Week 03: Lab Automation

Python Script for opentron

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

2. Writing the python script and results

Post-lab Questions

1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.4

Paper: Technical upgrade of an open-source liquid handler to support bacterial colony screening del Olmo Lianes et al., Frontiers in Bioengineering and Biotechnology, 2023. DOI: 10.3389/fbioe.2023.1202836

What it focuses one: This paper presents COPICK, a technical solution to automate colony picking using the Opentrons OT-2. The system mounts a camera directly onto the robot to capture images of Petri dishes and automatically detect microbial colonies. The software then selects the best colonies based on criteria like size, color, and fluorescence, and executes a protocol to pick and transfer them for further analysis.

Why it’s novel: Commercial colony pickers exist but their high price excludes small research laboratories and budget-limited institutions from high-throughput screening. COPICK democratizes this capability by turning an affordable OT-2 into a vision-guided colony picker. biorxiv

Results: Benchmark tests on E. coli and P. putida colonies achieved a raw picking performance of 82% with 73.4% accuracy at an estimated rate of 240 colonies per hour. nih

2. Write a description about what you intend to do with automation tools for your final project.

What automation I would be working with is still not clear with me as I am still trying to finalize a project direction and the goals. However, as I have been planning to focus on computation first, will try to simulate stuff first virtually and then move towards validation. I would use automation tools to accelerate two key steps: transformation screening and expression optimization, after virtual simulations.

Final Project Idea

I am still not very clear about my project idea, but I have been researching about biosensors, and oxidative stress as one of my broder target ideas. The three paths that I find myslef leaning towrads are, female reproductive health: quite a recent experience with a certain effect of periods, eye strain. During, after or before periods many women experinece eye strain bad enough for them to feel irritated by their prescribed power correcters. This is one of the things that has facinated me and would like to work on.

The second path that I have been brainstroming on is oxidative stress damage to cells, majorly focusing on cromosomnal damage and genetic disformity. In my reasearch in this direction I was able to find, few gaps in how oxidative stress in cells are measured and translated into readable data. The said gap is, we use florecence to map the levels of oxidative stress, the brighter the color the more the stress. I was brainstroming towards an idea to create some type of sensor that can not just take in the levels of stress but also take in some of the important nuances. We may then use that whole to train models to predict paths and changes we never thought of.

The third path is Neurodegenration in cells, or in genral neurodegenrative dieseases. What caused neural death, how it progresses, what things incraese the speed of the said dieseas. I would most probably focus on one diseases rather than the broader perspective.

The main goal for me from any of the mentioned above project will be to compuationalize biology as much as I can. See what can be compuatationalize and what not. To come up with a more adaptable framework for these issues. I have been highly leaning towards biosensors of some type, for either of the ideas.