Albert Einstein Science Park, Potsdam

May 17-18, 2017

9:00 - 18:00

Instructors: Martin Hammitzsch (GFZ), Stefan Lüdtke (GFZ), Marvin Reich (GFZ), Till Francke (UP), Berry Boessenkool (UP), Peter Evans (GFZ)

Helpers: Knut Günther (GFZ), Joachim Krois, and instructors

General Information

This workshop is a R-Workshop with a focus on scientific computing. Everyone with solid basic knowledge of R or a similar scripting language is invited to join and getting in touch with tools and structures to write scientific code with a high-quality, that is reproducible and follows a well-documented standard.

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 aims at scientists and researchers who are interested in extending their skills in data processing and techniques on "how to write good scientific code" and how to deal with this in a broader context. Solid knowledge of R or a similar scripting language is required. We start the workshop with a R-wrap-up to get everyone on board.

Where: GeoLab, A27 (Großer Refraktor), Albert-Einstein Wissenschaftspark, Telegrafenberg, 14473 Potsdam. Get directions with OpenStreetMap or Google Maps.

When: May 17-18, 2017. Add to your Google Calendar.

Requirements: Participants are highly encouraged to usw the provided IT-infrastructure (computer). This is a Linux system. Please note that the content taught can be used and easiliy be transfered later on to other operating systems. If you implicitly want to use your own laptop, we cannot guarantee full support. An installation routine (also only for Linux) will be provided in advance, so you can install the required software. Specific software packages required are 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. Please contact the organisers if you have any requirements and/or need assistance to access the workshop rooms.

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 and we will attempt to provide them.

Contact: Please email or for more information.

Organization: We're happy to announce that these workshops are jointly organised by the GFZ German Research Centre for Geosciences, the Potsdam Institute for Climate Impact Research (PIK), the University of Potsdam (UP), and others.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

09:00 Arrival & coffee
09:30 Welcome & introduction
09:45 Lightning talks by participants
10:30 Software set-up
11:00 Coffee
11:30 The Unix Shell
13:00 Lunch
14:00 Version Control with Git (and Gitlab)
15:30 Coffee
16:00 Introduction to R and Rstudio & Project Management
17:30 Wrap-up

Day 2

09:00 Arrival & coffee
09:30 Functions and Unittests
11:00 Coffee
11:30 Code optimization (Vectorization, profiling, parallelization)
13:00 Lunch
14:00 Debugging und Packages
15:30 Coffee
16:00 Tidyverse and ggplot
17:30 Wrap-up


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Resolving conflicts
  • Working on the web: clone, pull, push, ...
  • Where to host work, and why
  • Reference...

Programming in R

  • Introduction to GUI Rstudio and some R basics
  • Writing functions and testing them
  • How can you optimize your code and what do you have to do for that?
  • Debugging
  • Writing your own R-package
  • The tidyverse and ggplot2


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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X 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 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 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).

Mac OS X

Video Tutorial

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 yum install git.

Text Editor

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 Mac OS X 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.


Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software 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.

Mac OS X

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.


Video Tutorial

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.

Mac OS X

Video Tutorial

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 yum install R). Also, please install the RStudio IDE. To get the latest R version on Ubuntu, use:
sudo echo "deb xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get install r-base r-base-dev

Replace xenial with e.g. trusty if you have another Ubuntu version: Ubuntu 16.10 yakkety, 16.04 xenial, 14.04 trusty, 12.04 precise