Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.
We will focus on teaching R programming, using shell to do more tasks more quickly, version control to track and share your work, and reproducible research. Registration is free for GREZOSP and Faculté de médecine vétérinaire de l'Université de Montréal (UdeM) members, $50 for the UdeM community, and $200 otherwise. Seats are limited! (Note: the bootcamp will be given in English, but help support in French will also be available)
Instructors: John D. Blischak, Denis Haine, Marianne Corvellec, Gabriel Devenyi
Who: The course is aimed at graduate students and other researchers, especially in epidemiology and public health.
Classroom: Local 2950, entrance via main building.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail firstname.lastname@example.org for more information.
After registering, please complete the pre-bootcamp assessment. It will only take a few minutes. We need this information to help us prepare the bootcamp as well as assess the efficacy of our teaching. Also, do not worry about survey questions on topics that we are not covering. These are included because we use the same standard survey for all bootcamps.
Before leaving, please complete the post-bootcamp survey. It will only take a few minutes. It is really appreciated!
Join the Etherpad to ask questions and find useful information during the lessons.
|8:30 - 9:00||Setup help|
|9:00||Automating tasks with the Unix shell|
|12:00||Lunch break (on your own)|
|13:00||Building programs with R|
To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).
Git is a state-of-the-art version control system. It 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.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection.
After installing R and Git Bash:
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
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager, e.g. for Debian/Ubuntu
apt-get install r-base or
yum install R.
Also, please install the