Feb 1-3, 2016
9:30 am - 5:30 pm
Instructors: Andrew Rohl, Raffaella Demichelis, Philipp Bayer, Matthias Liffers, Lukas Weber, Chris Bording
Helpers: Mark Agostino, Marco De La Pierre, Carla de Tomas Andres, Paolo Raiteri, Bernhard Reischl, Kelly Rensing, Irene Suarez-Martinez, Amy Whitehead
Software Carpentry's mission is to help researchers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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.
Who: The course is aimed to PhD students from Western Australian Universities
Requirements: Participants must bring a laptop with a web browser. They are also required to abide by Software Carpentry's Code of Conduct.
|09:30||Automating tasks with the Unix shell|
|11:00||Automating tasks with the Unix shell|
|09:30||Programming with Python/R (all-day parallel sessions)|
|09:30||Version control with Git|
|11:00||Version control with Git|
Please note that we will be using the ResBaz cloud to do the Software Carpentry courses. So the only software you need is a web browser. However if you want to use the tools you learn about you should have them installed on your laptop. So please try to install the sofware below before you come to ResBaz and then you can get help if you have any problems.
This page has instructions on testing that you have the right software installed.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection.
After Git Bash:
Information about the SWC Windows Installer, including the source code, can be found at https://github.com/swcarpentry/windows-installer.
On Windows machines, you may experience a problem with Git Bash running nano, despite it being installed and in the path. The error message is “Redirection not supported”. To fix the error, Git for Windows needs to be reinstalled. On the 6th page of the installation wizard (the page titled ‘Configuring the terminal emulator...’) select ‘Use Windows’ default console window’.
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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.7) use the
most recent available installer for your
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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.
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 an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.
We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)
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).