Instructors:
Katrin Leinweber, Tobias Weiß, Marc Hanisch, Maximilian Dolling, Peter Evans, Bezaye Tesfaye, Stefan Lüdtke, Jannes Breier, Berry Boessenkool, Michael Dietze
Helpers:
Knut Günther, Matthias Rüster, Nils Brinckmann, Vivien Stender, Gesa Petersen, Tabea Rettelbach, Heidrun Matthes, Phillip Tiburtius, and instructors
General Information
Together with the advancement of new tools and techniques, and
the availability of large datasets in different research domains,
a solid understanding of common scripting languages and version
control systems is becoming more and more important for many researchers.
Having the knowledge and skills on how to use tools and techniques to
analyze data efficiently, to preserve research output and to collaborate
with peers benefit every research domain. So its important to close the
gap between researchers and the know-how for new tools and techniques.
Software Carpentry aims to provided this support.
It is an interactive workshop including sessions from concepts to practice on
topics that can be used in many research domain. The sessions are organized
in a friendly environment, where people can learn from each other and share
experience. Participants also get support throughout the whole sessions.
Who:
The workshop targets audience from graduate students to advanced researchers, and
doesn't require previous knowledge of topics that will be covered.
Where:
Albert Einstein Science Park, House H, Room V2+3, Telegrafenberg, 14473 Potsdam.
Get directions with
OpenStreetMap
or
Google Maps.
Requirements: Each participant must bring a laptop (not a tablet, Chromebook, etc.) pre-installed
with preferred operating system of his/her own and software packages listed HERE. And should have administrative right for it.
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:
There will be an eduroam wlan during the workshop.
We will provide WiFi guest tickets as a backup as well.
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.
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
Select "Use the nano editor by default" and click on "Next".
Keep "Git from the command line and also from 3rd-party software" 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.
Click on "Next".
Select "Use the native Windows Secure Channel library", and click "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" and click on "Next".
Leave all three items selected, and click on "Next".
Do not select the experimental option. Click "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press Enter)
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press Enter, you should see SUCCESS: Specified value was saved.
Quit command prompt by typing 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
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.
You will need an account at GitLab.com
for parts of the Git lesson. A basic, free account is sufficient and can be deleted after the lesson.
If you want to keep it, 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.
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.
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 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.
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.
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.