Wednesday, 18 March 2015

Laboratory automation in a functional programming language

Whenever I write code in Haskell instead of other programming languages, it feels cleaner. Not just more elegant, but also more obviously correct. And that's not just about the lack of side effects and mutable variables. Haskell has stronger typing, which gives the programmer many guarantees and allows you to express more information about the code. It also has tools such as QuickCheck, in which you can state and test further properties that you believe to be true.

We wanted to bring these ideas to the area of laboratory automation. We've had some fairly large and complex lab automation systems in our lab over the years, with multiple robot arms, and dozens of devices to be serviced. These robot arms pass plastic plates containing yeast around incubators, washers, liquid handlers, centrifuge devises and so on. If the plates get deadlocked or left out of the incubator for too long because scheduling operations went wrong, then the experiment is ruined. However, this can happen if the scheduler needs to be able to make decisions on the fly during the experiments. It may need to decide what to do next based on the current instrument readings and current system capacity. So either you make a scheduler that's so simple that you know exactly what it will do in advance (but it can't do the workflow you really need), or you make a scheduler that's complex and flexible, but it's very difficult to analyse its properties. Hmm, I think Tony Hoare already suggested that choice.

So we've written a paper to demonstrate the benefits of programming a lab automation scheduler in Haskell, and in particular to demonstrate the kinds of properties that can be expressed and checked. We illustrate the paper with a fairly simple system and a fairly simple scheduler, but it's immediately obvious that more complex systems and schedulers can be explored by tweaking the code.

This paper was written by the three of us, coming together with three very different perspectives. Colin is a functional programming researcher at the Uni of York who enjoys opportunities to demonstrate the benefits of FP in real world problems. Rob works for PAA, an excellent lab automation company, who build complex bespoke systems (and software) for their clients. They built one of our lab automation systems. I'm both a user of such lab automation systems, and also a user of Haskell, without ever actually being an FP researcher.

The code is available as a literate Haskell file. The entire code is in this file, along with a complete description of what's going on and how it all works, and this file can easily be turned into a readable PDF document (which also includes all the code).

If you've been inspired by the ideas in this work, do please cite the paper:
C. Runciman, A. Clare and R. Harkness. Laboratory automation in a functional programming language. Journal of Laboratory Automation 2014 Dec; 19(6):569-76. doi: 10.1177/2211068214543373.

After some years of use in academic and research settings, functional languages are starting to enter the mainstream as an alternative to more conventional programming languages. This article explores one way to use Haskell, a functional programming language, in the development of control programs for laboratory automation systems. We give code for an example system, discuss some programming concepts that we need for this example, and demonstrate how the use of functional programming allows us to express and verify properties of the resulting code.

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