Queen's University

Feb 21-23, 2017

9:00 am - 4:30 pm

Instructors: Jeff Stafford, Hartmut Schmider, Gang Liu, Robert Colautti

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific 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 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: Douglas Library Electronic Classroom (Room 416), Kingston, ON. 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.

Contact: Please mail jeff.stafford@queensu.ca for more information.

Lesson Materials

Link to repository with all of the workshop R scripts. Download these to your computer with the "Clone and Download" button, or fork this repository on Github.



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

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Programming with R
10:30 Coffee
12:00 Lunch break
13:00 Automating tasks with the Unix shell
14:30 Coffee
16:00 Wrap-up

Day 2

09:00 Version control with Git
10:30 Coffee
12:00 Lunch break
13:00 Programming with R (continued)
14:30 Coffee
16:00 Wrap-up

Day 3

09:00 Next Generation Sequencing Tutorial
10:30 Coffee
12:30 Wrap-up


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

  • Introduction to R and RStudio
  • Understanding R's data structures
  • Loops, conditionals, and functions
  • Dataframe manipulation with dplyr
  • Creating publication-quality graphics with ggplot2
  • Using R from the command line
  • Producing reports with knitr
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Where to host work, and why
  • Reference...

Next Generation Sequencing

  • Introduction to NGS -- technology and applications
  • Exploring short-read sequence data
  • Checking the quality of sequence data
  • De novo genome assembly
  • Aligning DNA and RNA sequences to a reference genome
  • Exploring gene expression with TopHat2 and Cufflinks
  • Reference...


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.


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.

The Bash Shell

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


Since Bash is not installed on Windows, we will use a lightweight version called MSYS2 to provide Bash and Git instead. Follow these instructions to install and setup MSYS2:

  • Download and install MSYS2 from msys2.github.io
  • Open MSYS2 (you can find it under "All Apps" -> "MSYS2_64bit")
  • Enter the command "pacman -S nano git" (if it asks for confirmation, select "y")

Mac OS X

The default shell in all versions of Mac OS X 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.


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.


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 github.com. 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 github.com 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.


Git should be installed on your computer as part of your Bash install (described above). If you wish to use the native Git client for Windows (Git Bash), you can download it here.

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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.


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 yum install git.

SSH Client

For the third day of the workshop, we will work remotely on servers provided by the Centre for Advanced Computing. To connect to these computers, you will need an SSH client.


Please install MobaXterm before the workshop. The home edition (either installer or portable version) will work fine.

Mac OS X

Your operating system includes an SSH client by default, though you may wish to install XQuartz to enable extra graphics features.


Your operating system includes an SSH client by default. You're all set!