Monash University

Faculty of Medicine, Nursing and Health Sciences (Krongold Centre (Building 5) / Room G19), Wellington Road, Clayton, Victoria 3800
Jun 02-04, 2014
1:00 pm - 5:00 pm

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This three half-day hands-on bootcamp will cover basic concepts and tools including Python, Git and using the command line; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors: Matthew Dimmock, Damien Irving

Who: This bootcamp is restricted to postgraduate students, post-docs and other researchers in the Australian biomedical imaging and the broader biomedicine community who have a basic familiarity with programming concepts like loops, conditionals, and arrays, but need help to translate this knowledge into practical tools to help them work more productively. Participation is primarily for, but not restricted to, Monash University people. There are 40 places available, so get in quick.

For those participants who do not have a basic familiarity with programming (i.e. first time programmers), we are running an optional "Introduction to the Command Line" session from 1-5pm on the Friday prior to the bootcamp (30 May). It will be held in computing room 143 in Building 17 (first floor of the Biology building).

Where: Faculty of Medicine, Nursing and Health Sciences (Krongold Centre (Building 5) / Room G19), Wellington Road, Clayton, Victoria 3800. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants are asked to bring their laptop with some specific software packages installed (see the setup instructions below for details). If you don't have a laptop, that's completely fine. We'll pair you up with someone who does.

Also, please download these four data files before arriving at the bootcamp:

Please download the IPython Notebook:

Registration: All participants are required to register at the Eventbrite page. The registration process involves a 5-minute questionnaire about your previous programming experience, so that we can tailor the teaching materials to the knowledge of the audience. We also require the head of each group to make a $50 donation to the Mozilla foundation for each PhD student or Post-doc that registers.

Links: Please view the Etherpad for answers to many FAQs.

Contact: Please mail Matthew.Dimmock@monash.edu for more information.

Schedule

Monday	13:00	Introduction to Python
	14:15	Break
	14:30	Loops and conditional statements
	16:00	Break
	16:15	Defensive programming
	17:00	Wrap-up
Tuesday	13:00	Defensive programming continued
	14:15	Break
	14:30	Command-line execution
	16:00	Break
	16:15	Image processing
	17:00	Wrap-up
Wednesday	13:00	Histogramming
	14:15	Break
	14:30	Scientific libraries
	16:00	Break
	16:15	An introduction to Git
	17:00	Wrap-up

Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

Git is a state-of-the-art version control system. It 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.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

Windows

Editor

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.

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Bash

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

Install Git for Mac by download and running the installer.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Linux

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

Python

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.
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).