Software Carpentry

An introductory programming workshop for UChicago BSD researchers

Thursday-Friday, Sep 20-21, 2018

Registration

Registration is required and is limited to those affiliated with the Biological Sciences Division.
Please register at 2018-09-20-chicago.eventbrite.com (password: uchicago)


General Information

This interactive workshop will cover the basics of R, the Unix shell, and version control. R is a computing environment that is especially powerful for data exploration, visualization, and statistical analysis.

Coffee and lunch will be provided.

When: 8:00 am - 4:30 pm, Thursday-Friday (Sep 20-21), 2018

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

Prerequisites: There are no prerequisites. Attendees are expected to have no (or little) previous programming experience.

Where: CLSC 119, 924 E 57th St, 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).

Instructors: Arjun Biddanda, Nicholas Knoblauch, Briana Mittleman

Faculty advisor: Allan Drummond

Administrator: Sue Levison

Funding: This workshop was made possible through the generous sponsorship of the Department of Human Genetics, and the Department of Biochemistry and Molecular Biology.

Contact: Please mail abiddanda@uchicago.edu or nwknoblauch@uchicago.edu for more information.


Schedule

Sep 20

08:00 am - 08:30 am - Installation and troubleshooting
08:30 am - 09:00 am - Introduction to RStudio
09:00 am - 10:00 am - Analyze data with R
10:00 am - 10:30 am - Break
10:30 am - 12:00 pm - Organize your code with R functions
12:00 pm - 01:00 pm - Lunch
01:00 pm - 02:30 pm - Automate tasks with loops
02:30 pm - 03:00 pm - Coffee break
03:00 pm - 04:30 pm - Make choices with if/else statements

Sep 21

08:00 am - 08:30 am - Installation and troubleshooting
08:30 am - 10:00 am - Introduction to the Unix shell
10:00 am - 10:30 am - Break
10:30 am - 12:00 pm - Introduction to the Unix shell (cont)
12:00 pm - 01:00 pm - Lunch
01:00 pm - 02:30 pm - Version control with Git and GitHub
02:30 pm - 03:00 pm - Break
03:00 pm - 04:30 pm - Using Git with RStudio

Syllabus

Introduction to RStudio

We will introduce the basic functionalities of RStudio, a useful integrated development environment (IDE) for writing R code.

Analyze data with R

We will demonstrate how to import a data set, calculate descriptive statistics, and create some basic plots.

Organize your code with R functions

We can extend R by converting common routines into functions. This allows us to execute the same commands on many different input arguments. Best of all, writing functions makes it easier to read and maintain your code. In this lesson, we convert the analysis we performed in the previous lesson into a function that can then be applied to any similar input data set.

Automate tasks with loops

One of the main advantages of writing code over using spreadsheet software is that it is easier to repeat the analysis on new data sets. In this lesson, we use loops to automatically apply the function we wrote in the previous lesson to process multiple data sets.

Make choices with if/else statements

Automated data analysis pipelines can be made even more powerful by allowing the code to make decisions based on the input parameters and data. In this lesson, we modify our code from the previous lessons so that it will save the analysis plots to a specific file only if we provide a filename as input. This allows us to choose whether to immediately view the results in the RStudio window or save the results to a file.

Introduction to the Unix shell

We will introduce the Unix shell and motivate it's usefulness. Specifically, we will quickly introduce how to manage files with the Unix shell and how to navigate the file system.

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.


Setup

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.

Windows

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.

Linux

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

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 github.com. 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 github.com 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.

Windows

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.

Linux

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

To create small files in this workshop, you will use the basic text editor nano. It's a much different experience from the text editor you are likely familiar with for creating documents, e.g. Microsoft Word, but it is very convenient for writing short scripts.

Warning: 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.

Windows

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.

Linux

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

R

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

Windows

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.

Linux

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.

Acknowledgments

This workshop was made possible by the instructor training and lesson development created by the Software Carpentry team and of course our generous sponsors (OGPA, HG, BMB).

This page was generated by GitHub Pages using the Architect theme by Jason Long.