A Data Carpentry Workshop

Organized by and for interdisciplinary biologists and environmental scientists.

iDigBio at University of Florida, Gainesville, FL

AMNH, New York, NY (via teleconference)


September 29-30, 2014

8:30 am - 5:30 pm

Instructors: Fran├žois Michonneau (FLMNH - iDigBio), Tracy Teal (MSU - BEACON), Matt Collins (ACIS - iDigBio), Katja Seltmann (TTD-TCN, AMNH)

Helpers: Dan Stoner (ACIS - iDigBio), Deborah Paul (FSU - iDigBio), Pam Soltis (FLMNH - iDigBio PI), Derek Masaki (USGS), Shari Ellis (iDigBio), Kevin Love (iDigBio), Juliet Pulliam (UF), Tommy Tang (UF), Bernardo Santos (AMNH), Jonathan Foox (AMNH)

Workshop Information

Information about the iDigBio Data Carpentry Workshop is maintained on the iDigBio Data Carpentry wiki page.

Acknowledgements & Support

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


To participate in a Data Carpentry workshop, 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 workshop.



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


We'll be using a spreadsheet program. If you already have a spreadsheet program installed, like LibreOffice, Excel or OpenOffice, you can use whatever you already have. If you don't have a spreadsheet program, please download and install LibreOffice from http://www.libreoffice.org/download/libreoffice-fresh/



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). The instructions to modify your path are available online here. 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.
  • A command window will open and then close again. The installer downloads and installs a couple of command line programs that we'll need for course.
  • If you saw it open and then close again, you're set!


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


Install the Firefox SQLite browser plugin described below.

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.


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


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


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



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.


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


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.


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


Extras - everyone needs to install these

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you will use this plugin for Firefox instead. If you don't already have firefox, install it first. To install the sqlite plugin:

  • 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.
  • To check that it was installed correctly, select "SQLite Manager" from the "Tools" menu.

Adobe Connect

We will be using Adobe Connect extensively in this workshop. Please perform the systems test using the link below. Windows and Mac users should install the Adobe Connect Add-In. Follow the link to begin the process.

Adobe Connect Systems Test