Week 3 HW: Lab Automation

Assignment: Python Script for Opentrons Artwork

This design is inspired by traditional Inca geometric art, particularly the tocapu textile patterns of the Inca Empire. The composition features a symmetrical stepped cross motif enclosed within a square, referencing the Andean worldview and the symbolic structure of the Chakana (Andean cross). The use of straight lines and geometric repetition reflects the mathematical precision and cosmological symbolism characteristic of Inca visual culture. (https://opentrons-art.rcdonovan.com/?id=6ef1d0494o5n1p7)

Post-Lab Questions

  1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

A relevant example is the paper “An open-source automated platform for high-throughput RT-qPCR testing” developed during the COVID-19 pandemic. In this work, researchers used the Opentrons OT-2 liquid handling robot to automate RNA extraction and RT-qPCR setup.

The system enabled scalable, low-cost diagnostic testing by reducing manual pipetting steps, minimizing human error, and increasing reproducibility. This study demonstrated how open-source automation tools can expand access to molecular diagnostics, especially in resource-limited settings.

The novelty of this application lies in democratizing laboratory automation—allowing smaller labs to perform high-throughput testing without expensive proprietary systems.

LINK: https://pubmed.ncbi.nlm.nih.gov/34260637/

  1. 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.

For my final project, I plan to use laboratory automation tools to develop controlled collagen-based biomaterials inspired by ancient Andean techniques. Collagen will serve as a structural matrix that mimics organic components found in archaeological artifacts such as textiles, adhesives, or composite materials. By using automated liquid handling, I aim to precisely control mixing ratios and spatial deposition of biological components within the collagen scaffold. This will allow the creation of reproducible material samples that can be used to study degradation processes, conservation strategies, or experimental archaeology models.

Automation ensures precision and repeatability, which are essential when comparing material behavior under different environmental conditions.

For my final project, I plan to use two main pieces of equipment to create collagen-based materials inspired by archaeological patterns. First, I will use the Opentrons OT-2 liquid handling robot. This robot allows precise mixing of liquids and can deposit the mixture in exact locations with consistent volumes. In my project, I will prepare different mixtures of collagen and pigments that mimic the colors and textures of ancient textiles or other organic components found in archaeological artifacts. The robot will then deposit these mixtures according to a predetermined pattern, such as geometric motifs inspired by Inca textiles. Using the robot ensures that each replica is precise and reproducible, allowing me to create multiple samples under the same conditions without human error.

Second, I will use 3D-printed holders or molds to support the materials during deposition. These molds will be designed to match the shape of specific archaeological patterns, such as squares or other geometric compartments. The robot will deposit the collagen mixtures into these molds, and once the collagen sets, the molds can be removed to reveal a precise replica of the intended pattern. This combination of automation and custom molds allows me to accurately reproduce complex designs and study how these materials behave, degrade, or can be conserved, providing a controlled and repeatable approach to experimental archaeology.

Final Project Ideas