FAQ & Notes

When I use the get_colours function and run an optimisation script, I get errors related to figures not appearing. What should I do?

If using a Linux OS, ensure that the Python bindings for the chosen graphical user interface backend are installed and up to date.

For the Tkinter backend, use the following command to update bindings.

$ sudo apt install python3-tk

For the Qt5 backend, use the following command to update bindings.

$ sudo apt install python3-pyqt5

Under Development

True Automated Optimisation

The current implementation of OptoBot was developed in an environment where the Opentrons OT-2 robot was not connected to the internet. This meant that 3rd-party Python packages could not be installed on the OT-2 (through SSH), limiting the complexity of the OT-2 protocol script. As a consequence, the current implementation of OptoBot handles the optimisation process on the user’s computer and generates an OT-2 protocol script between iterations of optimisation. The user has to upload the generated OT-2 protocol script at each iteration of optimisation, making the optimisation loop semi-automated. Despite its semi-automated nature, the current implementation of OptoBot is flexible and offers easier integration with custom measurement processes of experimental response variables.

A feature for users that have an environment where their Opentrons OT-2 is connected to the internet and want to take advantage of a true automated optimisation loop is under development. This feature will generate a OT-2 protocol script that contains the entire experimental optimisation workflow, where the instructions for the OT-2 are updated in real-time at each iteration of optimisation. The user will have to upload the generated OT-2 protocol script to the OT-2 just once and the whole process will be automated. Although this feature implements a true automated optimisation loop, it is less flexible as the measurement of experimental response variables between each iteration of optimisation have to be automated through the OT-2 itself. Manual measurement processes of experimental response variables will not be supported and users should use the default semi-automated version that OptoBot offers in its current implementation.