How well does a biologist need to be able to code to automate protocols?


How confident is the average wet lab biologist with coding? As questions go, this one is about as open-ended as ‘how long is a piece of string’.

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Wet lab biologists typically span an entire spectrum of coding experience, with scientists unaccustomed to ever using the command line at one end and those with extensive expertise in a range of programming languages such as R, Python and Perl, at the other. It is not surprising that many biological scientists are not well versed in programming. Programming has habitually not formed an essential part of undergraduate biology and biochemistry curricula and most traditional wet lab techniques, such as cloning, PCR, ELISA and so on, have no requirements for such skills. With modern developments in automation and data processing, however, the role that computing has in the wet lab environment is only set to grow.

Figure 1. Example of the Antha programming language


Antha is set to change how we work in the wet lab by providing the tools to rapidly automate and increase the throughput of biological protocols. This is powered by the Antha language (Figure 1), which enables users to program and execute their protocols in an incredibly flexible and transferable way. The language is designed such that users have high-level control over the protocol, so that it is executed effectively, without the user needing to worry about minutiae, such as detailing every liquid handling step, loading tips and resetting pipetting channel pistons. Writing a full protocol in Antha undoubtedly requires a good grasp of the language, this however is in no way beyond the reach of lab biologists, with tutorials and case studies provided to help all learners get to grips with the language. For those either not ready or not having the time to develop this level of expertise, other options exist, allowing you to get huge benefits from Antha, without devoting a  lot of time developing extensive coding skills.

Baked in workflows such as Type IIs Construct Assembly (Figure 2), allow you to carry out large, automated protocols without any complicated setup steps. In the case of Type IIs Construct Assembly, it is simply a case of uploading an Excel file containing your required assembly combinations and the Antha Job is created for you. As an extension to this, it is also possible to wire together existing elements in the Antha Work Flow Editor (Figure 3), for example read a plate layout file with solutions (“ParsePlate” in the example below) and then transfer these to a different location (“Transfer_multi”), or carry out a construct assembly and wire this directly into a transformation. Users can stitch existing elements or protocols together and alter parameters to be relevant for their experiment, all through an accessible user interface.

Figure 2. Baked in workflows can provide immediate, out-of-the-box functionality.

Figure 3. Wiring together established elements provides even greater flexibility without the need to develop in-depth coding skills

Therefore, how much a wet lab biologist needs to learn to code in order to use Antha, is flexible and up to individual requirements and interests. Certainly, an in-depth knowledge of the language can provide great flexibility when it comes to writing your own protocols but Antha also has plenty to offer the novice programmer, meaning whatever your level of coding experience, Antha can offer you huge gains in your lab automation.

About the author

Charlotte WardI came to work at Synthace after completing BSc and PhD degrees in biochemistry. I was really excited by how Synthace wanted to take a different approach to biology, particularly by applying developments in computer science to leverage what we can achieve in biology. I am now a senior research scientist working on developing protocols in Antha to automate biological processes
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