May 10-11, 2018
8:30 AM - 4.30 PM
Instructors: Timothy Moore, James Mickley, Pariksheet Nanda
Helpers: Henry Frye, Wanli Xu, Charlie Brown, Austin Spence, Kendra Maas
Software Carpentry 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.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students, advanced undergraduates, professors, and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Room #127, School of Business(BUSN), 2100 Hillside Rd, Storrs, CT 06269. Get directions with OpenStreetMap or Google Maps. Parking for non UConn folks is best at South Garage
When: May 10-11, 2018. 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 to install software 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 timothy.e.moore@uconn.edu , james.mickley@uconn.edu or pariksheet.nanda@uconn.edu for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 08:30 | Programming with R - Timothy Moore |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Version control with Git - Pariksheet Nanda |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
| 16:30 | END |
| 09:00 | Programming with R cont. - Timothy Moore & James Mickley |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | OpenRefine and Managing data with SQL - James Mickley |
| 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.
ggplot2dplyr and tidyrknitradd, commit, ...status, diff, ...clone, pull, push, ...SELECTWHEREJOININSERT, UPDATE, and DELETEdplyr, RSQLite, and DBIFirst and foremost, we recommend the lessons from Software Carpentry that we followed for this course. We've added links to those lessons in the syllabus above.
To participate in a Software Carpentry 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.
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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
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.
Github for Education offers a free 2-year plan for students and educators that allows you to have private repositories. You can apply for an education plan here
Alternatively, you can use UConn's GitHub at github.uconn.edu. Just login with your netID, and you will have unlimited free public and private repositories. However, you cannot collaborate on those repositories with those outside UConn.
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
After installing Git, there will not be anything in your /Applications folder,
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"
available here.
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.
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.
SQL is a specialized programming language used with a variety databases. We use a simple, file-based database manager called SQLite in our lessons.
We will also use a visual database browser called DB Browser for SQLite to see the results of our SQL queries.
sudo add-apt-repository -y ppa:linuxgndu/sqlitebrowsersudo apt-get updatesudo apt-get install sqlitebrowsersudo dnf install sqlitebrowser.
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.
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.
Download software from http://openrefine.org/
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
Go to your newly created OpenRefine directory.
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).
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.
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.
Download software from http://openrefine.org/.
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by double-clicking it.
Go to your newly created OpenRefine directory.
Launch OpenRefine by dragging the icon into the Applications folder.
Use Ctrl-click/Open ... to launch it.
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.
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
Download software from http://openrefine.org/.
Make a directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory.
Go to your newly created OpenRefine directory.
Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.
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.
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, try
typing the escape 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. See the Git installation video tutorial for an example on how to open nano. It should be installed when you install 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 Text Wrangler 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.