Albert Einstein Science Park, Potsdam, Germany

April 25-26, 2018

9:00 - 18:00

Instructors: Martin Hammitzsch (GFZ), Stefan Lüdtke (GFZ), Marvin Reich (GFZ), Till Francke (UP), Berry Boessenkool, Peter Evans (GFZ), Robert Gieseke (PIK), Daniel Beiter (GFZ)

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

An Introduction to Scientific Computing and Reproducible Research

General Information

This workshop focuses on scientific computing and reproducible research using tools such as the shell, git and R. The workshop is aimed at participants who already have basic experience with R. You should be comfortable with using R to read, subset and visualize a dataset, as well as perform tasks conditionally (with if-else statements) and repeatedly (with for and lapply loops).

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. Basic knowledge of R or a similar scripting language is required.

Where: PIK (Potsdam Institute for Climate Impact Research), Kuppel, Albert-Einstein Wissenschaftspark, Telegrafenberg, 14473 Potsdam. Get directions with OpenStreetMap or Google Maps.

When: April 25-26, 2018. Add to your Google Calendar.

Application: Register online for the workshop by April 03, 2018. There are limited places available. The application form is found here.

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. 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.

Contact: Please email swc-workshop-org@gfz-potsdam.de for more information.

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


Schedule

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, Profiling and Debugging
13:00 Lunch
14:00 Tidyverse
15:30 Coffee
16:00 Visualizations in R (ggplot)
17:30 Wrap-up

Etherpad: http://pad.software-carpentry.org/2018-04-25-Potsdam-Berlin.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

The Unix Shell

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

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...

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
  • The tidyverse and ggplot2

Setup

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.

Windows

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.

Linux

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

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.

Windows

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.

Linux

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.

Windows

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.

Linux

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

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

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.

Linux

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 http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --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