Data Carpentry for Genomics

New York University

March 26-27, 2020

9:30am - 5pm

Instructors: Alex Provo, Nick Wolf

Helpers: Vicky Steeves, Casey Hampsey

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. To attend, you must be able to enter Bobst Library. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room 743, Bobst Library, 70 Washington Sq South, New York, NY 10012. Get directions with OpenStreetMap or Google Maps.

When: March 26-27, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email vicky.steeves@nyu.edu or emily.mathis@nyu.edu for more information.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.This document also outlines how to report an incident if needed.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

BeforePre-workshop survey
09:30Project Organization and Management
11:00Morning break
11:20Introduction to the Command Line
12:00Lunch break
13:00Introduction to the Command Line - cont
14:30Afternoon break
14:50Introduction to the Command Line - cont
17:00END

Day 2

09:30Data Wrangling and Processing
11:00Morning break
11:20Data Wrangling and Processing - cont
12:00Lunch break
13:00Data Wrangling and Processing - cont
14:40Afternoon break
15:50Introduction to Cloud Computing for Genomics
16:50Post-workshop survey
17:00END

Syllabus


Setup

To participate in a Data Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

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.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.