A Data Carpentry Workshop
Boston University
April 12-13, 2016
9:00 am - 4:30 pm
Instructors:
Ivan Gonzalez, Sheldon McKay
Helpers:
Marianna Foos
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 iglpdc+bu@gmail.com for more information.
Etherpad: http://pad.software-carpentry.org/2016-04-11-bu.
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 |
| Wrap-up | |
| 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 |
Setup
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.