September 29-30, 2014
8:30 am - 5:30 pm
Instructors: François 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)
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.)
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.
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.
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.
Other tools used in Data Carpentry have been packaged up by Software Carpentry in an installer. This installer requires an active internet connection.
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
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
sqlite3 comes pre-installed on Linux.
Also install the Firefox SQLite browser plugin described below.
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.