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A Data Carpentry Workshop

Boston University

April 12-13, 2016

9:00 am - 4:30 pm

Instructors: Ivan Gonzalez, Sheldon McKay

Helpers: Marianna Foos

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 , , and . 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: . Get directions with OpenStreetMap or Google Maps.

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.

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

Agenda and Lessons

Day 1: 9AM - 5PM

If you have not already done so, please complete the pre-workshop survey
Intro, Data Processing, and Organization Instructor
Intro to Data Carpentry Sheldon
Getting started with cloud computing Sheldon
Introduction to the data Sheldon
Data tidiness Sheldon
Getting started with the data Sheldon
Getting your project started Ivan
Command line exploration of the data (unix shell) Ivan

Day 2: 9AM - 5PM

NGS Data analysis Instructor
Quality Control of NGS Data Sheldon
Know your data Sheldon
Automating a workflow with a shell script Sheldon
Automating a variant calling workflow Sheldon
Data analysis and visualization with R Ivan
Moving Your Data Ivan
Please complete the post-workshop Survey before you leave. Everyone

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


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.