Resources for learning and teaching

Table of contents

1. Markdown
2. Python and programming
3. Jupyter notebooks
4. GitHub’s interactive tools for learning skills
5. Example problems and teaching materials

The external materials linked here may be useful for the instructor to learn more about the material and/or to share in their classroom to assist in teaching their students.

Markdown

• The Markdown guide, GitHub Guide on Markdown and a blog post on Markdown syntax. Any are great references to understand the basics of Markdown.
• HackMD, a freemium browser tool for creating simple Markdown notes and websites
  • Register for a free account for a workspace. There you can create any number of notes that may be published as a website in a single click, organize them with folders and tags, and sync to your GitHub account.
  • The live editing feature of HackMD allows you to catch errors and see any formatting issue immediately. It can be a timesaver to type your markdown documents in HackMD first to add into your GitHub later.
  • HackMD is a great solution for a simple, one page website. It is also easily accessible through a smart phone to make edits or take notes while away from a computer.
  • HackMD’s Official Tutorial
• GitHub relies heavily on Markdown.
  • Learn how to communicate on GitHub using markdown
  • GitHub also makes it possible to create a full website with markdown and GitHub Pages. An example from Dr. Julin Maloof

Python and programming

• Plotting and programming with Python

  • A very nice tutorial for learning the basics of Python. This can be used with Jupyter notebooks to teach both very effectively.

  • https://plotnine.org/
  • https://python-graph-gallery.com/all-charts/
• The Python Tutorial
  • Created by Python developers for Python users, this is a comprehensive tutorial to deeply learn Python.
• The Python Standard Library
  • The information on all the base modules distributed with a Python install.

• https://www.w3schools.com/python/default.asp

• CS50 Python

Jupyter notebooks

https://github.com/ctb/2025-jupyterlite-template

Titus’ JupyterLite material

• Currently, there is a bug preventing exporting the files from JupyterLite. Instead of using File/Save and Export, Right-click and Download.

  https://github.com/jupyterlite/jupyterlite/discussions/1421

GitHub’s interactive tools for learning skills

1. Introduction to GitHub
   • Learn GitHub’s basic infrastructure. Branching, committing, pull request,
2. Communicate using markdown
3. Introduction to repository management
4. Introduction to creating static websites with GitHub Pages

Example problems and teaching materials

• Rosalind, real bioinformatic problem sets

• UC Davis’ DataLab Workshop Repos

• https://www.w3schools.com/datascience/default.asp

• https://www.w3schools.com/programming/index.php

  • w3schools is a wonderful static site that contains introductory material for the most commonly used programming languages like python
• https://www.youtube.com/@cs50
• https://www.youtube.com/@freecodecamp
• https://www.youtube.com/@DataWithBaraa