Week 3 HW: Lab Automation

Homework

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

Committed Listeners Required

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.
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!
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.

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

https://opentrons-art.rcdonovan.com/?id=86flkdas3nws5bs

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.

Bryant Jr, J. A., Kellinger, M., Longmire, C., Miller, R., & Wright, R. C. (2023). AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots. Synthetic Biology, 8(1), ysac032.

They published an open-source Python software package called “AssemblyTron” and it automates DNA assembly worfklows using the Opentrons OT-2 liquid handling opentrons.. it can automate PCR setupts, gradient optimization, Golden Gate assembly and homology based in vivo assembly.

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.

Idea 1, The engineering of extracted hematopoietic stem cells so their B-cell progeny produces bnAbs and after exposure to an HIV immunogen they can provide protection for a long time after autologous engraftment: AUTOMATION

So, with python I could generate safety kill-switch modules. I could Echo transfer plasmids into 96-well plates, Inhecho incubate the cells, automate ELISA plate reader for measuring antibody secretion.

Idea 2, Geroprotective psilocybin and hallucinogenic blockade/evasion: A liposome that evades the BBB with a geroprotective carrier: AUTOMATION

Automated drug loading quantification via plate reader,

Idea 3, Bioluminiscent trees: AUTOMATION

Echo transfer DNA fragments into 96-well plates, automate Agrobacterium transformation mixes, and potentially a Python image analysis that quantifies glow intensity.

There’s a lot that can be automated; it is not my strength just yet.

Final Project Ideas — DUE BY START OF FEB 24 LECTURE

Committed Listeners Required

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!