Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  9th February 2026

• Week 2 HW: DNA Read, Write, & Edit

  Part 1: Benchling & In-silico Gel Art Part 3: DNA Design Challenge 3.1. Choose your protein. I chose the PETase enzyme protein from the bacterium species Ideonella sakaiensis (strain 201-F6). I chose this protein as it was discovered to be important in plastic degradation. Its plastic degradation capabilities means that it allows bioremediation by reducing plastic pollution and promoting a circular economy.

• Week 3 HW: Lab Automation

  Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! A Blooming Daisy Flower PINK, PURPLE & BLUE DESIGN! :) INITIAL DESIGN: Python documentation from opentrons import types metadata = { 'author': 'Tammy Sisodiya', 'protocolName': ' HTGAA Dazzling Daisy', 'description': 'A blooming Daisy flower in Purple, Pink, and Blue.', 'source': 'HTGAA 2026 Opentrons Lab', 'apiLevel': '2.20' } ############################################################################## ### Robot deck setup constants ############################################################################## TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = 'A1' # UPDATED: Mapping the new lab colors to source wells well_colors = { 'A1' : 'Purple', 'B1' : 'Pink', 'C1' : 'Blue' } def run(protocol): # Tips tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips') # Pipettes pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul]) # Modules temperature_module = protocol.load_module('temperature module gen2', COLORS_DECK_SLOT) temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate') color_plate = temperature_plate # Agar Plate agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate') center_location = agar_plate['A1'].top() pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL) # Helper Functions def location_of_color(color_string): for well,color in well_colors.items(): if color.lower() == color_string.lower(): return color_plate[well] raise ValueError(f"No well found with color {color_string}") def dispense_and_detach(pipette, volume, location): assert(isinstance(volume, (int, float))) above_location = location.move(types.Point(z=location.point.z + 5)) pipette.move_to(above_location) pipette.dispense(volume, location) pipette.move_to(above_location) ### YOUR DESIGN DATA ### sfgfp_points = [(-4.4, 26.4),(1.1, 26.4),(2.2, 26.4),(3.3, 26.4),(4.4, 26.4),(-6.6, 25.3),(-5.5, 25.3),(-4.4, 25.3),(-3.3, 25.3),(1.1, 25.3),(4.4, 25.3),(-12.1, 24.2),(-11, 24.2),(-9.9, 24.2),(-8.8, 24.2),(-7.7, 24.2),(-6.6, 24.2),(-2.2, 24.2),(0, 24.2),(4.4, 24.2),(-13.2, 23.1),(-12.1, 23.1),(-7.7, 23.1),(-6.6, 23.1),(-2.2, 23.1),(4.4, 23.1),(6.6, 23.1),(7.7, 23.1),(8.8, 23.1),(-13.2, 22),(-7.7, 22),(-6.6, 22),(-2.2, 22),(0, 22),(4.4, 22),(5.5, 22),(6.6, 22),(8.8, 22),(-13.2, 20.9),(-7.7, 20.9),(-2.2, 20.9),(3.3, 20.9),(4.4, 20.9),(9.9, 20.9),(-13.2, 19.8),(-7.7, 19.8),(-2.2, 19.8),(3.3, 19.8),(9.9, 19.8),(-13.2, 18.7),(-2.2, 18.7),(8.8, 18.7),(9.9, 18.7),(-13.2, 17.6),(-2.2, 17.6),(-1.1, 17.6),(8.8, 17.6),(-18.7, 16.5),(-17.6, 16.5),(-16.5, 16.5),(-15.4, 16.5),(-14.3, 16.5),(-12.1, 16.5),(-2.2, 16.5),(7.7, 16.5),(8.8, 16.5),(-20.9, 15.4),(-19.8, 15.4),(-18.7, 15.4),(-14.3, 15.4),(-13.2, 15.4),(-12.1, 15.4),(-2.2, 15.4),(-1.1, 15.4),(7.7, 15.4),(-20.9, 14.3),(-13.2, 14.3),(-12.1, 14.3),(-11, 14.3),(-3.3, 14.3),(-2.2, 14.3),(5.5, 14.3),(6.6, 14.3),(-20.9, 13.2),(-9.9, 13.2),(-8.8, 13.2),(-3.3, 13.2),(4.4, 13.2),(5.5, 13.2),(-20.9, 12.1),(-8.8, 12.1),(-7.7, 12.1),(-3.3, 12.1),(-2.2, 12.1),(2.2, 12.1),(3.3, 12.1),(5.5, 12.1),(6.6, 12.1),(7.7, 12.1),(8.8, 12.1),(9.9, 12.1),(11, 12.1),(-20.9, 11),(-19.8, 11),(-6.6, 11),(-5.5, 11),(-4.4, 11),(0, 11),(1.1, 11),(2.2, 11),(3.3, 11),(4.4, 11),(11, 11),(-19.8, 9.9),(-4.4, 9.9),(-3.3, 9.9),(-2.2, 9.9),(-1.1, 9.9),(0, 9.9),(11, 9.9),(-23.1, 8.8),(-22, 8.8),(-20.9, 8.8),(-19.8, 8.8),(-18.7, 8.8),(-17.6, 8.8),(-5.5, 8.8),(-4.4, 8.8),(-3.3, 8.8),(-2.2, 8.8),(-1.1, 8.8),(0, 8.8),(9.9, 8.8),(11, 8.8),(15.4, 8.8),(16.5, 8.8),(17.6, 8.8),(18.7, 8.8),(19.8, 8.8),(20.9, 8.8),(22, 8.8),(23.1, 8.8),(24.2, 8.8),(-23.1, 7.7),(-3.3, 7.7),(-1.1, 7.7),(0, 7.7),(1.1, 7.7),(2.2, 7.7),(8.8, 7.7),(9.9, 7.7),(14.3, 7.7),(15.4, 7.7),(16.5, 7.7),(20.9, 7.7),(22, 7.7),(24.2, 7.7),(-24.2, 6.6),(-23.1, 6.6),(-5.5, 6.6),(-4.4, 6.6),(-3.3, 6.6),(-2.2, 6.6),(1.1, 6.6),(2.2, 6.6),(7.7, 6.6),(8.8, 6.6),(9.9, 6.6),(11, 6.6),(12.1, 6.6),(13.2, 6.6),(14.3, 6.6),(16.5, 6.6),(19.8, 6.6),(20.9, 6.6),(23.1, 6.6),(-22, 5.5),(-9.9, 5.5),(-7.7, 5.5),(-6.6, 5.5),(-5.5, 5.5),(-4.4, 5.5),(-2.2, 5.5),(3.3, 5.5),(4.4, 5.5),(13.2, 5.5),(16.5, 5.5),(18.7, 5.5),(19.8, 5.5),(23.1, 5.5),(-20.9, 4.4),(-19.8, 4.4),(-18.7, 4.4),(-17.6, 4.4),(-16.5, 4.4),(-15.4, 4.4),(-14.3, 4.4),(-13.2, 4.4),(-12.1, 4.4),(-9.9, 4.4),(-8.8, 4.4),(-7.7, 4.4),(-2.2, 4.4),(4.4, 4.4),(5.5, 4.4),(6.6, 4.4),(13.2, 4.4),(16.5, 4.4),(17.6, 4.4),(18.7, 4.4),(23.1, 4.4),(-12.1, 3.3),(-11, 3.3),(-2.2, 3.3),(5.5, 3.3),(7.7, 3.3),(8.8, 3.3),(9.9, 3.3),(11, 3.3),(12.1, 3.3),(13.2, 3.3),(16.5, 3.3),(17.6, 3.3),(23.1, 3.3),(-13.2, 2.2),(-12.1, 2.2),(-2.2, 2.2),(6.6, 2.2),(9.9, 2.2),(16.5, 2.2),(17.6, 2.2),(18.7, 2.2),(19.8, 2.2),(20.9, 2.2),(22, 2.2),(-14.3, 1.1),(-2.2, 1.1),(7.7, 1.1),(9.9, 1.1),(11, 1.1),(15.4, 1.1),(16.5, 1.1),(22, 1.1),(-15.4, 0),(-14.3, 0),(-2.2, 0),(7.7, 0),(11, 0),(14.3, 0),(15.4, 0),(22, 0),(-15.4, -1.1),(-2.2, -1.1),(3.3, -1.1),(8.8, -1.1),(13.2, -1.1),(14.3, -1.1),(20.9, -1.1),(-15.4, -2.2),(-14.3, -2.2),(-13.2, -2.2),(-12.1, -2.2),(-8.8, -2.2),(-7.7, -2.2),(-6.6, -2.2),(-2.2, -2.2),(3.3, -2.2),(8.8, -2.2),(11, -2.2),(12.1, -2.2),(13.2, -2.2),(20.9, -2.2),(-14.3, -3.3),(-11, -3.3),(-8.8, -3.3),(-7.7, -3.3),(-6.6, -3.3),(-3.3, -3.3),(-2.2, -3.3),(3.3, -3.3),(4.4, -3.3),(8.8, -3.3),(11, -3.3),(19.8, -3.3),(20.9, -3.3),(-13.2, -4.4),(-12.1, -4.4),(-11, -4.4),(-8.8, -4.4),(-3.3, -4.4),(-2.2, -4.4),(4.4, -4.4),(5.5, -4.4),(6.6, -4.4),(7.7, -4.4),(8.8, -4.4),(13.2, -4.4),(19.8, -4.4),(-16.5, -5.5),(-15.4, -5.5),(-14.3, -5.5),(-13.2, -5.5),(-8.8, -5.5),(-4.4, -5.5),(-3.3, -5.5),(-2.2, -5.5),(4.4, -5.5),(14.3, -5.5),(15.4, -5.5),(16.5, -5.5),(18.7, -5.5),(19.8, -5.5),(-19.8, -6.6),(-18.7, -6.6),(-17.6, -6.6),(-16.5, -6.6),(-8.8, -6.6),(-4.4, -6.6),(-1.1, -6.6),(3.3, -6.6),(4.4, -6.6),(17.6, -6.6),(18.7, -6.6),(-23.1, -7.7),(-22, -7.7),(-20.9, -7.7),(-19.8, -7.7),(-17.6, -7.7),(-16.5, -7.7),(-15.4, -7.7),(-8.8, -7.7),(-7.7, -7.7),(-6.6, -7.7),(-5.5, -7.7),(-4.4, -7.7),(-3.3, -7.7),(-2.2, -7.7),(-1.1, -7.7),(0, -7.7),(2.2, -7.7),(3.3, -7.7),(16.5, -7.7),(17.6, -7.7),(-24.2, -8.8),(-23.1, -8.8),(-14.3, -8.8),(-13.2, -8.8),(-8.8, -8.8),(-7.7, -8.8),(-3.3, -8.8),(-2.2, -8.8),(0, -8.8),(1.1, -8.8),(2.2, -8.8),(3.3, -8.8),(5.5, -8.8),(14.3, -8.8),(15.4, -8.8),(16.5, -8.8),(-26.4, -9.9),(-25.3, -9.9),(-24.2, -9.9),(-12.1, -9.9),(-11, -9.9),(-9.9, -9.9),(-8.8, -9.9),(-3.3, -9.9),(0, -9.9),(7.7, -9.9),(8.8, -9.9),(11, -9.9),(12.1, -9.9),(13.2, -9.9),(-27.5, -11),(-26.4, -11),(-25.3, -11),(-24.2, -11),(-23.1, -11),(-22, -11),(-20.9, -11),(-19.8, -11),(-18.7, -11),(-17.6, -11),(-16.5, -11),(-15.4, -11),(-14.3, -11),(-13.2, -11),(-12.1, -11),(-11, -11),(-3.3, -11),(0, -11),(-28.6, -12.1),(-27.5, -12.1),(-19.8, -12.1),(-18.7, -12.1),(-17.6, -12.1),(-15.4, -12.1),(-12.1, -12.1),(-4.4, -12.1),(-3.3, -12.1),(-2.2, -12.1),(0, -12.1),(-28.6, -13.2),(-27.5, -13.2),(-20.9, -13.2),(-19.8, -13.2),(-12.1, -13.2),(-4.4, -13.2),(0, -13.2),(-26.4, -14.3),(-25.3, -14.3),(-13.2, -14.3),(-12.1, -14.3),(-5.5, -14.3),(-2.2, -14.3),(0, -14.3),(-23.1, -15.4),(-20.9, -15.4),(-19.8, -15.4),(-13.2, -15.4),(-8.8, -15.4),(-7.7, -15.4),(-6.6, -15.4),(-1.1, -15.4),(0, -15.4),(-18.7, -16.5),(-16.5, -16.5),(-15.4, -16.5),(-14.3, -16.5),(-13.2, -16.5),(-12.1, -16.5),(-9.9, -16.5),(-8.8, -16.5),(-2.2, -16.5),(0, -16.5),(-2.2, -17.6),(0, -17.6),(0, -18.7),(-1.1, -19.8),(1.1, -19.8),(-1.1, -20.9),(1.1, -20.9),(2.2, -20.9),(0, -22),(3.3, -22),(12.1, -22),(13.2, -22),(14.3, -22),(15.4, -22),(0, -23.1),(4.4, -23.1),(5.5, -23.1),(9.9, -23.1),(11, -23.1),(12.1, -23.1),(13.2, -23.1),(1.1, -24.2),(2.2, -24.2),(5.5, -24.2),(6.6, -24.2),(7.7, -24.2),(8.8, -24.2),(9.9, -24.2),(11, -24.2),(12.1, -24.2),(2.2, -25.3),(3.3, -25.3),(4.4, -25.3),(9.9, -25.3),(11, -25.3),(5.5, -26.4),(6.6, -26.4),(7.7, -26.4),(8.8, -26.4)] mrfp1_points = [(-15.4, 12.1),(-14.3, 12.1),(-14.3, 11),(-13.2, 11),(-12.1, 11)] mscarlet_i_points = [(-11, 20.9),(-9.9, 20.9),(-11, 19.8),(-9.9, 19.8),(-9.9, 18.7)] mko2_points = [(3.3, 18.7),(4.4, 18.7),(5.5, 18.7),(6.6, 18.7),(4.4, 17.6)] mjuniper_points = [(6.6, 9.9),(7.7, 9.9),(4.4, 8.8),(5.5, 8.8),(6.6, 8.8),(7.7, 8.8),(-6.6, 2.2),(-9.9, 1.1),(-8.8, 1.1),(-7.7, 1.1),(-6.6, 1.1)] electra2_points = [(1.1, 4.4),(1.1, 3.3),(1.1, 2.2),(1.1, 1.1)] # 2. UPDATED Design Mapping # Purple for the large petals, Pink for highlights, Blue for details. layers = [ ('Purple', sfgfp_points), ('Pink', mrfp1_points), ('Pink', mscarlet_i_points), ('Pink', mko2_points), ('Blue', mjuniper_points), ('Blue', electra2_points) ] # 3. Execution Loop drop_vol = 1.0 for color_name, points in layers: if not points: continue source_well = location_of_color(color_name) for i in range(0, len(points), 15): chunk = points[i:i + 15] pipette_20ul.pick_up_tip() aspirate_vol = (len(chunk) * drop_vol) + 2.0 if aspirate_vol > 20.0: aspirate_vol = 20.0 pipette_20ul.aspirate(aspirate_vol, source_well) for x, y in chunk: if (x2 + y2) < 1600: target_point = center_location.point + types.Point(x=x, y=y, z=0) target_loc = types.Location(target_point, None) dispense_and_detach(pipette_20ul, drop_vol, target_loc) # Return residual to source well top to avoid contamination if pipette_20ul.current_volume > 0: pipette_20ul.dispense(pipette_20ul.current_volume, source_well.top()) pipette_20ul.drop_tip() Post-Lab Questions — DUE BY START OF FEB 24 LECTURE

• Week 4 HW: Protein Design Part I

  Part B: Protein Analysis and Visualization In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins.

1. Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions. Briefly describe the protein you selected and why you selected it. I chose the p53 protein, which triggers programmed cell death when ailments like cancer cause extensive DNA damage from oxidative stress like UV light, oxygen radicals or chemicals. In a cancerous cell, the p53 protein will travel to the nucleus and signal the mitochondria to release reactive oxygen species or increase calcium levels. Other death factors released include cytochrome c, which activates caspases and SMAC which blocks survival proteins (Fogg et al., 2011). I selected this protein as mutations in this protein can cause cancer and it is vital to protect the human genome from damage .