Week 3 HW: Lab Automation

Homework

Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME!

Assignees for this section

Your task this week is to Create a Python file to run on an Opentrons liquid handling robot.

0. Review this week’s recitation and this week’s lab for details on the Opentrons and programming it.
1. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com.

Response

https://opentrons-art.rcdonovan.com/?id=32iqzh4w9m44o5k

2. 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.

   Ask for help early!

   If you are having any trouble with scripting, contact your TAs as soon as possible for help.
   Do not wait until your scheduled robot time slot or you may not be able to complete this assignment!

3. 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:

   

   Use the download icon pointed to by the red arrow in this diagram.

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

5. 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.

6. Submit your Python file via this form.

Response

I utilized gemini pro 3.5 and I was able to have it create the nested for loops needed to dispense on a per color basis.

Colab available here: Open My Opentrons Colab Script

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

Assignees for this section

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:

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

Response

https://pmc.ncbi.nlm.nih.gov/articles/PMC11933169/ Enhanced production of bacterial cellulose with a mesh dispenser vessel-based bioreactor.

From my reading of the paper the team created structures for the Komagataeibacter out of mesh and automated nutrient dispensing, the quality and speed of Komagataeibacter’s cellulose production were significantly improved over the control of pellicle formation to produce the bacterial leather.

Loh J, Arnardottir T, Gilmour K, Zhang M, Dade-Robertson M. Enhanced production of bacterial cellulose with a mesh dispenser vessel-based bioreactor. Cellulose (Lond). 2025;32(4):2209-2226. doi: 10.1007/s10570-024-06367-w. Epub 2025 Jan 29. PMID: 40144312; PMCID: PMC11933169.

2. 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.

1. Echo transfer biosensor constructs and any required cofactors into specified wells.
2. Bravo stamp in CPFS reagent master mix into all wells of a 96-well / 384-well plate.
3. Multiflo dispense the CFPS lysate to all wells to start protein expression.
4. PlateLoc seal the plate.
5. Inheco incubate the plate at 37°C while the biosensor proteins are synthesized.
6. XPeel remove the seal.
7. PHERAstar measure fluorescence to compare biosensor responses.

Response

For my final project I can see the possibility of the Opentrons helping by inserting the plasmids into my target organism, automating PCRs for sequencing, and being able to test different combinations of variables very quickly such as growth media or quantity of plasmids needed to successfully express the cellulose synthase within my target organism.

For broader automation goals I would like to also implement automated nutrient delivery systems and leather harvesting systems in order to reduce human oversight of microbial leather production. I am thinking of implementing fluid transfer pumps, temperature controls, and computer vision models to monitor the growth of bacterial leather in my target organism. This would be done with custom made hardware and implementing transfer learning for the vision policies.

Final Project Ideas — DUE BY START OF FEB 24 LECTURE

Assignees for this section

As explained in this week’s recitation, add 1-3 slides with 3 ideas you have for an Individual Final Project in the appropriate slide deck for MIT/Harvard/Wellesley students or for Commited Listeners. Be sure to put your name on your slide(s); for CLs, also put your city and country on your slide(s) and be sure you’re putting your slide(s) in your Node’s section of the deck.

Response

Automated microbial leather production

• Utilizing sensors to monitor target organism (Komagataeibacter) health and nutrient conditions in growth tank

• Leveraging fluidics automations for a custom nutrient delivery fluidics system

• Computer vision learning to develop contamination detection models

Expressing cellulose growth in model organisms

• Utilizing Twist Biosci gene synthesis we can take the Komagataeibacter’s cellulose synthase and then insert that plasmid into a model organism such as yeast or E. coli to test whether a fast-growing model organism can produce bacterial cellulose.

Adapting fluorescent protein expression in Komagataeibacter

• We can genetically modify Komagataeibacter to express a fluorescent protein and see if that might carry over and last into the bacterial leather after the post processing of the pellicle.
• We could use gene synthesis to produce the required DNA strands prepackaged in a plasmid from Twist Biosci.
• The transformation of the plasmid into the Komagataeibacter can be automated by the Opentrons system in order to test variations on how we approach gaining fluorescence within Komagataeibacter