Python Script for Opentrons Artwork from opentrons import types import string metadata = { ‘protocolName’: ‘{Ashraful} - Opentrons Art - HTGAA’, ‘author’: ‘Ashraful’, ‘source’: ‘HTGAA 2026’, ‘apiLevel’: ‘2.20’ } Z_VALUE_AGAR = 2.0 POINT_SIZE = 0.75 sfgfp_points = [(-17.6,13.2), (-15.4,13.2), (-13.2,13.2), (-11,13.2), (-8.8,13.2), (11,13.2), (13.2,13.2), (15.4,13.2), (17.6,13.2), (-17.6,11), (-15.4,11), (-11,11), (-8.8,11), (8.8,11), (11,11), (13.2,11), (15.4,11), (17.6,11), (-15.4,8.8), (-13.2,8.8), (-8.8,8.8), (-6.6,8.8), (6.6,8.8), (8.8,8.8), (13.2,8.8), (15.4,8.8), (-13.2,6.6), (-11,6.6), (-6.6,6.6), (-4.4,6.6), (4.4,6.6), (6.6,6.6), (11,6.6), (13.2,6.6), (-11,4.4), (-8.8,4.4), (-4.4,4.4), (-2.2,4.4), (2.2,4.4), (4.4,4.4), (8.8,4.4), (11,4.4), (-8.8,2.2), (-6.6,2.2), (-2.2,2.2), (0,2.2), (2.2,2.2), (6.6,2.2), (8.8,2.2), (-6.6,0), (-4.4,0), (0,0), (4.4,0), (6.6,0), (-4.4,-2.2), (-2.2,-2.2), (0,-2.2), (2.2,-2.2), (4.4,-2.2), (-2.2,-4.4), (0,-4.4), (2.2,-4.4), (-2.2,-6.6), (0,-6.6), (2.2,-6.6), (-2.2,-8.8), (0,-8.8), (2.2,-8.8), (-2.2,-11), (0,-11), (2.2,-11), (-2.2,-13.2), (0,-13.2), (2.2,-13.2), (-11,-15.4), (-8.8,-15.4), (-6.6,-15.4), (-4.4,-15.4), (-2.2,-15.4), (0,-15.4), (2.2,-15.4), (4.4,-15.4), (6.6,-15.4), (8.8,-15.4), (11,-15.4), (13.2,-15.4), (-13.2,-17.6), (-11,-17.6), (-8.8,-17.6), (-6.6,-17.6), (-4.4,-17.6), (-2.2,-17.6), (0,-17.6), (2.2,-17.6), (4.4,-17.6), (6.6,-17.6), (8.8,-17.6), (11,-17.6), (13.2,-17.6), (15.4,-17.6), (-15.4,-19.8), (-13.2,-19.8), (-11,-19.8), (-8.8,-19.8), (-6.6,-19.8), (-4.4,-19.8), (-2.2,-19.8), (0,-19.8), (2.2,-19.8), (4.4,-19.8), (6.6,-19.8), (8.8,-19.8), (11,-19.8), (13.2,-19.8), (15.4,-19.8), (17.6,-19.8)] point_name_pairing = [(“sfgfp”, sfgfp_points)] # Robot deck setup constants TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = ‘A1’ # Place the PCR tubes in this order well_colors = { ‘A1’: ‘sfGFP’, ‘A2’: ‘mRFP1’, ‘A3’: ‘mKO2’, ‘A4’: ‘Venus’, ‘A5’: ‘mKate2_TF’, ‘A6’: ‘Azurite’, ‘A7’: ‘mCerulean3’, ‘A8’: ‘mClover3’, ‘A9’: ‘mJuniper’, ‘A10’: ‘mTurquoise2’, ‘A11’: ‘mBanana’, ‘A12’: ‘mPlum’, ‘B1’: ‘Electra2’, ‘B2’: ‘mWasabi’, ‘B3’: ‘mScarlet_I’, ‘B4’: ‘mPapaya’, ‘B5’: ’eqFP578’, ‘B6’: ’tdTomato’, ‘B7’: ‘DsRed’, ‘B8’: ‘mKate2’, ‘B9’: ‘EGFP’, ‘B10’: ‘mRuby2’, ‘B11’: ‘TagBFP’, ‘B12’: ‘mChartreuse_TF’, ‘C1’: ‘mLychee_TF’, ‘C2’: ‘mTagBFP2’, ‘C3’: ‘mEGFP’, ‘C4’: ‘mNeonGreen’, ‘C5’: ‘mAzamiGreen’, ‘C6’: ‘mWatermelon’, ‘C7’: ‘avGFP’, ‘C8’: ‘mCitrine’, ‘C9’: ‘mVenus’, ‘C10’: ‘mCherry’, ‘C11’: ‘mHoneydew’, ‘C12’: ‘TagRFP’, ‘D1’: ‘mTFP1’, ‘D2’: ‘Ultramarine’, ‘D3’: ‘ZsGreen1’, ‘D4’: ‘mMiCy’, ‘D5’: ‘mStayGold2’, ‘D6’: ‘PA_GFP’ } # Mapping for visualization colors VISUALIZATION_COLOR_MAP = { ‘sfGFP’: ‘green’, ‘mRFP1’: ‘red’, ‘mKO2’: ‘orange’, ‘Venus’: ‘yellow’, ‘mKate2_TF’: ‘purple’, ‘Azurite’: ‘blue’, ‘mCerulean3’: ‘cyan’, ‘mClover3’: ’lightgreen’, ‘mJuniper’: ‘darkgreen’, ‘mTurquoise2’: ’teal’, ‘mBanana’: ‘gold’, ‘mPlum’: ‘plum’, ‘Electra2’: ’navy’, ‘mWasabi’: ’lime’, ‘mScarlet_I’: ‘darkred’, ‘mPapaya’: ‘peachpuff’, ’eqFP578’: ‘brown’, ’tdTomato’: ’tomato’, ‘DsRed’: ‘indianred’, ‘mKate2’: ‘darkmagenta’, ‘EGFP’: ‘chartreuse’, ‘mRuby2’: ‘firebrick’, ‘TagBFP’: ‘slateblue’, ‘mChartreuse_TF’: ‘darkseagreen’, ‘mLychee_TF’: ‘palevioletred’, ‘mTagBFP2’: ‘darkblue’, ‘mEGFP’: ’limegreen’, ‘mNeonGreen’: ’lawngreen’, ‘mAzamiGreen’: ‘mediumseagreen’, ‘mWatermelon’: ‘pink’, ‘avGFP’: ‘forestgreen’, ‘mCitrine’: ‘khaki’, ‘mVenus’: ‘olivedrab’, ‘mCherry’: ‘crimson’, ‘mHoneydew’: ‘honeydew’, # This will likely be too light ‘TagRFP’: ‘rosybrown’, ‘mTFP1’: ‘dodgerblue’, ‘Ultramarine’: ‘mediumblue’, ‘ZsGreen1’: ‘springgreen’, ‘mMiCy’: ‘peru’, ‘mStayGold2’: ‘goldenrod’, ‘PA_GFP’: ‘darkgreen’ } volume_used = { ‘sfgfp’: 0 } def update_volume_remaining(current_color, quantity_to_aspirate): rows = string.ascii_uppercase for well, color in list(well_colors.items()): if color == current_color: if (volume_used[current_color] + quantity_to_aspirate) > 250: # Move to next well horizontally by advancing row letter, keeping column number row = well[0] col = well[1:] # Find next row letter next_row = rows[rows.index(row) + 1] next_well = f"{next_row}{col}" del well_colors[well] well_colors[next_well] = current_color volume_used[current_color] = quantity_to_aspirate else: volume_used[current_color] += quantity_to_aspirate break def run(protocol): # Load labware, modules and pipettes protocol.home() # 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]) # Deep Well Plate temperature_plate = protocol.load_labware(’nest_96_wellplate_2ml_deep’, 6, ‘Deep Well Plate’) # Agar Plate agar_plate = protocol.load_labware(‘htgaa_agar_plate’, AGAR_DECK_SLOT, ‘Agar Plate’) agar_plate.set_offset(x=0.00, y=0.00, z=Z_VALUE_AGAR) # Get the top-center of the plate, make sure the plate was calibrated before running this center_location = agar_plate[‘A1’].top() pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL) # Helper function (dispensing) def dispense_and_jog(pipette, volume, location): assert(isinstance(volume, (int, float))) # Go above the location above_location = location.move(types.Point(z=location.point.z + 2)) pipette.move_to(above_location) # Go downwards and dispense pipette.dispense(volume, location) # Go upwards to avoid smearing pipette.move_to(above_location) # Helper function (color location) def location_of_color(color_string): for well,color in well_colors.items(): if color.lower() == color_string.lower(): return temperature_plate[well] raise ValueError(f"No well found with color {color_string}") # Print pattern by iterating over lists for i, (current_color, point_list) in enumerate(point_name_pairing): # Skip the rest of the loop if the list is empty if not point_list: continue # Get the tip for this run, set the bacteria color, and the aspirate bacteria of choice pipette_20ul.pick_up_tip() max_aspirate = int(18 // POINT_SIZE) * POINT_SIZE quantity_to_aspirate = min(len(point_list)*POINT_SIZE, max_aspirate) update_volume_remaining(current_color, quantity_to_aspirate) pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color)) # Iterate over the current points list and dispense them, refilling along the way for i in range(len(point_list)): x, y = point_list[i] adjusted_location = center_location.move(types.Point(x, y)) dispense_and_jog(pipette_20ul, POINT_SIZE, adjusted_location) if pipette_20ul.current_volume == 0 and len(point_list[i+1:]) > 0: quantity_to_aspirate = min(len(point_list[i:])*POINT_SIZE, max_aspirate) update_volume_remaining(current_color, quantity_to_aspirate) pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color)) # Drop tip between each color pipette_20ul.drop_tip() Simulation # Execute Simulation / Visualization protocol = OpentronsMock(well_colors, VISUALIZATION_COLOR_MAP) run(protocol) protocol.visualize() Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
