Data Carpentry Genomics

University of Kansas

January 9-11, 2024

9:00 am - 4:30 pm, all days

Instructors: Caroline Kisielinski, Ph.D, Katherine Hanson

Helpers: Savannah Hay, Boryana Koseva, Ph.D, Daniel Montezano, Ph.D, Sarah Unkel, Jamene Brooks-Kieffer

Registration

This is an in-person workshop on KU's Lawrence campus. The workshop and waitlist are full.

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. You will need some familiarity with biological concepts, including the concept of genomic variance within a population.

Where: Clark Instruction Center, Watson Library, 1425 Jayhawk Boulevard, Lawrence, KS. Get directions with OpenStreetMap or Google Maps.

When: January 9-11, 2024. 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. For workshops at a physical location, 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 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.

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, called an Etherpad, 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

Tuesday, January 9, 2024

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 noonIntroduction to the Command Line
12:00 noon - 1:00 pmLunch on your own
1:00 pm - 3:30 pmIntroduction to the Command Line, continued
3:30 pm - 4:00 pmIntroduction to Cloud Computing for Genomics
4:00 pm - 4:30 pm Wrap up for the day

Wednesday, January 10, 2024

9:00 am - 9:30 am Computer setup and Q&A from Day 1
9:30 am - 12:00 noonData Wrangling and Processing
12:00 noon - 1:00 pmLunch on your own
1:00 pm - 4:00 pmData Wrangling and Processing, continued
4:00 pm - 4:30 pm Wrap up for the day

Thursday, January 11, 2024

9:00 am - 9:30 am Computer setup and Q&A from Days 1 & 2
9:30 am - 12:00 noonIntro to R and RStudio for Genomics
12:00 noon - 1:00 pmLunch on your own
1:00 pm - 4:00 pmIntro to R and RStudio for Genomics, continued
4:00 pm - 4:30 pmWrap up and post-workshop survey

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.

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

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Spreadsheet Program

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.

  1. Download the installer from https://www.libreoffice.org/download. The version for Windows should automatically be selected.
  2. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  3. Once the installer is downloaded, double click on it and LibreOffice should install.
  1. Download the installer from https://www.libreoffice.org/download. The version for Mac should automatically be selected.
  2. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  3. Once the installer is downloaded, double click on it and LibreOffice should install.
  1. Download the installer from https://www.libreoffice.org/download. The version for Linux should automatically be selected.
  2. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  3. Once the installer is downloaded, double click on it and LibreOffice should install.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

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".

Video Tutorial

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.