University of Melbourne

Alan Gilbert Building
Mar 18, 21, 26 & 28, 2014
9:00 am - 12:30 pm

Python for Bioinformatics Bootcamp

Researchers 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, an international volunteer organisation known as Software Carpentry has been running bootcamps for a number of years now, teaching basic lab skills for computing like program design, version control, data management and task automation. With support from the ITS Research Services department, The Hacker Within student group has been running Software Carpentry bootcamps at the University of Melbourne since 2013. For this particular bootcamp, we are teaming up with COMBINE to offer a course specifically for the computational biology and bioinformatics community.

Instructors: Damien Irving

Who: This bootcamp is restricted to postgraduate students, post-docs and other researchers in the Australian computational biology and bioinformatics 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 not restricted to University of Melbourne people - we'd love to see many computational biology and bioinformatics institutions represented.

Where: Alan Gilbert Building, University of Melbourne. We are in Theatre 4 for this first week of the bootcamp and Theatre 3 for the second.

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.

Requirements: Participants are asked to bring their laptop with some specific software packages installed and access to either the UniWireless or Eduroam wifi networks (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:

Contact: Please mail d.irving@student.unimelb.edu.au for more information.

Schedule

In order to accommodate as many people as possible, we are going to spread the content of the typical two-day bootcamp over four morning sessions. The following is an outline of what will be taught. During the bootcamp, additional notes on the teaching materials will be available at the bootcamp Etherpad.

Session 1: The basics
Tuesday 18 March, 9:00am-12:30pm, Theatre 4
The key to being a proficient programmer is solid fundamentals. In this session you'll learn the basics of the unix shell, which is the cornerstone of software carpentry.

Sessions 2 & 3: Programming like a programmer
Friday 21 March, 9:00am-12:30pm, Theatre 4
Wednesday 26 March, 9:00am-12:30pm, Theatre 3
Have you ever wondered how professional programmers write code? In this session you'll learn the common tricks of the trade, via an introduction to the Python programming language. From defensive programming, error handling and debugging to unit testing and test-driven development, the skills learned in this session are transferrable to any language.

Session 4: Version control
Friday 28 March, 9:00am-12:30pm, Theatre 3
Do you work in a small research team that shares code? Do you struggle to keep track of multiple versions of the same code? Would you like an easier way to backup your work? This session will teach you everything you need to know about git, a version control system that can solve all these problems and more.

Setup

Prior to the bootcamp, 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.

Besides a working wifi connection, you will also need working copies of the software described below. Please make sure to install everything before the start of the bootcamp.

Software installation: 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.

Software installation: 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.

Software installation: 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.

Software installation: 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).