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Pennsylvania State University

Jun 22-23, 2015

9:00 am - 4:30 pm

Instructors: Bradley Taber-Thomas, Emily Davenport

Helpers: Dan Nugent, Chloe Callahan-Flintoft, Greg Snow

General Information

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.

Where: Room 115 Keller Building, Penn State, University Park, PA 16802. Get directions with OpenStreetMap or Google Maps.

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 ( for more information.


Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Introduction to data processing in Matlab
14:30 Coffee
16:30 Wrap-up

Day 2

09:00 Testing and debugging in Matlab and reproducible research practices
10:30 Coffee
12:00 Lunch break
13:00 Version control with Git
14:30 Coffee
16:30 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
A saved version of the final etherpad is located here.


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...
  • Lesson notes ...

Programming in MATLAB

  • Analyzing Patient Data
  • Writing MATLAB Scripts
  • Repeating With Loops
  • Creating Functions
  • Making Choices
  • Defensive programming
  • Reference...
  • Lesson notes...
  • Download (transfer to your work folder on Hammer, or we will in class)

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...
  • Lesson notes ...


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.

#The Bash Shell

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.

Mac OS X

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 in /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 install anything.


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 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).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, 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" available here.


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.

#Text Editor

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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.


nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

#Matlab via Hammer

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:

  1. Request an account through the Institute for CyberScience-- click "Individual User Account" on the left menu at the ICS System Accounts page, log in, and provide the requested information. Be sure to check the "Hammer" box under "ICS Linux Clusters." In the computational and data requirements box enter "minimal; learning to use ICS clusters." Other questions can be answered individually.
  2. Follow the ICS instructions to install Exceed onDemand for your operating system. The instructions also describe how to log in to Hammer in Exceed onDemand; please make sure you can login before the workshop, as it will be difficult to address login issues during the workshop.
  3. We will go over opening Matlab on Hammer during the workshop.