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).
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:
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.
|Monday||13:00||Introduction to Python|
|14:30||Loops and conditional statements|
|Tuesday||13:00||Defensive programming continued|
|16:15||An introduction to Git|
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.
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.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
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 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.
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.
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
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
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.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).