Jun 22-23, 2015
9:00 am - 4:30 pm
Instructors: Bradley Taber-Thomas, Emily Davenport
Helpers: Dan Nugent, Chloe Callahan-Flintoft, Greg Snow
SLEIC is running a free two-day Software Carpentry bootcamp at Penn State, University Park. 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, using Unix, Matlab, and Git. 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".
Click here to REGISTER!
Who: The workshop is aimed broadly at graduate students and scientists of brain, cognition, and psychology.
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. No prior programming experience is required, but general computing skills and enthusiasm to learn programming will help you get the most out of the workshop!
Contact: Please mail Bradley Taber-Thomas (firstname.lastname@example.org) for more information.
|09:00||Automating tasks with the Unix shell|
|13:00||Introduction to data processing in Matlab|
|09:00||Testing and debugging in Matlab and reproducible research practices|
|13:00||Version control with Git|
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. If you are using a University computer and have any trouble getting Bash, Git, a code/text editor, and Exceed On Demand installed via the IT department, please get in touch so we can help. Bradley Taber-Thomas also has weekly programming office hours on Wednesdays, 2:30-4pm, in 267 Moore; feel free to stop by if you need assistance setting up.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by downloading 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. 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.
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Matlab is commercial software and an expensive liscense is needed to install it. Thus, we will be using Matlab via a virtual machine connected to Hammer, one of the University's computing clusters. This is a simple way to access Matlab, and will give you some familiarity with using the high performance computing clusters on campus. If you do not already have a Hammer account, or Exceed onDemand installed, follow these instructions to set them up: