Data Carpentry Workshop

National Museum of Natural History AND Remote

May 9,10,16,17, 2023

1:00PM - 4:00PM EDT

Instructors: Jenna Ekwealor, Jennifer Giaccai, Richie Hodel, Matt Kweskin, Mike O'Mahoney, Jennifer Spillane, Mike Trizna, Sue Zwicker

Helpers: Carpentries Instructor Team

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: Room WG33, 10th and Constitution, Washington, DC AND Remote via Zoom. Get directions with OpenStreetMap or Google Maps.

When: May 9,10,16,17, 2023. 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 carpentries@si.edu or hodelr@si.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.

Registration

We encourage learners to sign up for all 3 lessons (GitHub, OpenRefine, and R), but we are splitting up registration so that learners can sign up for the lessons that fit into their busy schedules.

Registration for all 3 lessons will open to the Smithsonian community on Tuesday, April 25, at 10AM. Here is an Outlook calendar invite to remind you of that date and time: registration_reminder.ics





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

Detailed schedule coming soon!

Day 1 (Tuesday, May 9)

Day 2 (Wednesday, May 10)

Day 3 (Tuesday, May 16)

Day 4 (Wednesday, May 17)

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.

GitHub

For this lesson you will need a GitHub account and GitHub Desktop installed on your machine.

To sign up for a GitHub account:

  1. Go to https://github.com/signup and enter your email address (preferably your @si.edu or @cfa.harvard.edu address), choose a secure password, and then choose a username.
  2. Complete the "puzzle" to prove you are not a robot, click Create Account, and then confirm your email address with the code provided.
  1. Open Software Center, click on GitHub Desktop, and then click Install.
  2. Check the Desktop for a GitHub Desktop icon. If it is not there, you may need to restart your computer.
  3. Open GitHub Desktop, click on File > Options, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Open the Self Service app, click on the Scientific category, and then click Install under the GitHub Desktop icon.
  2. Check the Desktop for a GitHub Desktop icon. If it is not there, you may need to restart your computer.
  3. Open GitHub Desktop, in the top menu click on GitHub Desktop > Preferences, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Go to https://desktop.github.com/ and click on the big Download for Windows button.
  2. Follow the prompts to install the software.
  3. Open GitHub Desktop, click on File > Options, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.
  1. Go to https://desktop.github.com/ and click on the big Download for macOS button.
  2. Follow the prompts to install the software.
  3. Open GitHub Desktop, in the top menu click on GitHub Desktop > Preferences, and then click the Sign In button on the Accounts tab. This will direct you to a browser, where you will sign in to the account you created previously.

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

  1. Open Software Center, click on OpenRefine, and then click Install.
  2. Check the Desktop for an OpenRefine icon. If it is not there, you may need to restart your computer.
  3. If you get a Windows Defender warning about running the software, select 'More Info', then select 'Run Anyway'.
  • Open the Self Service app, click on the Utilities category, and then click Install under the OpenRefine icon.
  • Check the Desktop for an OpenRefine icon. If it is not there, you may need to restart your computer.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.
    2. Download software from http://openrefine.org/
    3. Create a new directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
    7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.
    2. Download software from http://openrefine.org/.
    3. Create a new directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory by double-clicking it.
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by dragging the icon into the Applications folder.
    7. Use Ctrl-click/Open ... to launch it.
    8. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
    1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
    2. Download software from http://openrefine.org/.
    3. Make a directory called OpenRefine.
    4. Unzip the downloaded file into the OpenRefine directory.
    5. Go to your newly created OpenRefine directory.
    6. Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.
    7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

    If you ran into any difficulty installing OpenRefine on your machine, we have a browser-based back-up solution that will run at this link: Binder

    Python

    Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

    Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

    We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

    1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
    2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
    3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

    Video Tutorial

    1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
    2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
    3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

    Video Tutorial

    1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
    2. Download the Anaconda Installer with Python 3 for Linux.
      (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
    3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
    4. Type 
      bash Anaconda3-
      and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
    5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
    6. Close the terminal window.