June 23-24, 2015
9:00 - 17:00
Instructors: Geoff Fucile, Stefan Pfenninger, Thomas Guignard
Helpers: Silvia Witzig, Lionel Walter, Martin Reisacher, Paul Coray, Sebastian Schuepbach, Thomas Julou
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This could be applied to libarians as well. 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 is aimed at graduate students, researchers and librarians. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Language: The class will be taught in English, but the instructors do speak German and French as well.
Geoffrey Fucile works at the SIB Swiss Institute of Bioinformatics and sciCORE - the center for high performance computing at the University of Basel. He is involved in training and research activities in life sciences, with a focus on genomics and structural biology.
Stefan Pfenninger is a postdoc in the Climate Policy Group at ETH Zürich’s Department of Environmental Systems Science.
Thomas Guignard is a Swiss engineer turned librarian now based in Toronto, Canada. He's also a maker and hobby programmer, and strongly believes in empowering kids and adults through a better understanding of technology.
Contact: Please mail firstname.lastname@example.org for more information.
During the same week, Software Carpentry will also be held in Lausanne.
If you are interested in open data, skills learned at this workshop are a perfect introduction to the 2nd Swiss Open Cultural Data Hackathon to be held in Basel on the 1st and 2nd of July 2016.
Please be sure to complete these surveys before and after the workshop.
|09:00||Automating tasks with the Unix shell|
|13:00||Building programs with Python|
|16:30||Have a drink together (at unternehmen mitte)|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
/Applications/Utilities). 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
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).
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
After installing Git, there will not be anything in your
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"
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.
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.
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.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).
We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).
OpenRefine (formerly Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. Please look at the Installation Instructions from the OpenRefine project for more details on how to run OpenRefine on your machine. The instructions below are adapted from this link. We will be using version 2.6-rc2 during the workshop. A Java Runtime Environment (JRE) is required to run OpenRefine. If the installation procedure below fails, make sure you have a working JRE installed on your computer.
Ctrl-Cin the command window that is running OpenRefine. Wait until there's a message that says the shutdown is complete. That window might close automatically, or you can close it yourself. If you get asked, "Terminate all batch processes? Y/N", just press Y.
ctrl(Control) key and click on the app icon
Ctrl-Cin the shell that is running OpenRefine.
OpenRefine is operated from within a web browser (such as Chrome or Firefox). If your browser doesn't open automatically when you start OpenRefine (see above), navigate to http://127.0.0.1:3333/ in your favourite browser to open the OpenRefine window. Please note that even though you use a browser to operate OpenRefine, it is still run locally on your machine, and not on the web.