University of Melbourne
Feb 16-17, 2015
9:00 am - 5:00 pm
Instructors: Isabell Kiral-Kornek, Scott Kolbe, Bill Mills
Helpers: Bryan Paton, Kerry Halupka, Andrew Boyd, Gregory Bass
Research Bazaar - MATLAB Stream
Participants enrolled in the "Programming and Data Analysis in MATLAB" stream at the Research Bazaar conference will attend a Software Carpentry workshop on the first two days. The mission of the Software Carpentry project is to help researchers be more productive by teaching them basic computing skills. Researchers often spend much of their time wrestling with software, but most are self-taught programmers. As a result, they spend hours doing things that should take minutes, reinvent a lot of wheels, and still don't know if their results are reliable. To tackle this problem, Software Carpentry runs two-day workshops at hundreds of sites around the world. These hands-on workshops cover basic concepts and tools, including program design, version control, data management, and task automation. Participants are be encouraged to help one another and to apply what they have learned to their own research problems.
Who: The workshop is restricted to Research Bazaar attendees who signed up for the "Programming and Data Analysis with MATLAB" stream.
Where: Room 103, Old Metallurgy Building (map).
Requirements: Participants must bring a laptop that (a) has a few specific software packages installed, and (b) is able to connect to the wifi network at the University of Melbourne (see instructions for both below). They are also required to abide by Software Carpentry's Code of Conduct.
Also, please download these four data files before arriving at the workshop:
Contact: Please mail isa.kiral@gmail.com for more information.
Schedule
The class schedule can be found here. As well as attending this Software Carpentry workshop, people who signed up for the "Programming and Data Analysis with MATLAB" stream will have the opportunity to attend a number of other elective classes at ResBaz.
Etherpad: https://etherpad.mozilla.org/2015-02-16-resbaz-matlab.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
The Unix Shell
- Files and directories
- History and tab completion
- Pipes and redirection
- Looping over files
- Creating and running shell scripts
- Finding things
- Reference card...
- Lesson notes...
Programming in MATLAB
- Working with arrays
- Reading and plotting data
- Creating and using functions
- Loops and conditionals
- Defensive programming
- Lesson notes...
Version Control with Git
- Creating a repository
- Recording changes to files:
add,commit, ... - Viewing changes:
status,diff, ... - Working on the web:
clone,pull,push, ... - Resolving conflicts
- Reference card...
- Lesson notes...
Setup
Wifi
Prior to the workshop, University of Melbourne staff/students should ensure that their laptop can connect to UniWireless. Instructions on how to do this and where to get assistance can be found here. Attendees from other Australian universities should find out (from the IT website of their home institution) how to connect to the Eduroam wireless network.
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 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.
Windows
nano is the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
lesson material.
Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.
Mac OS X
We recommend
Text Wrangler or
Sublime Text.
In a pinch, you can use nano,
which should be pre-installed.
Linux
Kate is one option for
Linux users. In a pinch, you can use nano, which
should be pre-installed.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Windows
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
Software Carpentry Installer
This installer requires an active internet connection.
After installing Python and Git Bash:
- Download the installer.
- If the file opens directly in the browser select File→Save Page As to download it to your computer.
- Double click on the file to run it.
Mac OS X
The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
(found in
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
Linux
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 on github.com.
Windows
Git should be installed on your computer as part of your Bash install (described above).
Mac OS X
For OS X 10.8 and higher, install Git for Mac
by downloading and running
the installer.
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 (10.5-10.7) use the
most recent available installer for your
OS available
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
Linux
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.
MATLAB
MATLAB is a very popular data analysis environment. It's a commercial product, however most universities provide free licences to their staff and students. University of Melbourne people can find instructions on how to install Matlab on their personal laptop here. Participants from other institutions should ask their IT department for assistance.
The instructors at the workshop will be using latest version of Matlab (2014b). Since each new version has a slightly different look and feel (not to mention new functionality that isn't available in previous versions), it's important that participants also install the latest version.
During the installation process, you'll be asked whether you'd like to install any additional toolboxes (e.g. statistics, curve fitting, aerospace... there are many). The only specialised toolbox required to complete the workshop is the parallel computing toolbox, however if there's other toolboxes that look relevant to your research you may wish to install them for future use. Note that it's not a good idea to install all the available toolboxes, as this makes the installation process take much longer (i.e. don't install a toolbox unless you are very likely to use it - you can always install additional toolboxes later on).