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A Data Carpentry Workshop

University of Cambridge

11-12 Septemper 2017

9:30 - 17:30

Instructors: Marco Chiapello, Laurent Gatto, Hugo Tavares


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 and OpenRefine, Introduction to R, Data analysis and visualization in R and SQL for data management. Participants are expected 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.

Who: The course is aimed at graduate students and other researchers.

Where: Bioinformatics Training Room, Craik-Marshall Building, Downing Site. Get directions with OpenStreetMap or Google Maps.

Requirements: Computers with all necessary software for this course are available in the training room. However, if participants want to use their own computer, they will need a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail Gabriella Rustici for more information.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Course Schedule

Day 1


Data organization in spreadsheets (Laurent)

Data files for the lesson are available here.

  1. Introduction
  2. Formatting data
  3. Common formatting problems
  4. Dates as data
  5. Quality control
  6. Exporting data

Data cleaning with OpenRefine (Marco)

Data files for the lesson are available here.

  1. Introduction
  2. Basics of OpenRefine
  3. Filtering and sorting
  4. Examining numeric data
  5. Generating scripts
  6. Exporting data
  7. Other resources

Introduction to R (Hugo)

  1. Before we start
  2. Introduction to R
  3. Starting with data
Recap of R materials from Day 1

Day 2

Data analysis with R (Laurent)

  1. Manipulating data with dplyr

Data visualisation with ggplot2 (Marco)

  1. ggplot2

SQL for data management (Hugo)

Data files for the lesson are available here. This is a zipped file. Unzip it to a location that you can easily find on your computer.

  1. Introduction to SQL
  2. Basic queries
  3. Summarising data by aggregation
  4. Joins and aliases
  5. Using SQL from R (optional)


All of the software required for this Data Carpentry workshop will be installed on the computers at our training venue.

However, if you want to use your own laptop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants can bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.