Coordinates

red_points = [(0, 37.2),(-3.1, 34.1),(3.1, 34.1),(-6.2, 31),(6.2, 31),(-9.3, 27.9),(9.3, 27.9),(-12.4, 24.8),(12.4, 24.8),(-15.5, 21.7),(15.5, 21.7),(-18.6, 18.6),(18.6, 18.6),(-21.7, 15.5),(-18.6, 15.5),(-15.5, 15.5),(15.5, 15.5),(18.6, 15.5),(21.7, 15.5),(-18.6, 12.4),(18.6, 12.4),(-21.7, 9.3),(21.7, 9.3),(-24.8, 6.2),(24.8, 6.2),(-27.9, 3.1),(-24.8, 3.1),(-21.7, 3.1),(21.7, 3.1),(24.8, 3.1),(27.9, 3.1),(-18.6, 0),(18.6, 0),(-21.7, -3.1),(21.7, -3.1),(-24.8, -6.2),(24.8, -6.2),(-27.9, -9.3),(27.9, -9.3),(-31, -12.4),(-27.9, -12.4),(-24.8, -12.4),(-21.7, -12.4),(-18.6, -12.4),(-15.5, -12.4),(-12.4, -12.4),(-9.3, -12.4),(9.3, -12.4),(12.4, -12.4),(15.5, -12.4),(18.6, -12.4),(21.7, -12.4),(24.8, -12.4),(27.9, -12.4),(31, -12.4),(-9.3, -15.5),(9.3, -15.5),(-9.3, -18.6),(9.3, -18.6),(-9.3, -21.7),(9.3, -21.7),(-9.3, -24.8),(9.3, -24.8),(-9.3, -27.9),(9.3, -27.9),(-9.3, -31),(9.3, -31),(-9.3, -34.1),(9.3, -34.1),(-9.3, -37.2),(-6.2, -37.2),(-3.1, -37.2),(0, -37.2),(3.1, -37.2),(6.2, -37.2),(9.3, -37.2)]
green_points = []
orange_points = []

https://opentrons-art.rcdonovan.com/

Code optimization

Visualization and Simulation of Christmas Tree Coordinates for Opentrons Protocol

I had no prior experience of python, so I did face some difficulties while generating and optimizing the code for the opentrons art. The goal was to To create a visualization of a Christmas tree plotted inside a a petri dish, with a black background and colored tree pattern — using Python

1. First I could not get the petri dish background right and the christmas tree pattern was the only thing that was visualized.I tried plotting the Christmas tree pattern using a list of manually defined (x, y) coordinates. However, I couldn’t figure out how to include a black background or circular boundary, so the result only showed tree dots on a default white canvas.

2. So i tried to troubleshoot, I Chatgpt’s help to get the petri dish the code it helped me modify the code to make the black petri dish background, mainly by defining the boundary of the points and creating a plot

Create a black circular petri dish
circle = plt.Circle((0, 0), 40, color='black', zorder=1)
ax.add_patch(circle)
Plot tree points that fall within the circle
ax.scatter(x_inside, y_inside, c='red', s=100, zorder=2)

As a further phase, I would like to play with different patterns, add motion (lights blinking), or maybe create symmetrical art in numerous petri dishes.

Post Lab Questions | Mandatory for All Students

One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention. This year, a greater emphasis will be placed on utilizing the Opentrons to accelerate your final projects.

For this week, we’d like for you to do the following

1. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode or Python scripts, procedures you may need to automate, 3D printed holders you may need, and more.

I plan to work around synthetic biology based detectables for my final project so iI would like to use automation for some of the things like to program pipetting steps for assembling genetic constructs, preparing reagents, and running assay protocols, also to minimize errors and save as much time and focus on the standardization and scalability I am also thinking of creating Python scripts to communicate with sensors or plate readers so that biosensor data can be collected in real time For speedy result interpretation, automate data processing, standardization, and visualization.

1. Find and describe a published paper that utilizes the Opentrons or similar automation tools to achieve novel biological applications (eg automated PACE)

Han, Y., Thomas, C. T., Wennersten, S. A., Lau, E., & Lam, M. P. Y. (2021). Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot. Journal of visualized experiments : JoVE, (176), 10.3791/63092. https://doi.org/10.3791/63092

I found this paper Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot which mainly emphasizes on workflow for proteomics sample preparation that uses Opentrons OT-2. It explains how to set up the key sample preparation steps such as protein reduction, alkylation, digestion etc.

Automated pipetting robots are used in labs to prepare samples, saving time, lowering human error, and increasing consistency. However, the issue is that a lot of commercial automation systems are quite costly, making it difficult for many research or academic labs to purchase them. So this paper focuses on turning the protocol semi automated, by integrating opentrons