Week 3 HW: Lab Automation
Paper Discussion
Paper: AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots
This paper reports using the Opentrons robot to conduct PCR, Golden Gate assembly, and Gibson assembly. It appears that the robot was able to determine specific parameters for experiments such as annealing temperature. The paper did not go into much detail about how this occurred, but after looking at some of the supplementary materials, the script likely parses .csv files that include primer and fragement sequences.
Automation in Final Project
Since my final project will likely involve assembly techniques as described above, I could use automation by writing a Python script that automatically calculates experiment parameters such as temperatures and concentrations based on information that I put in such as DNA sequences and concentrations. This part of experiment planning is tedious and often involves multiple tools/pages (such as NEB’s Tm calculator, and various protocols for each method of assembly), so having one script that can do this automatically would be helpful. Additionally, it would be interesting to see how the Opentrons robot can run this script, though I predict that that would require some amount of troubleshooting that I may not have time for.