Coastal Institute, University of Rhode Island

Hazard Conference Room, 215 South Ferry Road, Narragansett, RI 02882
Jan 13-14, 2014
8:00 am - 4:00 pm

Etherpad Link

Hosts: Co-hosted by The Coastal Institute of the University of Rhode Island and the US Environental Protection Agency's, Atlantic Ecology Division

Instructors: Patrick Fuller, Ivan Gonzalez

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:

Contact: Please mail for more information.


Participants in the bootcamp should have installed some software in their laptops *prior* to arriving to the bootcamp. Please follow the instructions below for your operating system.

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.

Windows / Git Bash

Install Git Bash following these instructions. This gives you Git as well as Bash.

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.

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.


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.

Windows / Editor

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

Mac OS X / Editor

We recommend Text Wrangler or Sublime Text.

Linux / Editor

Kate is one option for Linux users.


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

Windows / Git Bash

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

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.

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).


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).

Bootcamp Schedule


Topic Date Time Instructor
Welcome and Introduction 01/13/2014 8:00 AM - 8:10 AM Jeff Hollister
Logistics and Software Test 01/13/2014 8:10 AM - 8:30 AM Ivan Gonzalez
Using the Shell 01/13/2014 8:30 AM - 10:00 AM Patrick Fuller
BREAK 01/13/2014 10:00 AM - 10:15 AM
Introduction to R and RStudio 01/13/2014 10:15 AM - 12:00 PM Patrick Fuller
LUNCH 01/13/2014 12:00 PM - 12:45 PM
Dealing with Data in R 01/13/2014 12:45 PM - 2:30 PM Jeff Hollister
BREAK 01/13/2014 2:30 PM - 2:45 PM
R Functions 01/13/2014 2:45 PM - 4:00 PM Jeff Hollister


Topic Date Time Instructor
Git 01/14/2014 8:00 AM - 10:00 AM Ivan Gonzalez
BREAK 01/14/2014 10:00 AM - 10:15 AM
Git and GitHub 01/14/2014 10:15 AM - 12:00 PM Ivan Gonzalez
LUNCH 01/14/2014 12:00 PM - 12:45 PM
Testing and Debugging with R 01/14/2014 12:45 PM - 2:30 PM Ivan Gonzalez
BREAK 01/14/2014 2:30 PM - 2:45 PM
Introduction to Databases 01/14/2014 2:45 PM - 2:30 PM Patrick Fuller


Topic Date Time Instructor
Intro to Data Viz in R 01/15/2014 8:00 AM - 10:00 AM Jeff Hollister
BREAK 01/15/2014 10:00 AM - 10:45 AM
Wrap-up and next steps 01/15/2014 10:45 AM - 12:00 PM
LUNCH 01/14/2014 12:00 PM - 12:45 PM

Reference Guides