Date: Sept. 11-21, 2023
Time: 8:30 am - 12:30 pm
Venue: University of California
Instructors: Scott Peterson, Reid Otsuji, Kim Thomas, Albert Lee, Echelle Burns, Geoffrey Boushey, David Palmquist, Elizabeth McAulay, Jamie Jamison, Derek Devnich, Saulo Soares
Helpers: Rosana Aguilera, Celeste Allaband, Jean Allen, Kristian Allen, Misha Coleman, Stephanie Labou, Devontae Baxter, Monique Surles-Zeigler, Ellen Davenport, Tim Dennis
The Carpentries aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This workshop is designed for researchers and enables non-experts to develop computing skills for research analysis. We will cover basic concepts and tools, such as - working with libraries and data frames; reading and plotting data; creating and using functions; the shell using command-line applications; cleaning and transforming data; and more. Participants will be encouraged to help one another and to apply what they This is a free workshop and is open to all University of California students, staff, and faculty. have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: This workshop is open to University of California students, staff, postdocs, and faculty. You don't need to have any previous knowledge of programming or the tools presented in the workshop to attend. A laptop is required for each session.
Requirements: Participants must have a laptop or desktop with a few specific software packages installed (listed below).
Contact: Please email firstname.lastname@example.org for more information.
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.
Please be sure to complete these surveys before and after the workshop.
|Sept 11||Day 1||The Unix Shell: Introduction, Navigating the file system, & working with files & directories|
|Sept 12||Day 2||Version Control with Git: Introduction, Creating a Repository, Tracking Changes, and Collaborating|
|Sept 13||Day 3||Intro to R & RStudio: basics, data structures, data import/export, dylyr|
|Sept 14||Day 4||Intro to R & RStudio: dplyr (cont.), tidyverse, plotting with ggplot2 and knitr|
|Sept 18||Day 5||Intro to Python: Running/writing, variables/assignment, data types/type conversions, built-in functions/help, libraries, reading/writing data in Dataframes, and Pandas Dataframes|
|Sept 19||Day 6||Intro to Python: plotting, lists, for loops, conditionals, looping over datasets, and writing functions|
|Sept 20||Day 7||Tidy Data: learn how to use this tool to clean, transform, and track changes made to data|
|Sept 21||Day 8||SQL:Introduction, Creating a Repository, Tracking Changes, and Collaborating|
For this workshop we will be referencing the The UNIX Shell, Version Control with Git, R for Reproducible Scientific Analysis, Plotting and Programming in Python, Tidy Data, and SQL Carpentries curricula.
We will be using the specific software downloads and data for each lesson. Please refer to the listing of downloads needed for each session you'll be attending as provided at this link.
We will use HackMD collaborative notes for taking notes, and sharing URLs and bits of code. The links to each session are listed at this link.
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:
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Video Tutorial: SWC R Install Windows
Video Tutorial: SWC R Install Mac
Instructions for R installation on various Linux platforms (debian,
fedora, redhat, and ubuntu) can be found at
sudo dnf install R and for Debian/Ubuntu, add a ppa
repository and then run
sudo apt-get install r-base).
Also, please install the
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).
Video Tutorial: SWC Install Python on Windows
Video Tutorial: SWC Install Python on Mac
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
yesand press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type
yesand press Enter (or Return) to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).
Bash is a commonly-used shell that gives you the power to do tasks more quickly.
Git 2.27.0 Setup
Adjusting your PATH environment
Choosing the SSH executable
Choosing HTTPS transport backend
This should mean that people stuck behind corporate firewalls that do MITM attacks with their own root CA are still able to access remote git repos.
Configuring the line ending conversions
Configuring the terminal emulator to use with Git Bash
Configuring extra options
Configuring experimental options
Completing the Git Setup Wizard
as of 2020-06-02, the Window will say "click Finish", but the button is labelled as "Next"
cmdand press Enter)
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing Enter
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial: Windows Installation
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
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
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 MacOS Installation
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
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash install (see the Shell installation instructions).
For macOS, install Git for Mac
by downloading and running the most recent "mavericks" installer from
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
Video Tutorial: SWC Install Shell, Git, and Nano on Mac
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.
SQLite comes pre-installed on Mac OS X.
SQLite comes pre-installed on Linux.