January 15-16, 2025
9:00 am - 4:30 pm, both days
Instructors: Caroline Kisielinksi, Ph.D, Boryana Koseva, Ph.D
Helpers: Taylor Conway, Vanna Hay, Daniel Montezano, Ph.D, Brian Sanderson, Ph.D, Jamene Brooks-Kieffer, other helpers TBD
This is an in-person workshop on KU's Lawrence campus that will not be recorded. The workshop is full and registration is closed.
The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.
Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/
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: Clark Instruction Center, Watson Library, 1425 Jayhawk Boulevard, Lawrence, KS. Get directions with OpenStreetMap or Google Maps. What3Words location: ///scenes.indeed.lock.
When: January 15-16, 2025; 9:00 am - 4:30 pm, both days 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:
We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your Carpentries experience accessible. To request an accommodation for this workshop, please fill out the accommodation request form. If you have questions or need assistance with the accommodation form please email us.
Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.
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, called an Etherpad, 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 |
| 9:00 am - 9:30 am | Introductions and computer setup |
| 9:30 am - 10:30 am | Project Organization and Management |
| 10:30 am - 12:00 noon | Introduction to the Command Line |
| 12:00 noon - 1:00 pm | Lunch on your own |
| 1:00 pm - 3:30 pm | Introduction to the Command Line, continued |
| 3:30 pm - 4:00 pm | Introduction to Cloud Computing for Genomics |
| 4:00 pm - 4:30 pm | Wrap up for the day |
| 9:00 am - 9:30 am | Computer setup and Q&A from Day 1 |
| 9:30 am - 12:00 noon | Data Wrangling and Processing |
| 12:00 noon - 1:00 pm | Lunch on your own |
| 1:00 pm - 4:00 pm | Data Wrangling and Processing, continued |
| 4:00 pm - 4:30 pm | Wrap up and post-workshop survey |
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.
The Data Carpentry Genomics workshop overview site contains additional setup instructions for working through the lesson on your own. You won't need these instructions for the workshop, but they may be helpful for your post-workshop practice.
.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 Mac OS X Ventura and newer versions is Zsh, but
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, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
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 Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.