Week 3 HW: Lab Automation
Question 1
Inspiration: I am reading project hail mary with my friends as a weekly book club before the movie is released in late March. A character in the book is Rocky, and that is who is represented in the bio-art.
AI Assistance: Google Gemini 2.5 Flash built into Google Collab
Prompts:
I want to make a design that resembles a rock with six legs like a spider, this is the starter code you have to build this image, the starter code is in the “your code” up to the ### YOUR CODE HERE to create your design line
————————————————————————— NameError Traceback (most recent call last) /tmp/ipython-input-2180272395.py in <cell line: 0>() 1 # Execute Simulation / Visualization – don’t change this code block —-> 2 protocol = OpentronsMock(well_colors) 3 run(protocol) 4 protocol.visualize() NameError: name ‘OpentronsMock’ is not defined I get this error when I try to visualize the code output with this code# Execute Simulation / Visualization – don’t change this code block protocol = OpentronsMock(well_colors) run(protocol) protocol.visualize() You’re encountering a NameError because the OpentronsMock class, which is used for simulating the Opentrons protocol and visualizing the results, hasn’t been defined in your current execution environment. While the example visualization works, its definition seems to be missing from the parts of the notebook you’re currently running.
sorry the code to make the rock with six legs is good, but I want the rock to have more curvature and the legs to have more volume
I mean curvature meaning that its more like fractial shape then a perfect circle Ah, I understand! You’d like the rock to have a more organic, less perfectly circular shape, resembling a fractal. I can achieve this by adding a small, random variation to the radius as each point of the rock is drawn. This will give it a rougher, more natural edge.
I also want one of the legs to be waving hi, and add some musical notes in a speech bubble somewhere, scale the image as necessary so that allt he compoents can be shown
————————————————————————— ValueError Traceback (most recent call last) /tmp/ipython-input-2180272395.py in <cell line: 0>() 1 # Execute Simulation / Visualization – don’t change this code block 2 protocol = OpentronsMock(well_colors) —-> 3 run(protocol) 4 protocol.visualize() 3 frames/tmp/ipython-input-2092617955.py in run(protocol) 140 leg_points.append(center_location.move(types.Point(x=x, y=y))) 141 –> 142 draw_shape(pipette_20ul, ‘Green’, leg_points, volume_per_point=leg_volume_per_point) 143 144 # Speech Bubble (Orange) /tmp/ipython-input-2092617955.py in draw_shape(pipette, color_string, points_list, volume_per_point) 93 current_aspirated_volume += aspirate_chunk_size 94 —> 95 dispense_and_detach(pipette, volume_per_point, point_location) 96 current_aspirated_volume -= volume_per_point 97 pipette.drop_tip() /tmp/ipython-input-2092617955.py in dispense_and_detach(pipette, volume, location) 79 above_location = location.move(types.Point(z=location.point.z + 5)) # 5mm above 80 pipette.move_to(above_location) # Go to 5mm above the dispensing location —> 81 pipette.dispense(volume, location) # Go straight downwards and dispense 82 pipette.move_to(above_location) # Go straight up to detach drop and stay high 83 /tmp/ipython-input-917671935.py in dispense(self, volume, location) 106 assert(isinstance(volume, (int, float))) 107 if (location.point.x2 + location.point.y2 > MAX_DRAW_RADIUS**2): –> 108 raise ValueError(f’Dispensing outside “safe” area: Point ({location.point.x}, {location.point.y}) is more than’ + 109 f" {MAX_DRAW_RADIUS}mm away from the petri dish’s center.") 110 if not self.has_tip: ValueError: Dispensing outside “safe” area: Point
make the speech bubble bigger, and make sure that the music note is fully in the speech bubble You got it! I’ll make the speech bubble larger by increasing its radii and adjust its position slightly to ensure all the musical notes are comfortably inside.
don’t double dip into the same locations, and no speech bubble, but just add a musical note in space somewhere
fill in the fractial shape, and make the musical note bigger Okay, I’ll make those adjustments! I will fill in the fractal rock shape by drawing multiple concentric outlines, and I’ll make the musical note noticeably bigger. This should give your design a more complete and emphasized look.
make the musical note look like a beam note
make the note smaller, and add a quaver next to it
make sure that with orange, I am aspirating the saem amoutn that I am dispensing
Question 2
Paper title: Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience
Paper citation: Mark A. DeAngelis, Philip R. LeDuc, Warren C. Ruder. Adv. Intell. Syst.. 2025; 000, e202500624. https://doi.org/10.1002/aisy.202500624
Paper Description: The paper walked through how it used a robot from opentrons to study how different culture conditions impacted duckweed growth, and how this system can be applied towards other multi-cellular organisms to similarly study varying climate and environmental impacts on their growth. The novalty in this paper involved developing an automated method to prepare, maintain, and characterize triplicates of different test conditions at the same time using an Opentrons OT-2 robot, a custom camera module, and Cellpose deep learning algorithm to analyze the images.
For plasmid construction and characterization, I wouold store all my materials in the 4 C TundraStore until I am ready to use my plasmid backbone and genes of interest. Between each step that requires plate sealed, I would use the PlateLoc, and when I need to analyze underneath the seal or apply a protocal that needs access to the contents, I would use the XPeel Plate Peeler. When the protocals call for centrifuge, I would use the HiG3, and when I need to incubate or shake my reagants I would use the Inheco. When I would want to amplify my components, I would use the ATC. When I am ready to combine reagants, I would use the Echo525 Liquid Transfer. Finally, when I am ready to read my plasmid designs, I would use the Spark Plate Reader.
Question 3
Ideas were thought of by myself, but the experiemntal details and automation integration was polished with ChatGPT 5.2 model.