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
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.
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 firstname.lastname@example.org for more information.
Please be sure to complete these surveys before and after the workshop.
|09:10||Introduction to R Part 1|
|11:00||Introduction to R Part 2|
|1:30||Unix Shell Part 1|
|3:15||Unix Shell Part 2|
|09:00||Writing R scripts|
|11:00||Data visualization with R|
|1:30||Reproducible Research Workflows with R|
|3:15||Version control with Git and Github|
We will use Etherpad collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
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
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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
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
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"
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.
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.
You can use your favorite text editor. If you do not have one, we recommend
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=$PATH:"C:\Program Files (x86)\Notepad++"
Note: if Notepad++ is installed in `Program Files` folder, use:
export PATH=$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.
You can use your favorite text editor. If you do not have one, we recommend Text Wrangler.
You can use your favorite text editor. If you do not have one, we recommend Gedit.
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.