Week 3 HW: Lab Automation
Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME!
I downloaded the script from the GUI website:
The script
from opentrons import types
import string
metadata = { ‘protocolName’: ‘{YOUR NAME} - Opentrons Art - HTGAA’, ‘author’: ‘HTGAA’, ‘source’: ‘HTGAA 2026’, ‘apiLevel’: ‘2.20’ }
Z_VALUE_AGAR = 2.0 POINT_SIZE = 0.75
mscarlet_i_points = [(5.5,36.3), (-16.5,34.1), (-14.3,34.1), (-12.1,34.1), (-9.9,34.1), (1.1,34.1), (3.3,34.1), (5.5,34.1), (7.7,34.1), (-18.7,31.9), (-16.5,31.9), (-14.3,31.9), (-12.1,31.9), (-9.9,31.9), (-7.7,31.9), (-1.1,31.9), (1.1,31.9), (3.3,31.9), (5.5,31.9), (7.7,31.9), (9.9,31.9), (-18.7,29.7), (-16.5,29.7), (-14.3,29.7), (-12.1,29.7), (-9.9,29.7), (-7.7,29.7), (-5.5,29.7), (-3.3,29.7), (-1.1,29.7), (1.1,29.7), (3.3,29.7), (5.5,29.7), (7.7,29.7), (9.9,29.7), (-18.7,27.5), (-16.5,27.5), (-14.3,27.5), (-12.1,27.5), (-9.9,27.5), (-7.7,27.5), (-5.5,27.5), (-3.3,27.5), (-1.1,27.5), (1.1,27.5), (3.3,27.5), (5.5,27.5), (7.7,27.5), (9.9,27.5), (-18.7,25.3), (-16.5,25.3), (-14.3,25.3), (-12.1,25.3), (-9.9,25.3), (-7.7,25.3), (-3.3,25.3), (-1.1,25.3), (1.1,25.3), (3.3,25.3), (5.5,25.3), (7.7,25.3), (-16.5,23.1), (-14.3,23.1), (-12.1,23.1), (-9.9,23.1), (-1.1,23.1), (1.1,23.1), (3.3,23.1), (5.5,23.1), (7.7,23.1), (-14.3,20.9), (-12.1,20.9), (1.1,20.9), (3.3,20.9), (5.5,20.9), (7.7,20.9), (-18.7,18.7), (-16.5,18.7), (-14.3,18.7), (-12.1,18.7), (1.1,18.7), (3.3,18.7), (5.5,18.7), (7.7,18.7), (-20.9,16.5), (-18.7,16.5), (-16.5,16.5), (-14.3,16.5), (-12.1,16.5), (-9.9,16.5), (-1.1,16.5), (1.1,16.5), (3.3,16.5), (5.5,16.5), (7.7,16.5), (9.9,16.5), (12.1,16.5), (-23.1,14.3), (-20.9,14.3), (-18.7,14.3), (-16.5,14.3), (-14.3,14.3), (-12.1,14.3), (-9.9,14.3), (-7.7,14.3), (-5.5,14.3), (-3.3,14.3), (-1.1,14.3), (1.1,14.3), (3.3,14.3), (5.5,14.3), (7.7,14.3), (9.9,14.3), (12.1,14.3), (14.3,14.3), (-25.3,12.1), (-23.1,12.1), (-20.9,12.1), (-18.7,12.1), (-16.5,12.1), (-14.3,12.1), (-12.1,12.1), (-9.9,12.1), (-7.7,12.1), (-5.5,12.1), (-3.3,12.1), (-1.1,12.1), (1.1,12.1), (3.3,12.1), (5.5,12.1), (7.7,12.1), (9.9,12.1), (12.1,12.1), (14.3,12.1), (16.5,12.1), (-25.3,9.9), (-23.1,9.9), (-20.9,9.9), (-18.7,9.9), (-16.5,9.9), (-14.3,9.9), (-12.1,9.9), (-9.9,9.9), (-7.7,9.9), (-5.5,9.9), (-3.3,9.9), (-1.1,9.9), (1.1,9.9), (3.3,9.9), (5.5,9.9), (7.7,9.9), (9.9,9.9), (12.1,9.9), (14.3,9.9), (16.5,9.9), (-23.1,7.7), (-20.9,7.7), (-18.7,7.7), (-16.5,7.7), (-9.9,7.7), (-7.7,7.7), (-5.5,7.7), (-3.3,7.7), (-1.1,7.7), (1.1,7.7), (3.3,7.7), (5.5,7.7), (7.7,7.7), (9.9,7.7), (12.1,7.7), (14.3,7.7), (16.5,7.7), (-9.9,5.5), (-7.7,5.5), (-5.5,5.5), (-3.3,5.5), (-1.1,5.5), (1.1,5.5), (-9.9,3.3), (-7.7,3.3), (-5.5,3.3), (-3.3,3.3), (-1.1,3.3), (1.1,3.3), (-9.9,1.1), (-7.7,1.1), (-5.5,1.1), (-3.3,1.1), (-1.1,1.1), (1.1,1.1), (-9.9,-1.1), (-7.7,-1.1), (-5.5,-1.1), (-3.3,-1.1), (-1.1,-1.1), (-9.9,-3.3), (-7.7,-3.3), (-5.5,-3.3), (-3.3,-3.3), (-7.7,-5.5), (-5.5,-5.5)] mjuniper_points = [(3.3,5.5), (5.5,3.3), (7.7,-3.3), (16.5,-5.5), (18.7,-5.5), (20.9,-5.5), (16.5,-7.7), (18.7,-7.7), (20.9,-7.7), (14.3,-9.9), (16.5,-9.9), (18.7,-9.9), (20.9,-9.9), (12.1,-12.1), (14.3,-12.1), (16.5,-12.1), (18.7,-12.1), (-9.9,-14.3), (12.1,-14.3), (14.3,-14.3), (16.5,-14.3), (-9.9,-16.5), (-7.7,-16.5), (9.9,-16.5), (12.1,-16.5), (14.3,-16.5), (-9.9,-18.7), (-7.7,-18.7), (-5.5,-18.7), (-3.3,-18.7), (9.9,-18.7), (12.1,-18.7), (-9.9,-20.9), (-7.7,-20.9), (-5.5,-20.9), (-3.3,-20.9), (7.7,-20.9), (9.9,-20.9), (-7.7,-23.1), (-5.5,-23.1), (-3.3,-23.1), (-1.1,-23.1), (7.7,-23.1), (-7.7,-25.3), (-5.5,-25.3), (-3.3,-25.3), (-1.1,-25.3), (1.1,-25.3), (-5.5,-27.5), (-3.3,-27.5), (-1.1,-27.5), (1.1,-27.5), (3.3,-27.5), (-1.1,-29.7), (1.1,-29.7), (3.3,-29.7), (5.5,-29.7), (5.5,-31.9)] mturquoise2_points = [(5.5,1.1), (7.7,-1.1), (7.7,-5.5), (7.7,-7.7), (14.3,-7.7), (7.7,-9.9), (7.7,-12.1), (5.5,-14.3), (7.7,-14.3), (18.7,-14.3), (-12.1,-16.5), (-5.5,-16.5), (5.5,-16.5), (16.5,-16.5), (-12.1,-18.7), (5.5,-18.7), (7.7,-18.7), (14.3,-18.7), (-1.1,-20.9), (5.5,-20.9), (12.1,-20.9), (1.1,-23.1), (5.5,-23.1), (5.5,-25.3), (5.5,-27.5), (-3.3,-29.7), (5.5,-34.1)] mrfp1_points = [(-5.5,25.3), (-7.7,23.1), (-5.5,23.1), (-3.3,23.1), (-9.9,20.9), (-7.7,20.9), (-5.5,20.9), (-3.3,20.9), (-1.1,20.9), (-9.9,18.7), (-7.7,18.7), (-5.5,18.7), (-3.3,18.7), (-1.1,18.7), (-7.7,16.5), (-5.5,16.5), (-3.3,16.5)]
point_name_pairing = [(“mscarlet_i”, mscarlet_i_points),(“mjuniper”, mjuniper_points),(“mturquoise2”, mturquoise2_points),(“mrfp1”, mrfp1_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’ }
volume_used = { ‘mscarlet_i’: 0, ‘mjuniper’: 0, ‘mturquoise2’: 0, ‘mrfp1’: 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)
# 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()
Post-Lab Questions
Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details.