Week 3 HW: Lab automation
HW 3: Lab automation
Assignment: Python Script for Opentrons Artwork
Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons. You may use AI assistance for this coding — Google Gemini is integrated into Colab (see the stylized star bottom center); it will do a good job writing functional Python, while you probably need to take charge of the art concept. If you’re a proficient programmer and you’d rather code something mathematical or algorithmic instead of using your GUI coordinates, you may do that instead.
Here are some drafts from my review of the website:
And finally the one i liked the most:
And its code:
Post-Lab Questions
Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
What they did: The researchers developed an automated method to manufacture “synthetic cells” (microscopic fat-based bubbles known as Giant Unilamellar Vesicles, or GUVs) using an Opentrons OT-2 liquid-handling robot. Previously, these synthetic cells were made by hand in a slow, tedious process that often produced inconsistent results.
Why it matters: By using a robot, the team was able to produce hundreds of identical synthetic cells in a single experiment with high precision. This allows researchers to study complex biological processes or test new medicines in a controlled environment that mimics the membrane structure of living cells, but without the complications of using complex living organisms.
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. While your description/project idea doesn’t need to be set in stone, we would like to see core details of what you would automate. This is due at the start of lecture and does not need to be tested on the Opentrons yet.
Final Project Description: Autonomous Fabrication of Synthetic Immune-Sensing Protocells Project Vision: My project aims to automate the production of synthetic cells (Protocells) that function as “sentinels” for the immune system. Instead of using living cells, which are difficult to standardize and maintain, I will build lipid-based vesicles from scratch. These synthetic cells will be “programmed” to detect specific antigens in a blood-like environment and produce a fluorescent signal in response.
Implementation Plan:
DNA Circuit Design (Ginkgo Nebula): I will use the Ginkgo Nebula platform to design a cell-free genetic circuit. This circuit will consist of a specialized promoter that triggers the expression of Green Fluorescent Protein (GFP) only when a specific immune marker (like a cytokine) is present.
Automated Assembly (Opentrons OT-2): I will utilize the Opentrons robot to perform a Phase Transfer Assembly. The robot will precisely pipette aqueous “cytoplasm” (containing the DNA and cell-free machinery) into a lipid-oil phase. The automation is critical to ensure that thousands of vesicles are produced with a uniform size and encapsulation efficiency.
Custom Hardware (3D Printing): I plan to design and 3D print a custom aluminum block adapter or a “Vesicle Collection Rack.” This holder will be optimized for the Opentrons deck to keep the lipid-oil mixtures at a stable temperature, preventing the lipids from aggregating during the delicate phase-transfer process.
Example Automation Pseudocode:
This script represents the logic for creating different “batches” of synthetic cells with varying sensitivity levels.
And the python:
Final Project: Synthetic Cell Assembly Logic
def run(protocol): # 1. Load Labware temp_mod = protocol.load_module(’temperature module gen2’, 6) lipid_plate = temp_mod.load_labware(‘opentrons_96_aluminumblock_generic_pcr_strip_200ul’)
# 2. Preparation of the "Synthetic Cytoplasm"
# Mixing Ginkgo-designed DNA with Cell-Free TX-TL system
pipette.pick_up_tip()
pipette.aspirate(10, dna_source)
pipette.aspirate(10, cell_free_mix)
pipette.dispense(20, mixing_vial)
pipette.mix(5, 15)
# 3. Vesicle Formation (Phase Transfer)
# Carefully layering the aqueous mix over the lipid-oil phase
for well in target_wells:
pipette.aspirate(2, mixing_vial)
# Slow dispense at the interface to form GUVs
pipette.dispense(2, lipid_plate[well].top(-2), rate=0.1)
pipette.drop_tip()