Jan 5-6, 2015
9:00 am - 4:30 pm
Instructors: Sarah Supp, Kara Woo, Christie Bahlai, Dana Bauer
Helpers: Alyxandria Schubert, Iris Holmes, Marian Schmidt, Michelle Berry
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: This workshop is for women in the University of Michigan research community. We welcome undergraduates, graduate students, faculty, and other researchers.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Contact: Please mail email@example.com for more information.
Sponsors: Thank you to our very generous sponsors for making this workshop possible.
We plan to have two rooms for each lesson: a novice room for learners who are just getting started with a particular tool or technology; and an intermediate room for folks who have some working knowledge of a particular tool or technology. The instructors will help workshop participants make decisions about which group to join.
We'll have coffee and refreshments in the morning and light snacks in the afternoon. Lunch is on your own.
|09:00||Novice room: Unix shell basics & intro to data management |
Intermediate room: Building programs with R
|13:00||Novice room: Getting started with R |
Intermediate room: Automating tasks with the Unix shell & data management topics
|09:00||Novice room: Version control with Git |
Intermediate room: Version control with Git
|13:00||Novice room: Getting started with SQL |
Intermediate room: Managing data with SQL
Etherpad links (for taking notes)
To participate in a Software Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.
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.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
Git is a state-of-the-art version control system. It 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.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection
After installing R and Git Bash:
nano is the editor installed by the Software Carpentry Installer,
it is a basic editor integrated into the lesson material.
Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.
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
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager, e.g. for Debian/Ubuntu
apt-get install r-base or
yum install R.
Also, please install the
sqlite3 comes pre-installed on Linux.
you may install the Firefox SQLite browser plugin described below.
Instead of using
sqlite3 from the command line,
you may use this plugin
for Firefox instead.
To install it:
In newer versions of Firefox, the menu bar isn't always displayed. To make
it appear, use the
Alt key next to the space bar on your
keyboard, or consult
page from Firefox for additional help.
Learners are not required to install a virtual machine (VM); however, if you run into trouble installing any of the above software onto your computer, you can use a VM instead to follow along with the lessons. To install: