General Information

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)

To register, please send this registration form to Liliane Fortin. For any question on the program, contact Denis Haine.

Thursday November 6

Friday November 7

The Unix Shell

• Files and directories: pwd, cd, ls, mkdir, ...
• History and tab completion
• Pipes and redirection
• Looping over files
• Creating and running shell scripts
• Finding things: grep, find, ...
• Reference...

Programming in R

• Working with vectors and data frames
• Reading and plotting data
• Creating and using functions
• Loops and conditionals: for, if, else, ...
• Using R from the command line
• 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
• Open licenses
• Where to host work, and why
• Reference...

Workflow for epidemiological data analysis

• Data structure
• Data manipulation
• Data visualization
• Reproducible research

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

R

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

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.

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

R

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

Software Carpentry Installer

This installer requires an active internet connection.

After installing R and Git Bash:

• Download the installer.
• If the file opens directly in the browser select File→Save Page As to download it to your computer.
• Double click on the file to run it.

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 in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

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.

R

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

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get or yum).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

R

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