University of Southern Queensland

24-25 June, 2019

9.00 am - 5.00 pm

Instructors: Francis Gacenga, Adam Sparks, Richard Young

Helpers: Anita Frederiks, Michael Lane, Mathieu Clerte, Dag Evensberget, Paul Melloy

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: Rooms T110 and T111 West Street Toowoomba. Get directions with OpenStreetMap or Google Maps.

When: 24-25 June, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that can join wireless networks. 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 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.


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

Pre-workshop Survey

Post-workshop Survey


Day 1 - Mon 24 Jun

Before Pre-workshop survey
09:00 Introduction to the Unix shell
10:30 Coffee
10:45 Automating tasks with the Unix shell
12:00 Lunch break
13:00 Working with shell scripts and finding things
14:30 Coffee
14:45 Programming in R
16:00 Wrap-up
16:30 END

Day 2

09:00 Programming in R
10:30 Coffee
10:45 Programming in R
12:00 Lunch break
13:00 Programming in R
14:30 Coffee
14:45 Programming in R
16:00 Wrap-up
16:30 Post-workshop Survey
16:40 END

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


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in R

  • Analyzing Patient Data, Creating Functions, Analyzing Multiple Data Sets, Making Choices
  • Command-Line Programs, Practices for Writing R Code
  • Dynamic Reports with knitr, Making Packages in R
  • Introduction to RStudio, Addressing Data, Reading and Writing CSV Files
  • Understanding Factors,Data Types and Structures,The Call Stack, Loops in R
  • Reference...


To participate in a Software Carpentry workshop, you will need to bring your own computer ready to use USQ's Wireless Network. In addition, you will need an up-to-date web browser.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly. We will supply participants access to a VM running Linux.

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. We will use Nano which will be pre-installed in the supplied VM.