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The Jackson Laboratory

Jun 23-24, 2015

9:00 am - 4:00 pm

Instructors: Jennifer Shelton, Sue McClatchy, Narayanan Raghupathy

Helpers: Judy Yau, Larry Jacobs, Xingyao Chen

Please add your name and e-mail address to the waiting list to be contacted when another Software Carpentry session becomes available.

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 R concepts and tools including program design, plotting, functions, loops and conditionals, and command line programming. 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 open to Jackson Laboratory employees and is aimed at all academic levels from undergraduate to senior faculty. No prior programming experience is expected or required. We will create a supportive environment in which instructors assist with programming exercises and participants help one another. For this reason on-site (rather than remote) participation is required.

Where: Breezeway Bioinformatics Training Room Bldg 1 Unit 5 Room 1500 600 Main Street Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps.

See the campus map where building 1 is shown in dark blue. We'll be in the wing labeled 01e. The training room is located on the first floor near the bottom of the stairs.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). If you are using a lab owned machine please have these installed by IT before the course. IT can install required software quickly and easily, but your instructors will not be able to do so. Participants are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail for more information.


Tuesday, June 23

09:00 Welcome and introduction to RStudio
09:30 Analyzing patient data
10:30 Coffee/tea break
10:45 Creating functions
12:00 Lunch break
13:00 Analyzing multiple data sets
14:30 Coffee/tea break
14:45 Making choices
15:45 Wrap-up

Wednesday, June 24

09:00 Best practices for using R and designing programs
10:30 Coffee/tea break
10:45 Dynamic reports with knitr
12:00 Lunch break
13:00 Making packages in R
14:30 Coffee/tea break
14:45 Publication quality graphics with R
15:45 Wrap-up and next steps

Data files: inflammation data.

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R from the command line
  • Reference...

The Unix Shell

  • Command-line programs
  • Arguments, flags and files in command-line programs
  • Reading data from standard input
  • Reference...


To participate in this Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser. If you are using a lab owned laptop please ask IT to install software for you before the workshop. Your instructors don't have administrative rights to your computer and can't install software for you.


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.

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 downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.

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.

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 Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.


nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask IT to help you do this.

Mac OS X

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 Text Wrangler or Sublime Text.


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.