Online
January 4, 6, 8, 11, 13, 15, 2021
1:00 pm - 4:30 pm
Instructors: Elizabeth Everman, PhD, Boryana Koseva, PhD, Casey Russell
Helpers: Tami Albin, Jamene Brooks-Kieffer, Camille Delavaux, Elizabeth Everman, Joe Gunn, Paul Klawinski, Boryana Koseva, Casey Russell, Greg Smith, Samantha Thomas, Paris Veltsos, Konner Winkley
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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: January 4, 6, 8, 11, 13, 15, 2021. 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 jamenebk@ku.edu for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
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.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
| Before starting | Pre-workshop survey |
| 1:00 pm - 2:00 pm | Welcome and getting started |
| 2:00 - 4:30 pm | Project Organization and Management for Genomics |
| 1:00 - 4:30 | Introduction to the Command Line for Genomics |
| 1:00 pm - 4:30 pm | Data Wrangling and Processing for Genomics |
| 1:00 pm - 2:30 pm | Introduction to Cloud Computing for Genomics |
| 2:30 pm - 4:30 pm | RStudio setup check and start Intro to R and RStudio for Genomics |
| 1:00 pm - 4:30 pm | Intro to R and RStudio for Genomics |
| 1:00 pm - 4:30 pm | Intro to R and RStudio for Genomics |
| End | Post-workshop survey |
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.
If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.
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:
This workshop requires a working spreadsheet program. If you don't have a spreadsheet program already, such as Microsoft Excel, you can use LibreOffice. It's a free, open source spreadsheet program. Directions to install are included for Windows, Mac OS X, and Linux systems below.
Bash is a commonly-used shell that gives you the power to do tasks more quickly.
cmd and press Enter)setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing EnterThis will provide you with both Git and Bash in the Git Bash program.
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else and you can run Bash by typing bash
If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".
The default shell is usually Bash and there is usually no need to install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the Enter key. If the message printed
does not end with '/bash' then your default is something else and you
can run Bash by typing bash.