Perl for biologists

Perl for biologists

An Advanced Workshop held at the School of Biological Sciences, UQ, 2009

This isn't intended to be a comprehensive programming course. Instead, this course will be tightly focused on teaching you just the things that you need to know to use Perl in your daily work. In my lab, that's often things like reformatting large data files, or telling your computer to repeat the same analysis on 100 different data sets. If you need Perl to do other kinds of tasks, let me know and I will include those skills in the course. But I won't be teaching you how to print "Hello World" to the screen nor discussing the finer technical points of algorithm design.

The course also works from the assumption that you don't know anything about Perl, programming, or using the command line. I start right from the basics. I also remember what it was like learning to program as someone with no programming background and I try (sometimes successfully) to give both intuitive and technical explanations.

If you're wondering what a Perl script looks like, I've put a couple of examples up here to give you an idea of what you'll be getting into.

Class format

Classes will consist of me talking for 30 minutes or so and then practical exercises for 60-90 minutes. I highly recommend staying and doing the exercises during class because extra info and tips will probably emerge in response to people's questions during that time - and because you'll need to have the exercises done before the next class in any case to keep up.

I'll run the class in one of the ILC rooms, so you can either bring your own laptop or work on one of the machines there.

Contacting me

The best place to catch me to ask questions will be at the classes. If you have questions outside those times, my office is room 214 in the Goddard Building, and you can come and see me there any day before 12 noon (afternoons are sacrosanct research time and I'm not available then). You can also email me at

More info

Class notes are indexed here.