Coastal Institute, University of Rhode Island
Jan 13-14, 2014
8:00 am - 4:00 pm
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:
- 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 igonzalez@mailaps.org for more information.
Setup
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.
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.
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
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.
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
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
MONDAY JANUARY 13, 2014
| 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 |
TUESDAY JANUARY 14, 2014
| 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 |
WEDNESDAY JANUARY 15, 2014
| 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 |