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Havard School of Public Health

Mar 23-24, 2015

9:00 am - 5:00 pm

Instructors: Ivan Gonzalez, Meeta Mistry

Helpers: Radhika Khetani, Mary Piper

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.

Who: The course is part of the NGS Data Analysis Course (Spring 2015).

Where: 260 Longwood Ave, Boston, MA 02115 (Toteson Medical Education Center, room 130). Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail for more information.

Pre-workshop office hours: We are holding office hours to help those who find problems installing the required software on Friday, March 20th (room 438B in HSPH building 2, this is the preferred option) and from 8:30 am to 9 am on workshop's first day. You need to schedule your slot here.

Files: Please download these files for the corresponding lessons: shell.


Day 1

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

Day 2

09:00 Introduction to R
10:30 Coffee
12:00 Lunch break
13:00 Analyzing data with R
14:30 Coffee
16:00 Wrap-up

We will use this Etherpad 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...

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...

Programming in R

  • Introduction to RStudio
  • Basic R syntax
  • Working with vectors and data frames
  • Installing packages and using functions
  • Calculating simple statistics and creating plots
  • Reference...


In addition to what is described below, you will need to install other software for the reminder of the NGS Data Analysis course.

The Bash Shell

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


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

Software Carpentry Installer

This installer requires an active internet connection.

After Git Bash:

  • Download the installer.
  • Double click on the file to run it.

Information about the SWC Windows Installer, including the source code, can be found at

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). 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


Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. 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 (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.


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.


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


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

Mac OS X

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.