Advanced Python for Biologists

Posted 2013-12-05 by Martin Jones in Announcements.

When I was writing Python for Biologists (see my previous guest post) I was extremely ruthless about leaving material out. I wanted the book to cover pretty much the same set of language features that I teach in my instructor-led introductory programming courses, which meant I had to limit the scope of the book to what an average, motivated beginner could take in in a full-time week of study. This restriction meant that, while I think the overall balance of material in Python for Biologists is still the most useful set for novice programmers, there are big topics that didn't make the cut. There's no mention of object-oriented or functional programming, nothing about Python's extremely elegant comprehension syntax, and nothing on recursion. As I was writing, I made a list of all these omissions, with the promise to myself that I would write about them some day.

Recently, a couple of things have been co-incidentally happening at the same time that have got me thinking again about the importance of exploring a programming language beyond the basics. Firstly, I've been writing the follow-up to Python for Biologists (it's called, unsurprisingly, Advanced Python for Biologists, and you can read about it here) and I've found myself concentrating on the chapters that discuss different approaches to programming: object-oriented programming, functional programming, and recursion. Secondly, I've been watching my current class of students make the conceptual leap from procedural to object-oriented programming in the MSc course on which I teach. Both of these things have left me thinking about the important role that knowledge of a programming language plays in determining how people solve computational problems.

For the new book, I've started each chapter by laying out a problem and showing how to solve it using procedural code, before showing an alternative, better solution that involve object-oriented/functional/recursive programming. What strikes me forcibly in each case is not only the degree to which the object-oriented/functional/recursive solutions are better, but how simply knowing that such techniques exist open up a whole new approach to problem-solving. Recursive functions are great for processing tree-like data, for example, but it's unlikely that anyone would come up with them without having been explicitly introduced to recursion. This isn't because the concept is especially hard to grasp—it's just that recursive solutions simply aren't part of the conceptual toolbox of a procedurally-trained programmer. The same goes for higher-order functions: they allow us to solve certain sets of problems very elegantly, but in a way that's completely non-obvious to someone who hasn't been taught about functional abstraction. And, as the examples of code I see from my students makes clear, switching from procedural to object-oriented code (which makes some types of problems much easier to solve) requires changing the way we think about state.

In a way, this line of thought is a programmer's version of the Sapir-Whorf hypothesis: the idea from linguistics which posits that the structure of the language you speak affects your mental model of the world. Not being a linguist, I don't know how the Sapir-Whorf hypothesis (Wikipedia tells me that it is know known as "linguistic relativism") is currently viewed as applied to natural languages, but as a instructor, I definitely think that it applies very well to programming languages. If the language you know and use (or rather: the subset of features in that language that you know and use) doesn't include classes, first-class functions, or recursion, then those approaches to looking at and solving problems are unlikely to be at your disposal.

That's why I'm currently concentrating on writing about advanced Python features for use in biological analyses—including object orientation, higher-order functions, and recursion. If a programmer never goes beyond the basics then they're not just missing out on language features that could make life easier, they're missing out on entire ways of thinking about problems and their solutions. Incidentally, this is part of the reason that I'm a big fan of Python as a first language for teaching. It allows (but does not enforce) object-oriented and functional approaches to problem-solving, and the syntax for each is lightweight enough to allow the student to concentrate on the structure of code rather than the specifics.

So if you're comfortable with the basics of programming—and maybe you've already written a fair few useful programs—I encourage you to seek out the corners of your programming language that you haven't yet ventured into. With any luck, what you'll find there is not just new features, but new ways of thinking.

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