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Washington State University

Apr 27-28, 2015

9:00 am - 4:30 pm

Instructors: Karl Broman, Kara Woo

Helpers: Matt Pennell, Ben Weinstein, Daniel Caetano, Matt Pruett

General Information

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.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at researchers who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively. First priority for registration will be given to affiliates of the Center for Environmental Research, Education, and Outreach, followed by the WSU community, and finally researchers from University of Idaho.

Where: Quality Inn Paradise Creek, SE 1400 Bishop Blvd rooms PC2/PC3, Pullman, WA 99163. 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.

Accessibility: The facilities for this workshop are located on the ground floor and are wheelchair accessible. Please let us know if you plan to bring a service animal, and likewise if you are allergic. Teaching materials will be available to participants before the workshop, and large print handouts can be provided on request. If you have other accessibility needs, questions, or suggestions about how we can make this workshop more accessible, please contact Kara Woo.

Contact: Please mail admin@software-carpentry.org for more information.


Schedule

Please arrive early if you have any difficulty following the software installation instructions below

Day 1

09:00 Intro to R
10:30 Coffee
10:45 Intro to R (cont'd.)
12:00 Lunch break
13:00 ggplot2
14:30 Coffee
14:45 The Unix Shell

Day 2

09:00 Version control with Git
10:30 Coffee
10:45 Version control with Git (cont'd.)
12:00 Lunch break
13:00 Functions in R; knitr
14:45 Coffee
15:00 Capstone exercise

Etherpad: https://etherpad.mozilla.org/2015-04-27-wsu.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

The Unix Shell

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

Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R from the command line
  • Reference...

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...

Setup

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection.

After installing R and Git Bash:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Double click on the file to run it.

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.

Linux

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

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.

Windows

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 installer. 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 (10.6-10.8) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.8.

Linux

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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.

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.

Windows

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.

Mac OS X

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Linux

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.