Data Carpentry Workshop

UCDavis

September 22-23, 2015
9:00 am - 4:30 pm

General Information

Workshop etherpad: https://datacarpentry.etherpad.mozilla.org/83

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required.

The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover project setup, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.

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.

Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.

Schedule

Day 1: 9AM - 5PM

Intro, Data Processing, and Organization
Intro to Data Carpentry Jason
Introduction Jason
Data dityness Jason
Getting started with the data Jason
Getting your project started Jason
Command line exploration of the data (unix shell) John
Quality Control of NGS Data Jason

Day 2: 9AM - 5PM

NGS Data analysis
Know your data Jason
Automating a workflow with a shell script Jason
Automating a variant calling workflow Jason
Data analysis and visualization with R Tracy
Wrap-up
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

Updates will be posted to this website as they become available.

Organizer: Titus Brown, Jason Williams

Instructors: Jason Williams, John Fonner, Tracy Teal

Assistants:

Who: The course is aimed at faculty, research staff, postdocs, graduate students, advanced undergraduates, and other researchers in any field. No prior computational experience is required.

Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We will provide instructions on setting up the required software several days in advance, and the classroom will have computers with the software installed). There are no pre-requisites, and we will assume no prior knowledge about the tools. Participants are required to abide by Software Carpentry's Code of Conduct.

Contact: Please email for questions and information not covered here.

Twitter: @datacarpentry

Acknowledgements & Support

Data Carpentry is supported by the Gordon and Betty Moore Foundation and a partnership of several NSF-funded BIO Centers (NESCent, iPlant, iDigBio, BEACON and SESYNC) and Software Carpentry. The structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry.


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