A Data Carpentry Workshop

Washington State University

Bustad Hall, Room 145
May 14-15, 2015
8:30 am - 4:30 pm

General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover data organization in spreadsheets, data cleaning, the command line, and R for data analysis and visualization using examples from biology. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

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.

Preliminary schedule:

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

Instructors: Kara Woo (Washington State University), Naupaka Zimmerman (University of Arizona)

Assistants: Matt Pruett, Peter Olsoy, Eliot Miller

Who: The course is aimed at faculty, research staff, postdocs, graduate students, advanced undergraduates, and other researchers in any field. No prior computational experience is required.

Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (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. Participants are required to abide by Software Carpentry's Code of Conduct.

Contact: Please email naupaka@gmail.com for questions and information not covered here.

Twitter: @datacarpentry #datacarpentry #dcwsu

Etherpad: https://etherpad.mozilla.org/2015-05-14-WSU-DataCarpentry

Acknowledgements & Support

Data Carpentry is supported by the Gordon and Betty Moore Foundation and 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

Registration is through EventBrite, see below.


Setup

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 bootcamp. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Overview

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.

OpenRefine

OpenRefine (formerly Google Refine) is a powerful tool for exploring and working with messy data.

Windows

R

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

SQLite

Download and unzip the SQLite3 software from this link. Also, please install the Firefox SQLite browser plugin described below.

OpenRefine

Download the OpenRefine software described below.

Mac OS X

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.

OpenRefine

Download the OpenRefine software described below.

Linux

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.

OpenRefine

Download the OpenRefine software 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.

OpenRefine

Head to the OpenRefine download page for information on how to install it. It will run through a browser, but will not need to use an internet connection, and your data will also be securely stored on your own computer.