Week 3 HW: Lab Automation

My Homework

DNA!

Assignment: Python Script for Opentrons Artwork

Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Review this week’s recitation and this week’s lab for details on the Opentrons and programming it. 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. If the Python component is proving too problematic even with AI and human assistance, download the full Python script from the GUI website and submit that:

If you use AI to help complete this homework or lab, document how you used AI and which models made contributions.

Sign up for a robot time slot if you are at MIT/Harvard/Wellesley or at a Node offering Opentrons automation. The Python script you created will be run on the robot to produce your work of art!

At MIT/Harvard? Lab times are on Thursday Feb.19 between 10AM and 6PM. At other Nodes? Please coordinate with your Node.

Submit your Python file via this form.

Yes, I used AI to help generate my code. The majority of the script was generated using ChatGPT. I provided detailed instructions describing what I wanted to achieve specifically, generating a Yin-Yang pattern using the Opentrons platform, including how I wanted the shape to look and how the points should be distributed. However, I still needed to review, test, and modify the code to ensure it behaved as expected. Some adjustments were required to correct positioning and curvature details.

My Google Colab

Post-Lab Questions — DUE BY START OF FEB 24 LECTURE

One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention, and design and deploy experiments remotely.

For this week, we’d like for you to do the following:

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

Malcı et al. (2026) developed Slowpoke, an automated Golden Gate cloning workflow for the Opentrons OT-2 and Flex platforms. The system automates DNA assembly, transformation, plating, and colony PCR, with manual colony picking and plasmid purification. The authors validated the workflow by assembling Level 1 transcription units in Saccharomyces cerevisiae using 19 promoters driving sfGFP expression, and five-part GFP constructs in Bacillus subtilis with different promoter and RBS combinations. They further demonstrated scalability by constructing 62 assemblies encoding secreted recombinant proteins such as endolysin and scFv fragments. Assembly efficiencies exceeded 90% for most constructs, demonstrating that affordable liquid-handling automation can enable high-throughput synthetic biology 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. 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. Example 1: You are creating a custom fabric, and want to deposit art onto specific parts that need to be intertwined in odd ways. You can design a 3D printed holder to attach this fabric to it, and be able to deposit bio art on top. Check out the Opentrons 3D Printing Directory. Example 2: You are using the cloud laboratory to screen an array of biosensor constructs that you design, synthesize, and express using cell-free protein synthesis. Echo transfer biosensor constructs and any required cofactors into specified wells. Bravo stamp in CPFS reagent master mix into all wells of a 96-well / 384-well plate. Multiflo dispense the CFPS lysate to all wells to start protein expression. PlateLoc seal the plate. Inheco incubate the plate at 37°C while the biosensor proteins are synthesized. XPeel remove the seal. PHERAstar measure fluorescence to compare biosensor responses.

For my final project, I intend to use automation tools to optimize a CRISPR-Cas12a diagnostic platform that combines RPA (Recombinase Polymerase Amplification) with cell-free CRISPR detection. The goal is to systematically screen primers, reaction conditions, and crRNAs using high-throughput liquid handling to accelerate assay development. RPA is an isothermal amplification reaction performed at 37-42°C (typically ~39°C). Small changes in primer design, Mg²⁺ concentration, and template input significantly affect performance. Instead of optimizing conditions manually, I will automate reaction matrix setup using an Opentrons OT-2 (or Flex). The robot will:

  • Dispense multiple primer pairs across rows
  • Generate Mg²⁺ concentration gradients across columns
  • Add template dilution series
  • Add RPA master mix

Plates will be sealed and incubated at controlled isothermal temperature using a thermocycler module or external heater. After identifying optimal RPA conditions, I will automate screening of CRISPR detection reactions in a cell-free format.

Variables to test include:

  • Multiple crRNAs targeting different regions
  • Cas12a enzyme concentrations
  • Reporter concentrations
  • Positive and negative controls

Echo transfer RPA products into designated wells. Echo transfer crRNA variants into specific wells. Bravo dispense Cas12a master mix across plate. Multiflo add fluorescent ssDNA reporter. PlateLoc seal plate. Inheco incubate at 37°C for collateral cleavage activation. PHERAstar measure fluorescence kinetics.

Fluorescence over time will be used to calculate signal-to-noise ratios and rank crRNA performance.

Using Ginkgo Nebula or a cloud lab platform, I could upload a crRNA design library and screen 50-200 crRNAs in parallel, integrating automated synthesis, liquid handling, and fluorescence analytics. This would significantly accelerate crRNA optimization.

Final Project Ideas — DUE BY START OF FEB 24 LECTURE

As explained in this week’s recitation, add 1-3 slides in your Node’s section of this slide deck with 3 ideas you have for an Individual Final Project. Be sure to put your name, city, and country on your slide!