University of Chicago

Sep 15-16, 2016

8:00 am - 4:30 pm

Instructors: John Blischak, Emily Davenport

Helpers: Nick Knoblauch, Sahar Mozaffari, Joyce Hsiao, Daniel Rabe, Gao Wang

The following links will be useful during the workshop:


Registration is required and is limited to those affiliated with the Biological Sciences Division. Please register at

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 is aimed at intermediate programmers that know the basics of R and want to learn more. It is ideal for past attendees of our novice Software Carpentry workshops (e.g. 2013, 2014), incoming graduate students that attended the MBL bootcamp, and graduate students or postdocs that currently use R for their research.

Coffee and lunch will be provided both days.

This workshop will cover the same material as last year's workshop.

Who: The course is limited to graduate students and other researchers in the Biological Sciences Division at the University of Chicago.

Prerequisites: Attendees should be familiar with the basics of navigating a filesystem in a Unix-like shell and writing functions and loops in R. If you are new to programming, you should consider attending our Introduction to R workshop.

Where: Stuart 101, 5835 South Greenwood Avenue Chicago, IL 60637. 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.

Funding: This workshop was made possible through the generous sponsorhip of the Office of Graduate and Postdoctoral Affairs, the Department of Human Genetics, and the Department of Biochemistry and Molecular Biology.

Faculty advisors: Allan Drummond, Matthew Stephens, Mark Abney

Administrators: Lisa Anderson, Candice Lewis

Contact: Please mail for more information.


Sep 15

08:00 am - 08:30 am - Installation help
08:30 am - 10:00 am - Review of Unix shell and R
10:00 am - 10:30 am - Coffee break
10:30 am - 12:00 pm - Writing reproducible reports
12:00 pm - 01:00 pm - Lunch
01:00 pm - 02:30 pm - Analyzing data with dplyr
02:30 pm - 03:00 pm - Coffee break
03:00 pm - 04:30 pm - Visualizing data with ggplot2

Sep 16

08:00 am - 08:30 am - Installation help
08:30 am - 10:00 am - Version control with Git
10:00 am - 10:30 am - Coffee break
10:30 am - 12:00 pm - Version control with Git
12:00 pm - 01:00 pm - Lunch
01:00 pm - 02:30 pm - Debugging
02:30 pm - 03:00 pm - Coffee break
03:00 pm - 04:30 pm - Defensive programming


Review of the Unix shell and R programming

We will start with a refresher on the Unix shell and R programming. Specifically, we will quickly review how to manage files with the Unix shell and write loops and functions in R. This will ensure that everyone is reminded of the relevant syntax needed for the rest of the workshop.

Writing reproducible reports

We will introduce the concept of literate programming, in which code, plots, and text are combined into one document. This makes it easier to organize a research project and share the results. Specifically, we will use knitr/rmarkdown/pandoc to convert R code into html, pdf, and Word documents.

Exploring and visualizing data

We will teach how to subset, summarize, and clean a data set using the R package dplyr. Furthermore, we will demonstrate how to visualize multivariate data using the popular graphics package ggplot2.

Tracking code development

We will cover how to track code development using the version control software Git. This facilitates both experimenting with new ideas and the ability to reproduce past results with a specific version of the code. Furthermore, we will teach how to share their code online and collaborate using the website GitHub.

Debugging, defensive programming, and automated testing

We will cover multiple aspects of ensuring that code is working correctly. This will include how to debug functions, programming defensively by including assertion statements to check code behavior, and writing tests that can be run automatically.


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.

The Bash Shell

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


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

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). 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 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 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).

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.

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.


Video Tutorial

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.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.


nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.


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.

R packages

Please install the following R packages using install.packages: