Getting Started in Bioinformatics coding – Python


Biologists often ask me about where to start learning how to code, and where I learned myself (however limited that may be!). Around 6 and a half years ago, I first began working with perl by editing/personalising a transcriptome pipeline which, like a major proportion of bioinformatics from back then, was probably written for a single purpose without much thought to implementation by other users. After that, I picked up an O’Reilly book (Google O’Reilly + your chosen language) and eventually did a coursera course which taught me some better practices than what I picked up from other people’s code and Google.

A significant complaint that I hear is that a lot of the tutorials that you can find online, in print, and in person (CodeAcademy, Coursera, O’Reilly books etc.) are targeted to learning the core principles, and as soon as you have finished, it quickly slips out of your brain. This is why I now recommend to the Undergraduate and Masters classes, or anyone else who asks, which comes in either in Book or Online form. They teach all of the core concepts in a beginner and advanced course, but are tailored to the kind of tasks you are probably considering taking up the art for. What’s more, the exercises which you perform are real-world applicable which means that a few weeks down the line when you want to do some computational analysis, you already have something saved on your personal computer that likely does half of what you want to do, and you can refresh your memory on.

I’ve just looked at the website and there seems to have been a whole host of new material added since I ran through it a couple of years ago, so it’s definitely worth a look!