June 12-13, 2018
9:00 am - 5:00 pm
Instructors: Paula Andrea Martinez, Stijn Van Hoey, Tina O'Grady, Christof De Bo
Helpers: Verónica Lloréns-Rico, Akuli Biche Osong, Frederiek-Maarten Kerckhof, Heidelinde Dehaene
Thank your for your interest in this Data Carpentry workshop. The ever-increasing digital nature of research requires researchers, postgraduate students, and research-support staff to equip themselves with the skills to create, manipulate and manage data in digital format. Today, researchers can perform simple to complex data management through open source tools and techniques which do not require highly specialist skills. This hands-on workshop will assist you to learn more about 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.
This workshop is funded by the Elixir-Carpentries agreement and organised by Elixir Belgium. The trainers are all certified carpentry instructors who come from LifeWatch INBO, VIB, and Giga institute.
Who: This workshop is aimed to life scientist at all career stages, from undergrads to senior scientists. It is an introductory workshop to data management, databases, and data analysis in R. We recommend participants to have a basic understanding of R and its data types. We can send resources for people who need an introduction to R before this workshop. The level of this workshop is from beginner to intermediate, we will not cover advanced materials. If you are already familiar with the topics listed in the schedule you might not benefit from this workshop. But please contact us if you would like a more advanced workshop in any of the topics listed here. Please also contact us if you would like to be a helper in this workshop.
Where: Generaal Jacqueslaan 271, 1050 Brussels. Get directions with OpenStreetMap or Google Maps.
When: June 12-13, 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 on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Registration: Please register through the VIB website. We have four categories of registrations, prices are only to cover for catering and all other expenses are sponsored by Elixir Belgium. Prices include VAT. Invoiced requests are accepted.
Contact: Please email paula.martinez@elixir-belgium.org for more information.
Please be sure to complete these surveys before and after the workshop.
| 09:00 | Data organization in spreadsheets |
| 11:05 | Motivation and use cases of databases and R resources |
| 13:00 | Databases introduction with SQLite |
| 17:00 | Optional self-organised getting together after the workshop |
| 09:00 | R projects and visualisation using ggplot2 |
| 11:00 | Data manipulation using dplyr and tidyr |
| 13:30 | R and databases using RSQLite |
| 15:00 | R and version control using git |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a Data 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.
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 (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.
Git should be installed on your computer as part of your Bash install (described above).
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.
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. To install it, download the Data Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
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.
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 databases. We use a simple database manager called SQLite in our lessons.
The Data 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 macOS.
SQLite comes pre-installed on Linux.
If you installed Anaconda, it also has a copy of SQLite
without support to readline.
Instructors will provide a workaround for it if needed.