Data Carpentry

Data Carpentry

Quick Links for Data Carpentry
Data Carpentry Agenda
Data Carpentry Biblio Entries
Data Carpentry Report

This wiki supports the Data Carpentry Workshop held simultaneously at the University of Florida at iDigBio and AMNH on September 29-30, 2014. It is the first in a series of four biodiversity informatics workshops planned in the upcoming year (2014-2015) for iDigBio. The next workshop in this series is Data Sharing, Data Standards, and Demystifying the IPT (January 13-14, 2015).

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: Better spreadsheet skills and introduction to more powerful tools
  • Day 1 afternoon: Introduction to databases, combining and querying data using SQL
  • Day 2 morning: Introduction to the shell, Introduction to R and managing data in R
  • Day 2 afternoon: Collaborative data management & publishing data

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.

Software Installation Requirements and additional information is available at the github web site for the project:

Planning Team

François Michonneau (FLMNH - iDigBio), Katja Seltmann (TTD-TCN, MNH), Matt Collins (ACIS - iDigBio), Dan Stoner (ACIS - iDigBio), Deborah Paul (FSU - iDigBio), Tracy K. Teal (BEACON), Pam Soltis (FLMNH - iDigBio PI), Derek Masaki (USGS - BISON), Shari Ellis (iDigBio), Kevin Love (iDigBio), Mike Smorul (SESYNC), Juliet Pulliam (UF), Ming Tang (Tommy) (UF), and assistance from Nirav Merchant at iPlant.


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

Assistants: 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)

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

Skill Level: Beginner. Data Carpentry courses are meant for novices.

Where: iDigBio in Gainesville, FL and AMNH (AMNH in New York City via teleconference)

Requirements: Participants must bring a laptop with a few specific software packages installed. If you will be travelling from out of town, you will need to make your own travel arrangements.

Contact: Please email for questions and information not covered here.

Twitter: #datacarpentry

Tuition for the course is free, but prior registration is required for attending. You can register here.

Workshop Evaluation

Software Installation Details

Software needed for Data Carpentry Workshop at iDigBio

We use Adobe Connect extensively in this workshop. Please perform the systems test using the link below. Also, you will also need to install the Adobe Connect Add-In to participate in the workshop.


Course Overview - Day 1
8:30-8:45 Introductions & Overview, Data Carpentry: Making data science more efficient All, Deb Paul
8:45-9:00 Linking Heterogeneous Data in Biodiversity Studies: the need for data carpentry Pam Soltis, iDigBio PI
9:00-10:00 Better use of spreadsheets, part I Tracy Teal
10:00-10:30 Break
10:30-12:00 Better use of spreadsheets part II Tracy Teal
12:00-1:30 Lunch (with OpenRefine Demo) Deb Paul
1:30-3:00 SQL Introduction Matt Collins
3:00-3:30 Break
3:30-5:00 SQL part II Matt Collins
5:00-5:30 Review / Wrap up for tomorrow
Course Overview - Day 2
8:30-10:00 Introduction to the shell Tracy Teal
10:00-10:30 Break
10:30-12:00 Introduction to R François Michonneau
12:00-1:30 Lunch
1:30-3:00 Manipulating and plotting data in R François Michonneau
3:00-3:30 Break
3:30-4:30 Getting data in and out of R: How to integrate R in your workflow François Michonneau
4:30-5:00 Sharing your data and your results: RMarkdown and Figshare François Michonneau
5:00-5:30 Review / Wrap up / Evaluation and Feedback

Future plan: Scaling it up: Demo using the iPlant Discovery Environment (DE)

Link to Workshop Report

Data Carpentry - Please can we have some more?!


Adobe Connect Access

Adobe Connect will be used to provide access for a remote classroom at the American Museum of Natural History. Workshop participants will be encouraged to be logged in to the Adobe Connect room to facilitate sharing with this remote group: Already registered and accepted?

Presentation Documents and Links

Links to any presentations (like power points) here.

Workshop Recordings

Day 1


Data Carpentry Resources and Links

Links from You

Related Blog Posts and Photos

Digitization Training Workshops Wiki Home