June 20-21, 2016
9:00 - 17:00
Instructors: Julia Gustavsen, Diana Marek, Thomas Guignard
Helpers: Julien Delafontaine, Raphaël Grolimund, Pablo Iriarte, Igor Milhit, Pablo Iriarte, Jan Krause, Séverine Duvaud, Panu Artimo
This workshop is hosted by the SIB Swiss Institute of Bioinformatics, at the University of Lausanne (UNIL) with support from SIB, Library Information Switzerland (BIS), the swissbib project and the Scientific Information School.
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.
Where: Université de Lausanne, room 2020 (2nd floor, same floor as main entrance), Bâtiment Génopode, UNIL Sorge, 1015 Lausanne. Find the room on Planète UNIL, get directions on OpenStreetMap or Google Maps.
Language: The class will be taught in English, but the instructors do speak French as well.
Julia Gustavsen is a PhD student at the University of British Columbia in Biological Oceanography. Her thesis work focuses on the changes in marine viral communities over time and space.
Diana Marek works at the SIB Swiss Institute of Bioinformatics, where she is involved in scientific collaborations, teaching bioinformatics for postgraduates, as well as in coordinating training and outreach activities, such as scientific fairs, conferences, seminars and workshops for the layperson as well as for scientists.
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, another Software Carpentry workshop will also be held in Basel.
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|
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).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.
SQLite comes pre-installed on Mac OS X.
SQLite comes pre-installed on Linux.
If you installed Anaconda, it also has a copy of SQLite
without support to
Instructors will provide a workaround for it if needed.