• Bash shell, called Windows Subsystem for Linux (WSL), is available on Windows 10+! There are many online guides to activating it.
  • If you are working on a new Mac, you will likely have zsh as your default command-line environment when you open a terminal. To change this, type chsh -s /bin/bash in the terminal.
  • To work with python3, we have converted the example scripts. You can download them here. Let us know if you find any incompatibilities.
  • We have made available the Reference Tables from the Appendices! These handy tables can be used as a quick PDF reference guide (cheat sheets) for regular expressions, bash shell, python, and mysql commands.
  • Good news: you don't have to download the full XCode to get a compiler. Just sign up at the Apple Developer Page and scroll down to the Command Line Tools for your OS.
  • A review appeared in the Quarterly Review of Biology. Don't pay the $14 to download, but take our word for it: they liked the book ;^)
  • We got a very nice blog review. Some great quotes in there.
  • We got a nice little recommendation in Nature Reviews Genetics. (Look for reference 92.)
  • We were the subject of an insightful review in the journal Cell!
  • There was also a friendly notice in the Software Carpentry blog.


This is the companion site of the book Practical Computing for Biologists by Steven Haddock and Casey Dunn, available from Oxford University Press.

The book shows you how to use general computing tools to work more effectively. In one place, it pulls together a broad range of powerful and flexible tools that are applicable to ecologists, molecular biologists, physiologists, and anyone who has struggled with large or complex data sets. Training in python and data processing is essential for biologists and other scientists. Going beyond the subjects taught in most programming and bioinformatics courses, the book covers:

• Reformatting data with regular expressions
• The Unix command line
• Combining and automating analyses
• Python programming and debugging
• Creating and editing graphics
• Databases
• Performing analyses on remote computers

A one-page flyer describing the book can be downloaded here

On this site you can download example files, seek help from other researchers, and give feedback about the book. You can also enter into conversation via our Facebook page.