University of Missouri - Kansas City

TBD
Feb 15-16, 2014
9:00 am - 4:30 pm

Instructors: Emily Jane McTavish, Jonah Duckles

What: Our goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. Attendants are offered online office hours: regular events to get one-on-one help from Software Carpentry instructors, online.

Who: The course is aimed at postgraduate students and other scientists 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.

Requirements: Participants must bring a laptop with a few specific software packages installed. (The list will be sent to participants a week before the bootcamp.)

Content: The syllabus for this bootcamp will include:

using the shell to do more in less time
using version control to manage and share information
basic R programming
how (and how much) to test programs
documentation and debugging

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

Etherpad

Etherpad for shared notes

Setup

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

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.

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.

R

R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

The instructions for installing each of these components is organzed below by operating system.

MacOSX

Mac OS X / Bash

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.

Mac OS X / Editor

We recommend Text Wrangler.

Mac OS X / Git

Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.

For Mac OS X 10.7 and 10.8:

Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.

For Mac OS X 10.6

If you have Mac OS X 10.6, first get XCode by going to the Apple developer site. You have to sign in with an Apple ID linked to a Developer account. If you don't have one, you can register and create one. Once you log in, go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard". Click to open that section, and then download the .dmg file. Finally, install just git.

Mac OS X

Install R by downloading and running this .pkg file from The Comprehensive R Archive Network (CRAN). Also, please install the RStudio IDE.

Windows

Windows / Git Bash

Install Git Bash following the instructions here. This gives you Bash as well as Git.

Windows / Editor

Notepad++ is a popular free code editor for Windows.

Windows

Install R by downloading and running this .exe file from The Comprehensive R Archive Network (CRAN). Also, please install the RStudio IDE.

Linux

Linux / Bash

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.

Linux / Git

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Linux / Editor

Kate is one option for Linux users.

GNU/Linux

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

Testing

Reference Guides

The Unix Shell