Apr 18-19, 2015
9:00 am - 4:30 pm
Instructors: Gabriel Devenyi, Rachel Schwartz
Helpers: Tara Furstenau, David Winter, Ryan Middleton
Software Carpentry's mission is to help scientists and engineers 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 graduate students, post docs, and other researchers, primarily at Arizona State University.
Parking: ASU Parking Information. The Fulton Structure is the closest ($8 / day). However, other lots will be free on weekends. You may be able to park in the church parking lot on the west side of Wrigley Hall. It is $5 per day during the week, but I am not sure if they charge on the weekend. However, Sunday they are likely to be using it for services.
Contact: Please mail email@example.com for more information.
|09:00||Automating tasks with the Unix shell|
|13:00||Building programs with R|
|14:30||Iced tea / lemonade (provided)|
|09:00||Version control with Git|
|13:00||Managing data with SQL|
|14:30||Iced tea / lemonade (provided)|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
This is the saved etherpad.
This page has instructions on testing that you have the right software installed.
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.
We will be using the open-source software nano, which will be installed as part of the package listed under the sql installation.
The following alternative editors are closed-source, but are very popular alternatives.
We will be using the open-source software nano, which is pre-installed on Mac. To enable syntax highlighting (I recommend doing this after you feel comfortable on the command line) do the following:
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Download this file and unzip it into a local folder so we can work through an example together.
Install Git for Windows by download and running the installer. 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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.7) use the
most recent available installer for your
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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.
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Download the Software Carpentry Windows installer. Double click on the file to run it.
sqlite3 comes pre-installed on Mac OS X.
sqlite3 comes pre-installed on Linux.