Feb 11-12, 2019
9:00 am - 4:30 pm
Instructors: Brian Stucky, Ellen Bledsoe, Joe Andreoli, Sasha Lavrentovich
Helpers: Philip Chase, Falcon Restrepo, Eduardo Bongiolo, Elise Morrison, Mariandreina Kostantinov
Space is limited to 24 participants for this workshop and registration is required. A fee of $46.00 will be charged and lunch will be provided both days. Please plan on attending the entire time for both days. You can register in UF's conference system here:
Registration is now full
The UF Carpentries Club is offering a two day Carpentries-inspired workshop to help the UF community get started learning R and common software development tools such as the Unix shell, and Git. Need to learn some programming for a class? Want to collaborate effectively with your peers? We were there once too. Come start learning with us.
Our instructors are trained by the Carpentries in evidence-based pedagogy and our materials have been developed collaboratively over years by dozens of contributors. The University of Florida Informatics Institute and Biodiversity Institute have generously volunteered space and resources for this workshop in order to advance the skillset of the UF community. The organizers, instructors, and helpers are volunteering their time to help UF, and you!
The international Carpentries organization aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: The course is open to all members of the UF community: students, staff, and faculty. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: UFII Lecture Room, Computer Sciences/Engineering Building (0042), Gainesville, FL. Get directions with OpenStreetMap or Google Maps.
When: Feb 11-12, 2019. 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). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. 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 haoye@ufl.edu for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | R for Reproducible Scientific Analysis (part I) |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
| 16:30 | END |
| 09:00 | R for Reproducible Scientific Analysis (part II) |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Version control with Git |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
add, commit, ...status, diff, ...clone, pull, push, ...To participate in a this Carpentries-inspired workshop, you will need access to the software 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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of macOS is Bash, 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.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.
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 (described above).
Please open the Terminal app, type git --version and press
Enter/Return. If it's not installed already,
follow the instructions to Install the "command line
developer tools". Don't click "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your /Applications
folder, as they and Git are command line programs.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
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 in the pop-up dialog. You can watch
a video tutorial about this case.
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.
When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.
nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.
Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Others editors that you can use are BBEdit or Sublime Text.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Others editors that you can use are Gedit, Kate or Sublime Text.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
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.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.