A Data Carpentry Workshop
Organized by and for interdisciplinary biologists and environmental scientists.
NESCent
2024 W. Main Street, Suite A200, Durham, NCMay 8-9, 2014
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: Collaborative data management & publishing data.
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, and NESCent does have a few loaner laptops if you can't bring one.) 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: Karen Cranston (NESCent), Hilmar Lapp (NESCent), Tracy Teal (BEACON), Ethan White (Utah State U.)
Assistants: Darren Boss (iPlant), Matt Collins (iDigBio), Deb Paul (iDigBio), Mike Smorul (SESYNC)
Who: The course is aimed at graduate students, postdocs, research staff, and other researchers.
Where: 2024 W. Main Street, Suite A200, Durham, NC. NESCent has directions on its website; or get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a few specific software packages installed. If you will be traveling from out of town, you will need to make your own travel arrangements; note also that the course dates are right before the start of Duke graduation weekend, and therefore please secure needed accomodations before registering!
Contact: Please email datacarpentry@nescent.org for questions and information not covered here.
Twitter: #datacarpentry
Etherpad: https://etherpad.mozilla.org/nescent-2014-05
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.
Registration
Tuition for the course is free, but prior registration is required for attending it. Registration is through EventBrite, see below.
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 | Automating data workflows | |
| 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.