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A Data Carpentry Workshop

BPS room 1455(A)

Sep 28-29, 2016

9:00 am - 5:00 pm

Instructors: Amanda Charbonneau, Will Pitchers

Helpers: Anne Sonnenschein, Emily Dolson

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 Genomics Data and Organization, Shell and Scripting, Automation and Variant calling and Introduction to 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.

Where: Biomedical and Physical Sciences Building, 567 Wilson Road. 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.

Agenda and Lessons

Day 1: 9AM - 5PM in BPS room 1455(A)

If you have not already done so, please complete the pre-workshop survey
Intro, Data Processing, and Organization Instructor
Intro to Data Carpentry Amanda
Getting started with the HPC Amanda
The dataset Amanda
Data tidiness Amanda
Getting started with the data Amanda
Getting your project started Will
Command line exploration of the data (unix shell) Will

Day 2: 9AM - 5PM BPS room 1455(A)

NGS Data analysis Instructor
Quality Control of NGS Data Amanda
Know your data Amanda
Automating a workflow with a shell script Amanda
Automating a variant calling workflow Amanda
Introduction to R
Data analysis and visualization with R Will
Moving Your Data Will
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

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.