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Material for Computing Skills for Biologists
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Git repository accompanying the book:

Computing Skills for Biologists --- A Toolbox by Stefano Allesina & Madlen Wilmes, Princeton University Press, 2019.

See also the website for news, errata, and extra material.

How to download the material:

Install Git

To download all the material, you first need to install Git. The instructions are here.

Once you have installed Git, open a Terminal:

Linux Ubuntu

Press Ctrl + Alt + T or open the dashboard and type terminal.


The application Terminal is located in Utilities within Applications.


When you install Git, the program GitBash is installed automatically. Open GitBash.

Clone the repository

The terminal should open in your home folder. Type

git clone

The command downloads all the material on your computer. To make sure you everything went well, type:

ls CSB/

If you see a list of directories, everything is good. You can close the terminal.

Organization of the material

For each of the chapters, we provide a directory containing:

  • installation: instructions on how to install the software.
  • data: the data used for example and exercises; for each data set, see the about file for a reference to the original article and a link to the Dryad record.
  • sandbox: where you should be working.
  • solutions: contains the solution to the exercises at the end of each chapter. A full solution is provided in the appropriate language (e.g., Python, R, SQL), as well as a pdf file. A markdown file contains the description of the solution in plain English: if you are stuck on an exercise, check this file out first, and get inspired to solve the problem.


Much of the data used for the exercises and examples was published through the Dryad Digital Repository. We want to thank all the scientists who made their data available without restrictions. For each data set, a citation for the original paper and a link to the Dryad record are provided.


For any question, or to signal a bug, typo, etc. please contact us at

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