Supplemental Material

This section contains a growing list of links to supplemental material that can be used as further reference and to deepen the understanding of the topics. Reading this content is not required to pass the course, but sometimes gives a different view on topics from the course material or goes deeper and provides more examples.

Unix shell, Bash, Shell Scripting

• Software Carpentry Lesson: The Unix Shell
• Vi / vim tutorial by IBM: vi intro – the cheat sheet method, PDF
• …

Python

• General
  • Python 3.6.1 Documentation: https://docs.python.org/3.6/
  • Software Carpentry Lessons:
    • Programming with Python
    • Plotting and Programming in Python
  • Python for Everybody:
    • Lessons (most of them containing videos) and Material: http://www.py4e.com/
    • Free eBook (PDF, epub, …): https://www.py4e.com/book
    • printed copies of the book are available for ca. Cdn$ 14 .
  • Think Python, 2nd edition (Python 3):
    • Free eBook (read online, PDF, …): http://greenteapress.com/wp/think-python-2e/
    • Python for Everybody is actually derived from this book.
    • There are also printed copies, but they are more expensive than the those of Python for Everybody.
  • The Hitchhiker’s Guide to Python:
    • Free eBook (read online, PDF, epub): http://docs.python-guide.org/
    • A guide to Pyhton that describes best practices, useful packages and helpful tips.
    • Has something to offer for both novices as well as for experts.
    • Also available as printed O’Reilly book.
• Jupyter Notebooks:
  • Notebook Help
• Regular Expressions:
  • Reqular Expressions: Regular Expression Exercises
  • Download Regular Expressions Notebook (Jupyter Notebook)
  • Download Data.zip for regexp (zip file)
• NumPy Documentation
• Pandas DataFrames
  • Data Carpentry Lesson: Python for ecologists
  • Pandas Documentation
  • Book: Python for Data Analysis - Data Wrangling with Pandas, NumPy, and IPython* by Wes McKinney; Publisher: O’Reilly Media; A second edition has been released.
• Plotting with Matplotlib
  • Pyplot tutorial
  • Matplotlib gallery
• Software Testing
  • Software Carpentry Lesson on Testing with Python
  • Python Testing Frameworks:
    • nose - nicer testing for python
    • nose2
    • pytest
    • Python unittest module

Version Control with Git

• Software Carpentry Lesson: Version Control with Git
• Book Pro Git by Scott Chacon and Ben Straub; in print or as free eBook
• Interactive Git Cheatsheet: http://ndpsoftware.com/git-cheatsheet.html
• Bitbucket Git tutorials: https://www.atlassian.com/git/tutorials
• GitHub: Learn the basics of Git in 15 minutes: https://try.github.io/levels/1/challenges/1
• GitHub Videos: https://services.github.com/resources/videos/
• Git for Ages 4 And Up Video (99 minutes)

Task automation / Building Pipelines

• A Simple Makefile Tutorial

Markdown

• Original Markdown site and Markdown Syntax definition.
• GitHub Mastering Markdown

LaTeX

• Wikibook Latex
• Q&A Forum: Tex Stackexchange
• Collaborative LaTeX Editor Sharelatex