • Python docs
• Exercise:
  • Exercise 2 of Python translation project

Topic 7: Reading and writing files

• Notes and exercise:
  • python-file-io

Topic 8: Debugging

• Notes and exercise:
  • python-debugging

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

• Notes and exercise:
  • python-tabular-data

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

• Notes and demo:
  • python-argparse-demo
• No exercise

Topic 11: Classes in Python

Extras

Extra Topic 1: SSH Keys

• Notes and video here

Acknowledgments

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

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