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A Data Carpentry Workshop

American Society of Plant Biology

July 30-31, 2015

1 pm - 4 pm (day 1); 8am - 5pm (day 2)

Instructors: Sheldon McKay, Jason Williams, Ryan Williams

Helpers: Jon Badalamenti, Christos Noutsos, Nowlan Freese

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 processing at the command line, Working with NGS data and Data analysis and visualization in R. 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.

Requirements: Participants must bring a laptop with 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.

Note on Cloud Computing
The servers used in workshop are run in Amazon Web Services, courtesy of a grant from Amazon. If you want to run your instance of the server used for this workshop, launch a t2.large instance with AMI ami-6516b30e, available under "Community AMIs" in the Amazon EC2 Managemant Console.
Getting started with AWS


Day 1: 1PM - 5PM

Data Processing and Organization
Introduction Jason
Getting started with the data Jason
Getting your project started Jason
Command line exploration of the data (unix shell) Sheldon

Day 2: 8AM - 5AM

NGS Data analysis
Quality Control of NGS Data Jason and Sheldon
Know your data Jason
Automating a workflow with a shell script Sheldon
Automating a variant calling workflow Sheldon
Data analysis and visualization in R
Visualization with R
Note: data available here
Moving Your Data Jason
Please complete the post-workshop Survey
Post-workshop: Launch your own cloud instance after the workshop
Launching your own instance
Note: Start here if you are working on the lessons on your own
On your own
On your own

Post-Workshop (or using these lessons on your own)

Launching cloud instances after the workshop
Launching your own instance
Note: Start here if you are working on the lessons on your own
On your own

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


To participate in a Data Carpentry workshop, 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 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.