https://colab.research.google.com/drive/1paKij1Uiu7vJOUQpVmkJXCnruU4QnEni?usp=sharing

Post Lab Questions | Mandatory for All Students

One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention. This year, a greater emphasis will be placed on utilizing the Opentrons to accelerate your final projects.

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

  1. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode or Python scripts, procedures you may need to automate, 3D printed holders you may need, and more.
  2. Find and describe a published paper that utilizes the Opentrons or similar automation tools to achieve novel biological applications (eg automated PACE)

While your idea doesn’t need to be set in stone, we would like to see core details of what you would automate. This is due right before class and does not need to be tested on the Opentrons for now.

Example: 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.

Ans:

  1. While my final project is software-based (A DNA based data storage algorithm), the next phase could make extensive use of opentrons and other automations for DNA Mixing and assembly, PCR and amplification, Barcoding etc. 3D printed holders can be used to store the data/DNA safely.

  2. Paper:

"Accelerated evolution of engineered proteins using automated PACE (Phage-Assisted Continuous Evolution)"

(eLife, 2021. by Chen et al.)

This paper describes an automated version of PACE, where Opentrons is used to precisely handle transfer of phage, media, and bacteria between growth vessels, monitor real-time evolution of proteins under selective pressure, reduce human error and allow 24/7 uninterrupted evolution experiments etc. It shows how Opentrons enables low-cost, high-throughput bioengineering which is exactly the kind of workflow that could be used to test synthetic DNA stability, mutation rates, or even DNA barcodes over evolutionary time, which ties back into my project’s future vision.