Genomics Data Carpentry @ UW-Madison

August 5-6 & 12, 2019

8:30 a.m. - 4:30 p.m.

Instructors: Trisha Adamus, Steve Goldstein, Christina Koch, Tobin Magle, Elizabeth McDaniel, Sarah Stevens, Sailendharan Sudakaran

Helpers: Cid Freitag, Matt Stone

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Orchard View Room, Discovery Building, 330 N. Orchard St., Madison, WI, 53715. Get directions with OpenStreetMap or Google Maps.

When: August 5-6 & 12, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.


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

Pre-workshop Survey

Post-workshop Survey


Day 3

Day 3 will be on August 12. Attending Day 3 is optional, requires a separate registration, and will be held in the Researcher's Link Room at the Discovery Building.

Intro to R and R Studio for Genomics

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



This workshop will use Cyverse and Atmosphere to provide a remote working environment for attendees, so no software needs to be installed prior to the workshop. To gain access to the workshop materials, you will need to create an account with Cyverse and register with the workshop on Cyverse, after registering for the workshop via Eventbrite. In addition, you will need an up-to-date web browser.