Introduction

Experimental Automation & Optimisation

The automation of experimental processes has the potential to revolutionise workflows of scientists in both academic and industrial laboratories. Leveraging robotics enables experiments to become more accurate, safe and reproducible while decreasing the overall experimental time. Scientists can also focus on the more important aspects of their research through automating laborious and repetitive tasks.

A major benefit of experimental automation is the opportunities it brings for implementing automated, closed-loop experimental optimisation. Experimental optimisation is the procedure of finding parameter values that optimise a response in the least number of trial runs. Traditional experimental optimisation procedures, such as grid-search optimisation, are often time and resource inefficient. Automation enables the integration of more efficient optimisation algorithms, such as particle swarm optimisation, within a closed-loop framework. This gives scientists the power to harness the full capabilities of both experimental automation and modern experimental optimisation techniques.

Although experimental automation and optimisation offer great potential, in practice there are a wide range challenges that arise when integrating them into laboratories. Automation is an expensive endeavour with logistical factors such as the cost of equipment, installation, maintenance, consumables and lab space requiring careful consideration. Technical factors like retraining staff or hiring staff with programming experience can further increase the costs and time needed. In particular, these challenges are pronounced in the settings of small to medium scale laboratories, such as in academia, where budgets are limited and research goals are ever changing.

Opentrons OT-2 Robot

Opentrons is a US-based biotech business that specialises in manufacturing liquid handling robots to further the field of experimental automation. Their mission is to make robotics more accessible to laboratories, tackling the challenges mentioned in the previous section and empowering scientists with experimental automation.

The Opentrons OT-2 is an affordable bench-top liquid handling robot designed to automate lab work such as dispensing, mixing and transferring liquids. It supports the use of up to two single-channel or eight-channel pipette heads, enabling the handling of liquids between 1μL and 1000μL in volume. The OT-2 is a modular robot and compatible with ANSI/SLAS-compliant lab equipment, making it a flexible platform that can be customised to perform more complex tasks and experiments.

A highlight of the OT-2 is its open-source software, which allows scientists to develop custom protocols that meet their experimental requirements. Opentrons provides the Opentrons API through the opentrons package for developing custom protocols that control the OT-2. Developed protocols can be uploaded to the OT-2 through the Opentrons App which offers a straightforward graphical user interface for robot calibration, protocol management and protocol execution.

What Does OptoBot Do?

OptoBot is a package for implementing automated experimental optimisation using the Opentrons OT-2 liquid handling robot. It aims to provide scientists with a simple interface for implementing closed-loop experimental optimisation in their own work with minimal programming experience.

In its current implementation OptoBot focuses on automating and optimising colorimetric experiments. These are experiments where the experimental products can be assessed based on their measured RGB colour using a camera. For example, an experiment where red, yellow and blue liquids (e.g. food colouring) along with water are mixed to produce a pre-defined target colour. The experimental setup of such an experiment is shown below.

Figure: An example experimental setup for a colorimetric experiment.

OptoBot can also be used to semi-automate and optimise other experiments but manual measurements of experimental products and manual inputs are required. We aim to develop features for automating a wider range of experiments in the future.

OptoBot addresses the wider challenge of decreasing the programming barrier for integrating automated experimental optimisation in small to medium scale laboratories. While the Opentrons API provides a powerful and comprehensive interface for controlling the OT-2, it does not come with built-in features for experimental optimisation. Furthermore, the lack of open-source packages in this area is an important driving factor for development of OptoBot.