I took help from Alireza Hekmati’s google colab note for Opentron. My google colab and generated image for Opentron is given below.

https://colab.research.google.com/drive/1czwpeGag9LB52HvWOOkhJOkoCdZaRXq_?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.

While your idea doesn’t need to be set in stone, we would like to see core details of what you would automate.

I intend to design (and if possible, build) a novel synthetic gene circuit with defined functions for my final project.

  **From my week 2 SynBio DNA write assignment:** 

I heard about Opentrons for the first time in HTGAA lecture this year, and what I only know about Opentrons is that it automates the regular SynBio labworks to make them more easy and reproducible.

To synthesis a novel gene circuit, it will require lots of DNA synthesis: promoters, genes and terminators. Then it will require assembly, even in different permutations. But the first step would be computational design and simulation of these gene circuits. Then in-vivo validation of these circuits to actually produce the function. Opentrons might help here?

As far as I know, there are some platforms which actually do gene circuit design automation (such as Cello). But I don’t know how they function.

1. Find and describe a published paper that utilizes the Opentrons or similar automation tools to achieve novel biological applications (eg automated PACE)

AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots

“AssemblyTron, an open-source Python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention.

1. AssemblyTron can perform polymerase chain reactions across a range of fragment lengths and annealing temperatures by using an optimal annealing temperature gradient calculation algorithm.