Week 3 HW: Lab automation

Generate an artistic design using the GUI at opentrons-art.rcdonovan.com.

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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.

A) I have obtained the GUI coordinates, but by the time i got around to run the coordinates on the opentron Colab, the website had stopped responding to the codes. and so i was unable to use the website as instructed or access the coordinates again.

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.

A) Soh, B. W., Chitre, A., Tan, S. Z., Wang, Y., Yi, Y., Soh, W., Hippalgaonkar, K., & Wilson, D. I. (2025). Opentrons for automated and high‑throughput viscometry. Digital Discovery, 4, 711–722. https://doi.org/10.1039/d4dd00368c

this paper demonstrates their use for opentron OT2 liquid handling robot by turning it into a viscometer. the traditional way of measuring the viscosity for several liquids is time consuming and hard to scale. the researchers using the robot developed a method where the opentron pipettes dispensed liquids at different flow speeds and recorded the difference between how each liquid dispended and what it means in terms of viscosity. the despensing patterns are recorded and fed into learning models to help with the accuracy of viscosity prediction.

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.

A) My main final project idea is to create rapid sepsis test strips that use a cell free system with GFP based biosensors that respond to sepsis biomarkers like IL-6. Cell free systems are very sensitive to errors, thus, opentron automation can significantly help in reproducibility and reliability in the procedure. it can also help me set up several CFPS reactions parallel to each other, containing different concentrations of the biomarkers, different biosensors, or different GFP trigger designs. designing and optimizing a biosensor strip requires many trials and screening many combinations– experimenting with different promoters, RBSs, sensor domains and outside conditions. going through this process manually would be extremely slow and prone to many errors if the procedure is not consistant in the way an automated procedure can be.