Git should be installed on your computer as part of your Bash install (described above).
Nov 20-22 2019
9:30 am - 5:00 pm
Instructors: Marc Galland1, Zsófia Koma2, Tijs Bliek1
Helpers: Stacy Shinneman2, Johannes de Groeve2, Huub Hoefsloot1
1: member of the SILS institute, 2: member of the IBED institute
This lesson will introduce you to open data science so you can work with data in an open, reproducible, and collaborative way. Open data science means that methods, data, and code are available so that others can access, reuse, and build from it without much fuss. Here you will learn a workflow with R, RStudio, Git, and GitHub.
This is going to be fun, because learning these open data science tools and practices is empowering! This training book is written (and always improving) so you can use it as self-paced learning, or it can be used to teach an in-person workshop where the instructor live-codes. Either way, you should do everything hands-on on your own computer as you learn.
This workshop is organized by the core members of the Amsterdam Science Park Study group. This small community of computational biologists aims to promote skill sharing and collaboration through the organisation of interactive workshops. It acts as the main local hub to set-up Software and Data Carpentry workshops (official workshops and Carpentry-style). All are welcome to this study group, regardless of scientific research area, affiliation or training level.
For more information on what we teach and why, see our website: "scienceparkstudygroup".
Who: The course is aimed at master students and other researchers (PhD. and postdoc). You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Science park 904, Amsterdam. Get directions with OpenStreetMap or Google Maps.
Rooms: Unfortunately we were signed to multiple rooms:
Included: Coffee and tea will be included, Lunch is not included.
When: Nov 20-22 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).
Code of Conduct: 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.
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.
Helpers: Experts helping in the room.:
Etherpad: The group etherpad to ask question or place commands can be found under this link
Contact: Please email bliek@uva.nl for more information.
Links to the lesson materials:
| Morning (9:30-11:00) |
Data Organization in Spreadsheets part 1 (Marc) |
| Coffee | |
| Morning (11:15-12:45) |
Data Organization in Spreadsheets part 2 (Marc) |
| Morning (9:30-11:00) |
R session 1 (Zsófia) Introduction |
| Coffee | |
| Morning (11:15-12:45) |
R session 2 (Zsófia) Visualization with ggplot2 |
| Lunch | |
| Afternoon (13:45-15:15) |
R session 3 (Tijs) Data transformation w dplyr |
| Tea | |
| Afternoon (15:30-17:00) |
R session 4 (Tijs) Data tidying with tidr |
| Morning (9:30-11:00) |
R session 5 (Tijs) Programming with R |
| Coffee | |
| Morning (11:15-12:45) |
R session 6 (Marc) Version Control with Git |
| Lunch | |
| Afternoon (13:45-15:15) |
R session 7 (Marc) Collaborating with Github |
| Tea | |
| Afternoon (15:30-17:00) |
Open (data) science Alexandra Sarafoglou |
add, commit, ...statusclone, pull, push, ...To participate in a this 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.
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.
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 on the pop up window.
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, 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.