March 19-20, 2016
9:00 am - 4:00 pm
Instructors: James Desjardins
Helpers: Allan Campopiano, Stefon VanNoordt, Pawel Pomorski
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 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 and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Contact: Please mail email@example.com for more information.
|09:00||Orientation and Basics of Unix shell|
|10:45||Automating tasks with the Unix shell|
|13:00||Version control with Git|
|14:45||Version control with Git|
|09:00||Introduction to Octave/Matlab basics|
|09:00||Handling data and writing functions in Octave/Matlab|
|13:00||Introduction to SHARCNet basics|
|14:45||Using Octave on SHARCNet systems|
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.
For the Octave/Matlab session using either Octave or Matlab will work. If you already have a Matlab license and it is installed on your computer you do not need to install Octave. If you wish to purchase a Matlab license or install a trial version visit MathWorks (note that a trial installation may take up to a week to set up). Octave is an open source scientific computing language that is highly compatible with Matlab. The instructor of this session will be using Octave 4.0.0 in the demonstrations. For Octave installation instructions visit the Octave Download page.
SHARCNet is a High Performance Computing (HPC) consortium that offers free resources to Canadian researchers and their international collaborators. The HPC resources come in the form of compute and storage hardware, documentation and training, as well as expert support. In order to take part in the hands on SHARCNet session, attendees are required to have a SHARCNet account prior to arriving at the session. In order to get a SHARCNet account follow these getting a SHARCNet account instructions (note that a SHARCNet account may take up to a week to set up).