Software Carpentry: Murdoch University

General Information

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.

This workshop is supported by Curtin Institute for Computation, Curtin University, Edith Cowan University, Murdoch University, The University of Notre Dame. The University of Western Australia,

Who: The course is aimed to PhD students from Western Australian Universities

Where: Learning Link, Murdoch University.

Requirements: Participants must bring a laptop with a web browser. They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please email a.rohl@curtin.edu.au or raffaella.demichelis@curtin.edu.au for more information.

Schedule

February 1

09:30	Automating tasks with the Unix shell
10:30	Coffee
11:00	Automating tasks with the Unix shell
13:00	Lunch

February 2

09:30	Programming with Python/R (all-day parallel sessions)
10:30	Coffee
13:00	Lunch
15:30	Coffee
18:00	Wrap-up

February 3

09:30	Version control with Git
10:30	Coffee
11:00	Version control with Git
13:00	Lunch

Etherpad: for the python stream and for the R stream.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

Introducing the Shell
Files and directories
Creating things
Pipes and filters
Loops
Shell scripts
Finding things
Reference...

Programming in Python

Analysing patient data
Repeating actions with loops
Store multiple values in lists
Analysing data from multiple files
Making choices
Creating functions
Errors and exceptions
Defensive programming
Debugging
Command-line programs
Reference...

Programming in R

Analyzing patient data
Creating functions
Analyzing multiple data sets
Making choices
Command-Line Programs
Best practices for using R and designing programs
Dynamic reports with knitr
Making packages in R
Reference...

Version Control with Git

Automated Version Control
Setting Up Git
Creating a Repository
Tracking Changes
Exploring History
Ignoring Things
Remotes in GitHub
Collaborating
Conflicts
Open Science
Licensing
Hosting
Reference...

Setup

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.

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 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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

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 Git Bash:

Download the installer.
Double click on the file to run it.

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’.

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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.

Python

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.

Windows

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Linux

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.)

Download the installer that matches your operating system and save it in your home folder. Download the default Python 2 installer (do not follow the link to version 3).
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).