Genomics Data Carpentry Workshop

Carnegie Mellon University

Online

March 23-25, 2022

9:00 am - 1:00 pm EST

Instructors: Huajin Wang, Christina Akirtava, Ben Busby

Helpers: Hannah Gunderman, Emma Slayton, Melanie Gainey, Srilakshmi Chaparala

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. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: March 23-25, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer 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 dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email huajinw@cmu.edu or c.akirtava@gmail.com for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to the public. However, priority will be given to Carnegie Mellon University affiliates.

Registration Link: register on Eventbrite

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.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before starting	Pre-workshop survey
08:45 am	Installation Problems
9:00 am	Project organization and management
10:00 am	Break
10:10 am	Introduction to the command line (Part I)
11:30 am	Break
11:40 am	Introduction to the command line (Part II)
1:00 pm	End

Day 2

9:00 am	Introduction to the command line (Part III)
10:00 am	Break
10:10 am	Data Wrangling and Processing (Part I)
11:30 am	Break
11:40 am	Data Wrangling and Processing (Part II)
12:30 pm	Work on your own data + Q & A
1:00 pm	End

Day 3

9:00 am	Data Wrangling and Processing (Part III)
10:30 am	Break
10:40 am	Introduction to cloud computing for genomics
11:10 am	Add-on: UK Biobank
12:00 pm	Work on your own data + Q & A
12:45 pm	Post-workshop survey
1:00 pm	End

Setup

To participate in a Data Carpentry workshop, you will need access to software as 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.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

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