Week-03-hw-Lab-Automation
Python Script for Opentrons Artwork
My Inspiration
In taxonomy, Bucardo belongs to the genus Capra (goats). In my Opentrons practice, I discovered that the mosaic pattern formed by fluorescent bacteria blurred the boundaries between specific species and macroscopic classification. I am not depicting an exact sheep, but rather using the universality of the “Capra” attribute to reconstruct an image of “Resurrection for 7 Minutes”. This mosaic-like visual language is not only a numerical metaphor for Bucardo’s shattered life, but also a vague expression about ’existence and disappearance’ that transcends species classification.
Process
Firstly, I initially used the Automatic Art Interface to generate the image I desired. However, due to the color restrictions mentioned in the Colab document, I had to limit the use of the design sheep’s colors.
Since I had no coding experience, at the beginning I simply copied the coordinates and fed them to the AI along with the reference seven, in order to generate the code.
However, during the process, several errors occurred, including confusion between instructions and spaces, a situation where the machine pipette’s printing exceeded the capacity, and undefined terms such as: mko2_points and mrfp1_points.
After resolving these minor errors, when I copied the code given by the AI, there were still several errors in the generated code. I did not achieve the pattern I wanted.
After reflection, taking into account the previous mistakes, I realized that I had not clearly stated where to draw specifically. Therefore, I shifted my focus to how to make the coordinates and colors I obtained clearly expressed in the coding. After correcting the overflow error, I continued to give instructions to the AI.
Promote：Based on the code you provided, the image I generated is the first one. Please refer to the coordinates I set in the generator and help me modify the code further.
This time, the instruction, combined with the errors I had already fixed before, enabled me to generate my target image. The coding is divided into two parts. 1.Define the coordinate list 2.The drawing process.
Coding
Outcome
Post-Lab Questions
I have found two papers that I am particularly interested in.
Automation of protein crystallization scaleup via Opentrons-2 liquid handling
Description: This paper demonstrates how to scale up and automate the sitting drop protein crystallization process using the Opentrons-2 (OT-2) robot. The research focuses on using Python scripts to precisely control microliter-level liquid handling to optimize crystallization conditions for proteins such as lysozyme. Technical Highlights: The authors developed a flexible automated workflow, including: Serial Dilution: The robot can automatically configure gradients of different precipitant concentrations. Custom Hardware: To accommodate non-standard crystallization plates, the authors used 3D printing to create dedicated adapters. High Throughput and Accuracy: The system can automatically set up 24-well crystallization plates, ensuring highly consistent component proportions in each tiny droplet (approximately 4 μL).
What I intented to do
I plan to use the OT-2 automation platform to create a project titled “Crystal Architecture: Programming Microscopic Landscapes”. This project aims to leverage the self-organizing nature of protein crystallization, under artificial intervention (code), to “grow” microscopic artworks with complex geometric structures on specific biological substrates.
Automation of protein crystallization scaleup via Opentrons-2 liquid handling
Description: This paper introduces a highly integrated automated system called Piccolo, which is specifically designed to address the bottlenecks in protein production. The core innovation of this system lies in its ability to automate the entire process from cell culture, growth monitoring (OD value), induction of expression, to protein purification. Technical highlights: Unlike traditional timed operations, the Piccolo system can dynamically adjust (Reschedule) the induction time based on the real-time growth curve of cells in each 24-well bioreactor. This means that the robot can “sense” the rhythm of life and add the inducer at the most appropriate moment.
What I intented to do
This system not only supports the cultivation of Escherichia coli, but also that of insect cells (animal-derived cells). In my exploration of biological art, this provides an opportunity to view the “molecular purification” process as “artistic transformation of matter”. It demonstrates how, through precise automated control, pure biological art media with specific colors (such as fluorescent proteins) can be extracted from turbid biomass.
Final Idea
