Newcastle University

11 - 13 April, 2022

09:00 - 16:30

Instructors: Dr. Jannetta Steyn, Dr. Kate Court

Helpers: Imre Draskovits, Stuart Lewis

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: TBA. Get directions with OpenStreetMap or Google Maps.

When: 11 - 13 April, 2022. Add to your Google Calendar.

Requirements: Please bring your own laptop if you wish. Otherwise, there will be computers available for you to use.

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Etherpad link:

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1
Day 2
Start End Length Episode
09:00 09:15 00:15:00 Intro and pre-workshop survey
09:00 09:30 00:30:00 Introduction to MarkDown
09:45 09:50 00:05:00 Introducing the Shell (5 minutes)
09:50 10:30 00:40:00 Navigating Files and Directories (40 minutes)
10:30 10:45 00:15:00 BREAK
10:40 11:30 00:50:00 Working With Files and Directories (50 minutes)
11:30 12:05 00:35:00 Pipes and Filters (35 minutes)
12:05 13:00 00:55:00 LUNCH
13:00 13:50 00:50:00 Loops (50 minutes)
13:50 14:20 00:30:00 Shell Scripts (45 minutes)
14:35 14:50 00:15:00 Shell Scripts
14:50 15:05 00:15:00 BREAK
15:00 15:45 00:45:00 Finding Things (45 minutes)
15:45 15:45 FINISH
Start End Length Episode
09:00 09:15 00:15:00 Introduction (15 minutes)
09:15 09:20 00:05:00 1. Automated Version Control
09:20 09:25 00:05:00 2. Setting Up Git
09:25 09:35 00:10:00 3. Creating a Repository
09:35 09:55 00:20:00 4. Tracking Changes
09:55 10:20 00:25:00 5. Exploring History
10:20 10:25 00:05:00 6. Ignoring Things
10:25 11:10 00:45:00 7. Remotes in GitHub
11:10 11:25 00:15:00 Break (15minutes)
11:25 11:50 00:25:00 8. Collaborating
11:50 12:05 00:15:00 9. Conflicts
12:05 12:15 00:10:00 10. Open Science
12:15 12:20 00:05:00 11. Licensing
12:20 12:25 00:05:00 12. Citation
12:25 12:35 00:10:00 13. Hosting
12:35 12:35 Lunch
Start End Length Episode
13:35 13:45 00:10:00 1. Introduction
13:45 14:20 00:35:00 2. Working with OpenRefine
14:20 14:40 00:20:00 3. Filtering and Sorting with OpenRefine
14:40 14:55 00:15:00 BREAK
14:55 15:15 00:20:00 4. Examining Numbers in OpenRefine
15:15 15:35 00:20:00 5. Using scripts 
15:35 15:50 00:15:00 6. Exporting and Saving Data from OpenRefine
15:50 16:00 00:10:00 7. Other Resources in OpenRefine
16:00 16:00 FINISH
Day 3
Start End Length Episode
09:00 09:30 00:30:00 1. Python Fundamentals
09:30 10:30 01:00:00 2. Analyzing Data
10:30 10:45 00:15:00 BREAK
10:45 11:15 00:30:00 3. Visualizing Data
11:15 12:00 00:45:00 4. Storing Multiple Values in Lists
12:00 12:30 00:30:00 5. Repeating Actions with Loops
12:30 13:30 01:00:00 LUNCH
13:30 14:30 01:00:00 6. Analyzing Data From Mutliple Files
14:30 14:45 00:15:00 BREAK
14:30 15:00 00:30:00 7. Making Choices
15:00 15:30 00:30:00 8. Creating Functions
15:30 15:40 00:10:00 Post workshop survey
15:40 16:00 00:20:00 Questions and Answers
16:00 16:00 FINISH


We will provide access to the required software through a web browser. If you wish to setup the software on your own device in the future, you can find instructions below. Please note you may need administrative privileges.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    7. Ensure that "Use Windows' default console window" is selected and click on "Next".
    8. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    9. Ensure that "Git Credential Manager Core" is selected and click on "Next".
    10. Ensure that "Enable file system caching" is selected and click on "Next".
    11. Click on "Install".
    12. Click on "Finish" or "Next".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.


Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on You will need a supported web browser.

You will need an account at for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.


Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

  1. Open with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

Video Tutorial

  1. Open with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.