All code written by Owen Melville with contributions by Ilya Yakavets, Monique Ngan, ChatGPT and Claude. Workflow code is written by individual users.
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North_Safe.py Contains the reusable code for the control of the North Robot and the North Track which goes between the Cytation 5 and the North Robot. This is the most in-depth file.
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biotek_new.py Contains the code for control of the Cytation 5.
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master_usdl_coordinator.py Contains reusable workflow code that uses multiple instruments: Cytation 5, North Robot & Track & Heater & Solid Dispenser, Photoreactor
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photoreactor_controller Controls the photoreactor via Raspberry Pi Pico. reactor_test.py is the local Pico program.
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requirements.txt What packages need installation to use all this?
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slack_agent.txt Controls messages sent to slack from the robot. Mostly written by ChatGPT.
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vial_manager_gui.py Helps the user ensure the initial state of the system matches the digital state
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robot_state Contains configuration files that abstract objects in the setup, such as pipet tips, racks, positions etc.
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analysis : Contains programs that analyze data from the robot to produce a result usable by the recommenders
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recommenders: Contains programs (eg using Baybe) to recommend conditions
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status: Because we move between different workflows, we keep digital versions of each workflows vial status state.
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tests: Contains short test or commonly used programs for the setup.
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workflows: Contains active workflows that are designed for the setup, such as the color matching workflow.
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photo-reactor : Contains the RPi program for the photoreactor.
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logs : Contains logs from every digital and simulated run
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output : Contains output data. This is gitignored so that data remains locally.
The sample workflow contained in this video is labelled and contains the programming elements in the sample_workflow.py program in the "workflows" directory.
