University of Southern Queensland

24-25 June, 2019

9.00 am - 5.00 pm

Instructors: Francis Gacenga, Adam Sparks, Richard Young

Helpers: Rachel King, Anita Frederiks, Michael Lane, Mathieu Clerte, Ron Ward, Jake Clark, Dag Evensberget

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 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 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 eResearchServices@usq.edu.au for more information.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

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.


Syllabus

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...

Setup

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.

Windows

We will supply Windows participants access to a VM running Linux. For Windows computers please install PuTTY. PuTTY is an SSH and telnet client. Install from PuTTY installer or or if using a USQ computer from within USQ install from USQ KACE.

macOS

The default shell in all versions of macOS is Bash, 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.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

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.

Windows

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

Others editors that you can use are Atom is cross-platform, works on all three major OS and is easy to use or Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

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.

Others editors that you can use are BBEdit or Sublime Text.

Linux

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

Others editors that you can use are Gedit, Kate or Sublime Text.

R

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

Windows

Video Tutorial

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.

macOS

Video Tutorial

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

Linux

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 dnf install R). Also, please install the RStudio IDE.