Week 3 HW: Lab Automation

Part 1: Python Script for Opentrons Artwork

I used Ronan’s provided GUI and a nice little pixelart of a kidney to try out the design and figure out coordinates. Python coding was new and quite… surprising. But using the toad.py provided by the USFQ node I figured out how to get the code to work. This is a kidney art that i’ll try to print. Hopefully it actually resembles something!

This is a small test of the gui and code, it reads nefrologia (nephrology in portuguese) and has a small heart.

Part 2: Post lab

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details.

https://www.nature.com/articles/s44172-025-00575-3 is the paper I picked because it initially uses opentrons for a small scale production of a living cell hydrogel. I found it quite alike my proposed final project product so it may serve as a nice starting point to figure out fabrication. Although the paper uses their product for drug trialing instead of what I proposed.

I reckon the best use of automation for my idea is to help with the fabrication with properly placing the scaffolds and the microvesicules in between them.

Part 3: Final project ideas

I uploaded my ideas to the slide deck. Here is a copy of my slide and ideas.