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
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 archerc5@msu.edu 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 |
| Wrap-up | |
| 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 |
Etherpad: https://etherpad.wikimedia.org/p/MSU_DC_genomics.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.