University of Maryland

A Data Carpentry Workshop

Organized by and for interdisciplinary biologists and environmental scientists.

SESYNC and Maryland's iSchool

University of Maryland

2119 Hornbake South, College Park, MD
Jan 15-16, 2015
9:00 am - 5 pm

General Information

Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.

Our curriculum includes:

Day 1 morning: Getting data out of Excel and into more powerful tools
Day 1 afternoon: Managing data in R.
Day 2 morning: Introduction to databases, combining and querying data using SQL.
Day 2 afternoon: An end-to-end example showing one possible workflow

The concepts, skills, and tools we teach are domain-independent, but example problem cases and datasets will be taken from organismal and evolutionary biology, biodiversity science, ecology, and environmental science.

Data Carpentry's teaching is hands-on, so participants are required to bring their own laptops. (We will provide instructions on setting up the required software several days in advance There are no pre-requisites, and we will assume no prior knowledge about the tools.

Updates will be posted to this website as they become available.

Instructors: Ian Munoz, Mike Smorul

Assistants: Donal Heidenblad, Andrea Wiggins, Susan Winters

Who: The course is aimed at doctoral students, postdocs, research staff, and other researchers.

Where: 2119 Hornbake South, College Park, MD. Get directions with OpenStreetMap or Google Maps The class will be in 2119 Hornbake South (enter through the doors closest to Campus Drive, not the main doors to the Hornbake Library).

Requirements: Participants must bring a laptop with a few specific software packages installed.

Contact: Please email msmorul@sesync.org for questions and information not covered here.

Twitter: #umddc

Etherpad: https://etherpad.mozilla.org/umd-2015-01-15

Acknowledgements & Support

This class is supported by the National Socio-Environmental Synthesis Center (SESYNC), Maryland's iSchool, and the Center for the Advanced Study of Communities and Information (CASCI)

Data Carpentry is a partnership of several NSF-funded BIO Centers (NESCent, iPlant, iDigBio, BEACON and SESYNC) and Software CarpentryThe structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry.

Registration

Tuition for the course is free, but prior registration is required for attending it. In order to provide the best experience class size is limited to 30. Registration is through EventBrite, see below.

Registration Form

Schedule

Thursday	09:00	Thinking beyond Excel; data wrangling in the shell
		Coffee will be served at 10:30.
	12:00	Lunch break
	13:00	Data analysis in R
		Coffee will be served at 14:30.
	16:00	Wrap-up
Friday	09:00	Managing data with SQL
		Coffee will be served at 10:30.
	12:00	Lunch break
	13:00	Bringing it all together, an end-to-end workflow
		Coffee will be served at 14:30.
	16:00	Wrap-up

Additional Resources

shell

R

Where to learn more about R

http://www.statmethods.net/ - good for data organization, basics stats and graphs
http://www.gardenersown.co.uk/Education/Lectures/R/anova.htm - basic parametric and non-parametric stats
http://www.cyclismo.org/tutorial/R/index.html - R tutorial
R in Action - good book as an R reference
http://www.twotorials.com/
http://www.r-bloggers.com/
http://tryr.codeschool.com/
Advanced R Programming by Hadley Wickham
Beginner's Guide to R from Computer World
R for Journalists
R Bloggers
inside-R
rOpenSci

Plotting in R

http://www.harding.edu/fmccown/r/ - Very simple graphs
A variety of R gallery recommendations
ggplot gallery - extensive and comprehensive; a great resource
R Graphics Cookbook - highly recommended
Some of R Graphics Cookbook plots - a set of some of the plots from the R Graphics Cookbook by Winston Chang
R Graphical Manual - plots from apparently every R CRAN package

Setup

To participate in a Data Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

Editor

When you're writing scripts or text, 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. (This will lose any unsaved changes to the file.)

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.

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).

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

Windows

Editor

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.

Git Bash

Install Git (version control) and a Bash shell for Windows from the msysGit project's homepage. This will provide you with Bash in the Git Bash program.

Software Carpentry Installer

Other tools used in Data Carpentry have been packaged up by Software Carpentry in an installer. This installer requires an active internet connection.

Download the installer.
Double click on the file to run it.
Accept all defaults.

R

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

SQLite

Install the Firefox SQLite browser plugin described below.

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.

Editor

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

R

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

SQLite

sqlite3 comes pre-installed on Mac OS X. Also install the Firefox SQLite browser plugin described below.

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

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

R

You can download the binary files for your distribution from 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.

SQLite

sqlite3 comes pre-installed on Linux. Also install the Firefox SQLite browser plugin described below.

Miscellaneous

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

Start Firefox.
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
Select "SQLite Manager" from the "Tools" menu.