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University of Southern Queensland

25 September, 2017


Instructors: Rachel King, Russell Waldron, Francis Gacenga

Helpers: Samanthi Suraweera, Richard Young, Ron Ward

General Information

Software Carpentry's mission is to help researchers get more research done in less time and with less pain by teaching them basic lab skills for research computing. 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 research staff and students. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room T110, West Street Toowoomba. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible toilets are available.

Contact: Please mail for more information.



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

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 R for Reproducible Scientific Analysis
10:30 Tea/Coffee
10:45 R for Reproducible Scientific Analysis
11:30 R for Reproducible Scientific Analysis
12:00 Lunch break
12:30 Automating tasks with the Unix shell
14:00 Tea/Coffee
14:15 Version control with Github
16:45 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

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 simple tasks more quickly. We will use Jupyter.


For Windows computers please also install PuTTY. PuTTY is an SSH and telnet client. Install from PuTTY or if using a USQ computer from within USQ install from: USQ Software Repo PuTTY.


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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

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.


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


Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.


You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.