Online
Sep 22-30 2020
10.00 AM - 15.00 PM
Instructors: Thomas Lind, Joakim Philipson, Glenn Haya, Lina Andrén
Helpers: Rosa Lönneborg
The Carpentries aims to help researchers get their work done in less time and with less pain by teaching them basic research computing and data skills. This hands-on workshop will cover the basics of a data workflow, starting with SQL databases and going on to introduce data cleaning with OpenRefine and basic programmig and plotting using Python. 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".
Click here to sign up for the workshop
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: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Sep 22-30 2020. 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 dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email linaandr@kth.se for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
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.
| Before | Pre-workshop survey |
| 10:00 | Databases and SQL |
| 11:00 | Morning break |
| 11:15 | Databases and SQL (continued) |
| 12:00 | Lunch break |
| 13:00 | Databases and SQL (continued) |
| 14:00 | Afternoon break |
| 14:15 | Databases and SQL (continued) |
| 15:00 | END |
| 10:00 | Data cleaning and OpenRefine |
| 11:00 | Morning break |
| 11:15 | Data cleaning and OpenRefine (countinued) |
| 12:00 | Lunch break |
| 13:00 | Data cleaning and OpenRefine (countinued) |
| 14:00 | Afternoon break |
| 14:15 | Data cleaning and OpenRefine (countinued) |
| 15:00 | END |
| 10:00 | Plotting and programming in Python part 1 |
| 11:00 | Morning break |
| 11:15 | Plotting and programming in Python part 1 (continued) |
| 12:00 | Lunch break |
| 13:00 | Plotting and programming in Python part 1 (continued) |
| 14:00 | Afternoon break |
| 14:15 | Plotting and programming in Python part 1 (continued) |
| 15:00 | END |
| 10:00 | Plotting and programming in Python part 2 |
| 11:00 | Morning break |
| 11:15 | Plotting and programming in Python part 2 (continued) |
| 12:00 | Lunch break |
| 13:00 | Plotting and programming in Python part 2 (continued) |
| 14:00 | Afternoon break |
| 14:15 | Plotting and programming in Python part 2 (continued) |
| 15:00 | END |
We will use the following documents for taking collaborative notes during the workshop:
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.
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:
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).
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
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).
SQL is a specialized programming language used with databases. We use a database manager called SQLite in our lessons.
curl -fsSL https://linajandren.github.io/2020-09-22-stockholmtrio-online/getsql.sh | bash3.27.2 2019-02-25 16:06:06 ...If you want to do this manually, download sqlite3, make a bin directory in the user's home directory, unzip sqlite3, move it into the bin directory, and then add the bin directory to the path.
SQLite comes pre-installed on macOS.
SQLite comes pre-installed on Linux.
bashIf you installed Anaconda, it also has a copy of SQLite
without support to readline.
Instructors will provide a workaround for it if needed.
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.
openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser)../refine into the terminal within the OpenRefine directory.