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A Data Carpentry Workshop

SUNY Upstate Medical University

May 04-05, 2017

9:00 am - 4:30 pm

Instructors: Daren Card, Lingling Jiang

Helpers: Wayne Decatur, Jonathan Hess

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 Introduction to the Shell and Cloud Computing, Advanced Shell and Genomics Data Introduction, Genomics Workflow Overview and Automation and Data Summary, Statistical Analysis, and Visualization. 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.

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

Where: Weiskotten Hall, Room 103, 766 Irving Avenue, Syracuse, NY 13210. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring 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 for more information.

Preliminary Schedule


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

Post-workshop Survey

Day 1

Morning Introduction to the Shell and Cloud Computing
Afternoon Advanced Shell and Genomics Data Introduction

Day 2

Morning Genomics Workflow Overview and Automation
Afternoon Data Summary, Statistical Analysis, and Visualization

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


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things

Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Performing basic statistical analyses


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything before the start of your workshop. Participants should 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.