Jan 24-27, 2023
9:00-17:30
Instructors: Renato Alves, Gaurav Diwan, Florian Huber, Supriya Khedkar, Eleonora Mastrorilli, Lisanna Paladin, Fotis Psomopoulos
Helpers: Christian Schudoma
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: Meyerhofstraße 1, 69117 Heidelberg, Germany. Get directions with OpenStreetMap or Google Maps.
When: Jan 24-27, 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 renato.alves@embl.de or lisanna.paladin@embl.de 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.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
Before the course - Setup all required software
See detailed programme on the event page
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.
You can download all of the data used in this workshop by clicking this download link. The file is 38.4 MB.
Clicking the download link will automatically download all of the files to your default download directory as a single compressed
(.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder
application).
For a full description of the data used in this workshop see the data page.
| Software | Install | Manual | Available for | Description |
|---|---|---|---|---|
| Spreadsheet program | Link | Link | Linux, MacOS, Windows | Spreadsheet program for organizing tabular data. |
| OpenRefine | Link | Link | Linux, MacOS, Windows | Program for reproducibly cleaning data. |
| Git | Link | Linux, MacOS, Windows | Content tracking and versioning software. | |
| R | See install instructions below. | Linux, MacOS, Windows | Programming language for data analysis and visualisation. | |
| RStudio | Link | Cheatsheet | Linux, MacOS, Windows | Integrated development environment for R. |
To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other programs. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. For this workshop, we recommend using either Microsoft Excel (paid software) or LibreOffice (free and open source). Other spreadsheet programs may not have all of the features we will be exploring in this workshop.
To install LibreOffice, go to their download page. The website should automatically select the correct option for your operating system. Click the “Download” button. You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically. Once the installer is downloaded, double click on it (you may need to open your Downloads folder) and LibreOffice should install.
OpenRefine is a Java program that runs on your local machine (not on the cloud). Although it displays in your browser, no web connection is needed and your data remains local. You need to have a ‘Java Runtime Environment’ (JRE) installed on your computer to run OpenRefine. If you don’t already have one installed then you can download and install from http://java.com by going to the site and clicking “Free Java Download”.
To install OpenRefine, go to their download page. From the download page, select either “Windows
kit”, “Mac kit”, or “Linux kit” - depending on your operating system - and follow the instructions next to your download link. This
lesson has been tested with all versions of OpenRefine up to the latest tested version, 3.2. If you are using an older version, it is
recommended you upgrade to the latest tested version. After installing, you can delete the installer .dmg file.
You may get an error message: “OpenRefine.app can’t be opened because it is from an unidentified developer.” If you get this message, open your system preferences and click “Security & Privacy”. You will see a message “OpenRefine.app was blocked from opening because it is from an unidentified developer.” Click “Open Anyway” and “Yes”. OpenRefine should open in your default web browser.
OpenRefine does not support Internet Explorer or Edge. Please use Firefox, Chrome or Safari instead.
tidyverse and other packages.If you already have R and RStudio installed
- Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type
sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.- Follow the steps in the instructions for everyone at the bottom of this page.
If you don’t have R and RStudio installed
- Download R from the CRAN website.
- Run the
.exefile that was just downloaded- Go to the RStudio download page
- Under Installers select RStudio x.yy.zzz - Windows Vista/7/8/10 (where x, y, and z represent version numbers)
- Double click the file to install it
Once it’s installed, open RStudio to make sure it works and you don’t get any error messages
- Follow the steps in the instructions for everyone at the bottom of this page.
If you already have R and RStudio installed
- Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
- To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type
sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.- Follow the steps in the instructions for everyone at the bottom of this page.
If you don’t have R and RStudio installed
- Download R from the CRAN website.
- Select the
.pkgfile for the latest R version- Double click on the downloaded file to install R
- It is also a good idea to install XQuartz (needed by some packages)
- Go to the RStudio download page
- Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers)
- Double click the file to install RStudio
Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.
- Follow the steps in the instructions for everyone at the bottom of this page.
sudo apt-get install r-base, and for Fedora sudo yum install R), but we
don’t recommend this approach as the versions provided by this are
usually out of date. In any case, make sure you have at least R 3.5.1.sudo dpkg -i
rstudio-x.yy.zzz-amd64.deb at the terminal).install.packages(c("tidyverse", "corrplot", "corrr", "hexbin", "patchwork", "ggfortify", "broom", "RSQLite", "BiocManager")).
You can also do this by going to Tools -> Install Packages and
typing the names of the packages you want to install, separated by a comma.
Finally, install ComplexHeatmap from BioConductor using: BiocManager::install("ComplexHeatmap")