Oct 15-16, 2016
9:00 am - 5:00 pm
Instructors: Daren Card, Devendra Umbrajkar, Gaurav Kolekar, Kevin Vilbig, James Titus-McQuillan, Heath Blackmon
Helpers: Sailee Pawar, Anna Williford
Software Carpentry's mission is to help scientists across all disciplines 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 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.
Who: The course is aimed at anyone who is interested in learning new tools. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
|09:00||Unix Shell 1 Linux lesson; Linux Commands|
|11:00||Unix Shell 2 Data; Shell History|
|1:30||Version Control with Git 1: Git Intro; Git lesson Lesson materials for both afternoon sessions|
|3:15||Version Control with Git 2|
|09:00||Introduction to R 1: R basics lesson|
|11:00||Introduction to R 2: R functions lesson; R functions files|
|1:30||Reproducible Research Workflows with R 1 Data analysis with R Lessons materials for both afternoon sessions|
|3:15||Reproducible Research Workflows with R 2|
Lessons: Our lessons are based on lessons developed by Software Carpentry Foundation
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Saved latest version of Etherpad (after the workshop) is here.
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.
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
/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
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).
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
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 yum 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 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.
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++"
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.