University of Texas at Arlington

Sep 22-23, 2018

9:00 am - 5:00 pm

Instructors: Balan Ramesh, Adnan Qureshi, Farah Shamma, Joe Cloud, Rich Adams, James Titus-McQuillan

Helpers: Peace Ossom-Williamson, Nitin Kanwar, Daren Card, Anna Williford, Raisa Mustafi

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is for everyone who is interested in learning basic computational tools. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: UTA campus, Main Library, 6th floor. Get directions with OpenStreetMap or Google Maps.

When: Sep 22-23, 2018. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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.

Contact: Please email awillifo@uta.edu for more information.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1 Sep 22

09:00 Pre-workshop survey
09:10 Introduction to R Part 1
10:45 Coffee
11:00 Introduction to R Part 2
12:30 Lunch break
1:30 Unix Shell Part 1
3:00 Coffee
3:15 Unix Shell Part 2
5:00 END

Day 2 Sep 23

09:00 Writing R scripts
10:45 Coffee
11:00 Data visualization with R
12:30 Lunch break
1:30 Reproducible Research Workflows with R
3:00 Coffee
3:15 Version control with Git and Github
4:50 Post-workshop Survey
5:00 END

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



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 below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select “Use the nano editor by default” and 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. Select "Use Windows' default console window" 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.

macOS

The default shell in all versions of macOS 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).

macOS

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. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. 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 dnf 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 macOS 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

You can use your favorite text editor. If you do not have one, we recommend Notepad++. Be aware that you must add its installation directory to your system path. To add Notepad++ to the path:
1) Open Git-Bash from the start menu.
2) Type: cd [enter] to make sure you are in your home directory.
3) Type: notepad .bashrc [enter]. This will create .bashrc file in Notepad. Add the following text to the file:
export PATH=$PATH:"C:\Program Files (x86)\Notepad++"
alias npp=notepad++
Note: if Notepad++ is installed in `Program Files` folder, use:
export PATH=$PATH:"C:\Program Files\Notepad++"
4) Save the file and exit Notepad.
5) Open a new Git-Bash window.
You should now be able to launch Notepad++ by typing: npp [enter]. If you run into trouble please ask your instructor to help you with this.

macOS

You can use your favorite text editor. If you do not have one, we recommend Text Wrangler.

Linux

You can use your favorite text editor. If you do not have one, we recommend Gedit.

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. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

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 dnf install R). Also, please install the RStudio IDE.