Data Carpentry Genomics Workshop

Weizmann Institute of Science

October 29-31, 2024

9:00am-4:30pm (Day 1 & Day 2)
9:00am-12:00pm (Day 3)

Instructors: Dan Kerchner, Dr. Danny Ben-Avraham

Helpers: Dayana Yahalomi

General Information

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: Weizmann Institute of Science, Rehovot, Israel. Get directions with OpenStreetMap or Google Maps.

When: October 29-31, 2024; 9:00am-4:30pm (Day 1 & Day 2)
9:00am-12:00pm (Day 3) Add to your Google Calendar.

Language: The workshop will be conducted in English.

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 kerchner@gwu.edu or dan.ben-avraham@weizmann.ac.il for more information.

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


Acknowledgements

This workshop is made possible by the generous financial support of The United States Research Software Engineer Association (US-RSE), by The Carpentries, by the Weizmann Institute of Science, by The George Washington University Libraries, and by ELIXIR.


Registration

To register, please fill out and submit the registration form:


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

Schedule is approximate.


Setup

To participate in the workshop, you will need a laptop with an up-to-date web browser. In addition, Windows users may need to install additional software (see instructions below).

A list of common issues that occur during installation can be found on the Carpentries Configuration Problems and Solutions wiki page.

The Bash Shell

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

Open your Command Prompt app by searching for "cmd". At the command prompt, type ssh. Confirm that this prints out the usage information for the ssh command - if this is the case, then you do not need to install anything. However, if the result is Command not found then you have two options:
  • Set up the Ubuntu Subsystem for Windows. This option is only available for Windows 10 - detailedinstructions are available at https://docs.microsoft.com/en-us/windows/wsl/install.
  • Download the Git for Windows installer. 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 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. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    7. Ensure that "Use Windows' default console window" is selected and click on "Next".
    8. Ensure that "Default (fast-forward or merge) is selected and click "Next".
    9. Ensure that "Git Credential Manager Core" is selected and click on "Next".
    10. Ensure that "Enable file system caching" is selected and click on "Next".
    11. Click on "Install".
    12. Click on "Finish".
    13. Check the settings for you your "HOME" environment variable.
    14. If your "HOME" environment variable is not set (or you don't know what this is): Open command prompt (Open Start Menu then type cmd and press [Enter]). Type the following line into the command prompt window exactly as shown: setx HOME "%USERPROFILE%". Press [Enter], you should see SUCCESS: Specified value was saved.. Quit command prompt by typing exit then pressing [Enter]. </ol> </ul> </article> </div> </div> </div>