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Lab Automation

Part 1: Phyton Code & Agar Design

Documentation:

• For the first part of the Lab Automation assignment, I worked with Opentrons Python code using Google Colab. During this process, I used ChatGPT primarily as a debugging and learning aid. It helps me resolve execution errors, install missing packages (via pip), and understand how to structure the notebook so the design can be visualized correctly.
• Because the shared notebook relies on Opentrons hardware-specific functions (such as load_labware), the code was adapted to allow local visualization without a physical robot. My draft version originally included labware definitions intended for real laboratory execution, but these were temporarily removed to enable Plotly-based visualization.
  • If you are interested in reading my code, please enter the following link: https://colab.research.google.com/drive/18Pb0JAgtB5Sv8v3VHhfop3mpF-nUiMp8?usp=drive_link

The agar design was inspired by the ducks from Spirited Away (Studio Ghibli), based on my own drawing, combined with online references.

The final pixel-art layout was generated using the Opentrons Art Generator and can be viewed here:

https://opentrons-art.rcdonovan.com/?id=5s7w0mpt758a7af

Code Building Pipeline

To make the workflow clearer, the notebook was divided into three logical blocks:

flowchart TD
    A[OpentronsMock Definition] --> B[Main Protocol Code]
    B --> C[Visualization with Plotly]

• Block 1: Defines the virtual Opentrons environment and data recording
• Block 2: Executes the dispensing logic and color mapping
• Block 3: Displays the final agar pixel-art model

1. Opentrons Mock Definition:

This block defines a mock version of the Opentrons protocol (OpentronsMock).