Week 3 HW: Lab Automation
| GUI design | Opentron |
|---|---|
 |  |
Python Script for Opentrons Artwork
from opentrons import protocol_api
from opentrons.protocol_api import SINGLE
from opentrons.types import Point
metadata = {
'protocolName': 'Multichannel Color Dispensing (Single Tip) - Dani',
'author': '',
'description': 'Aspirate colors column-wise with a single tip on an '
'8-channel pipette and dispense into virtual grid '
'positions in a reservoir.',
'apiLevel': '2.20'
}
# ---------------------------------------------------------------------------
# USER CONFIGURATION
# ---------------------------------------------------------------------------
VOLUME_PER_DROP = 2
DISPENSE_HEIGHT = 0
START_TIP = "E1"
DROP_TIP_IN_TRASH = True
# Usable volume per well (leave margin below 250 µL max)
WELL_CAPACITY = 220 # µL
# ---------------------------------------------------------------------------
# COLOR MAP
# IMPORTANT: use "source_wells" (plural), not "source_well"
# ---------------------------------------------------------------------------
mscarlet_i_points = [(-7.7, 38.5),(-5.5, 38.5),(-3.3, 38.5),(-1.1, 38.5),(1.1, 38.5),(3.3, 38.5),(5.5, 38.5),(7.7, 38.5),(-14.3, 36.3),(-12.1, 36.3),(-9.9, 36.3),(-7.7, 36.3),(-5.5, 36.3),(-3.3, 36.3),(-1.1, 36.3),(1.1, 36.3),(3.3, 36.3),(5.5, 36.3),(7.7, 36.3),(9.9, 36.3),(12.1, 36.3),(14.3, 36.3),(-20.9, 34.1),(-18.7, 34.1),(-16.5, 34.1),(-14.3, 34.1),(-12.1, 34.1),(-9.9, 34.1),(-7.7, 34.1),(-5.5, 34.1),(-3.3, 34.1),(-1.1, 34.1),(1.1, 34.1),(3.3, 34.1),(5.5, 34.1),(7.7, 34.1),(9.9, 34.1),(12.1, 34.1),(14.3, 34.1),(16.5, 34.1),(18.7, 34.1),(20.9, 34.1),(-23.1, 31.9),(-20.9, 31.9),(-18.7, 31.9),(-16.5, 31.9),(-14.3, 31.9),(-12.1, 31.9),(-9.9, 31.9),(-7.7, 31.9),(-5.5, 31.9),(-3.3, 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),(12.1, 31.9),(14.3, 31.9),(16.5, 31.9),(18.7, 31.9),(20.9, 31.9),(23.1, 31.9),(-25.3, 29.7),(-23.1, 29.7),(-20.9, 29.7),(-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, 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-25.3),(-27.5, -27.5),(-25.3, -27.5),(-23.1, -27.5),(-20.9, -27.5),(-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),(12.1, -27.5),(14.3, -27.5),(16.5, -27.5),(18.7, -27.5),(20.9, -27.5),(23.1, -27.5),(25.3, -27.5),(27.5, -27.5),(-25.3, -29.7),(-23.1, -29.7),(-20.9, -29.7),(-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),(12.1, -29.7),(14.3, -29.7),(16.5, -29.7),(18.7, -29.7),(20.9, -29.7),(23.1, -29.7),(25.3, -29.7),(-23.1, -31.9),(-20.9, -31.9),(-18.7, -31.9),(-16.5, -31.9),(-14.3, -31.9),(-12.1, -31.9),(-9.9, -31.9),(-7.7, -31.9),(-5.5, -31.9),(-3.3, -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),(12.1, -31.9),(14.3, -31.9),(16.5, -31.9),(18.7, -31.9),(20.9, -31.9),(23.1, -31.9),(-20.9, -34.1),(-18.7, -34.1),(-16.5, -34.1),(-14.3, -34.1),(-12.1, -34.1),(-9.9, -34.1),(-7.7, -34.1),(-5.5, -34.1),(-3.3, -34.1),(-1.1, -34.1),(1.1, -34.1),(3.3, -34.1),(5.5, -34.1),(7.7, -34.1),(9.9, -34.1),(12.1, -34.1),(14.3, -34.1),(16.5, -34.1),(18.7, -34.1),(20.9, -34.1),(-14.3, -36.3),(-12.1, -36.3),(-9.9, -36.3),(-7.7, -36.3),(-5.5, -36.3),(-3.3, -36.3),(-1.1, -36.3),(1.1, -36.3),(3.3, -36.3),(5.5, -36.3),(7.7, -36.3),(9.9, -36.3),(12.1, -36.3),(14.3, -36.3),(-7.7, -38.5),(-5.5, -38.5),(-3.3, -38.5),(-1.1, -38.5),(1.1, -38.5),(3.3, -38.5),(5.5, -38.5),(7.7, -38.5)]
azurite_points = [(-5.4, 23.4),(-1.8, 23.4),(1.8, 23.4),(5.4, 23.4),(-9, 19.8),(-5.4, 19.8),(-1.8, 19.8),(1.8, 19.8),(5.4, 19.8),(9, 19.8),(12.6, 19.8),(12.6, 16.2),(12.6, 12.6),(-12.6, 9),(-1.8, 9),(1.8, 9),(5.4, 9),(12.6, 9),(-12.6, 5.4),(12.6, 5.4),(-12.6, 1.8),(12.6, 1.8),(-12.6, -1.8),(-9, -1.8),(-5.4, -1.8),(-1.8, -1.8),(1.8, -1.8),(5.4, -1.8),(-12.6, -5.4),(-5.4, -12.6)]
mko2_points = [(9, 23.4),(-12.6, 16.2),(12.6, -1.8),(-9, -5.4),(1.8, -5.4),(16.2, -9),(-12.6, -12.6),(-9, -16.2),(-5.4, -16.2),(-1.8, -16.2),(-12.6, -23.4),(-9, -23.4),(-5.4, -23.4),(-1.8, -23.4),(1.8, -23.4),(5.4, -23.4),(9, -23.4),(-5.4, -30.6),(-1.8, -30.6),(1.8, -30.6),(5.4, -30.6),(9, -30.6),(12.6, -30.6),(16.2, -34.2)]
sfgfp_points = []
COLOR_MAP = [
{'name': 'Red', 'source_wells': ['A1','B1','C1','D1','E1','F1','G1','H1'], 'points': mscarlet_i_points}
]
# ---------------------------------------------------------------------------
# RESERVOIR BOUNDS
# ---------------------------------------------------------------------------
RESERVOIR_X_MM = 107.0
RESERVOIR_Y_MM = 67.0
ALLOW_OUT_OF_BOUNDS = False
# ---------------------------------------------------------------------------
# PROTOCOL
# ---------------------------------------------------------------------------
def run(protocol: protocol_api.ProtocolContext):
# --- Labware ---
tip_rack = protocol.load_labware('opentrons_96_tiprack_20ul', 6)
plate = protocol.load_labware('scienfocus_96_wellplate_250ul', 1)
reservoir = protocol.load_labware('thermo_1_reservoir_90000ul', 2)
# --- Pipette ---
pipette = protocol.load_instrument('p20_multi_gen2', 'left',
tip_racks=[tip_rack])
pipette.configure_nozzle_layout(style=SINGLE, start="H1")
# --- Reference locations ---
reservoir_well = reservoir['A1']
dispense_base = reservoir_well.bottom(DISPENSE_HEIGHT)
# --- Tip ordering ---
ordered_tips = []
for col in tip_rack.columns():
ordered_tips.extend(col)
start_tip_well = tip_rack.wells_by_name()[START_TIP]
try:
next_tip_index = ordered_tips.index(start_tip_well)
except ValueError as exc:
raise RuntimeError(f"START_TIP '{START_TIP}' is not in the loaded tip rack.") from exc
# -----------------------------------------------------------------------
# MAIN LOOP
# -----------------------------------------------------------------------
for color in COLOR_MAP:
if not color['points']:
continue
source_wells = [plate.wells_by_name()[w] for w in color['source_wells']]
current_well_index = 0
remaining_volume = WELL_CAPACITY
n_dispenses = len(color['points'])
protocol.comment(
f"--- {color['name']} | {len(source_wells)} wells | "
f"{n_dispenses} × {VOLUME_PER_DROP} µL ---"
)
# Pick up one tip per color
if next_tip_index >= len(ordered_tips):
raise RuntimeError("Out of tips for the configured colors.")
pipette.pick_up_tip(ordered_tips[next_tip_index])
next_tip_index += 1
for (x_offset, y_offset) in color['points']:
# --- Bounds check ---
if (abs(x_offset) > RESERVOIR_X_MM / 2) or (abs(y_offset) > RESERVOIR_Y_MM / 2):
protocol.comment(
f"WARNING: {color['name']} point ({x_offset}, {y_offset}) mm is out "
f"of bounds ±{RESERVOIR_X_MM/2:.1f} x ±{RESERVOIR_Y_MM/2:.1f}"
)
if not ALLOW_OUT_OF_BOUNDS:
continue
# --- Switch wells if needed ---
if remaining_volume < VOLUME_PER_DROP:
current_well_index += 1
if current_well_index >= len(source_wells):
raise RuntimeError(
f"Ran out of volume for {color['name']} "
f"(increase number of source wells)"
)
remaining_volume = WELL_CAPACITY
protocol.comment(
f"Switching to well {color['source_wells'][current_well_index]}"
)
source_well = source_wells[current_well_index]
# --- Aspirate ---
pipette.aspirate(VOLUME_PER_DROP, source_well)
remaining_volume -= VOLUME_PER_DROP
# --- Move & dispense ---
target = dispense_base.move(Point(x=x_offset, y=y_offset, z=0))
pipette.move_to(target)
pipette.dispense(VOLUME_PER_DROP, target)
# --- Tip handling ---
if DROP_TIP_IN_TRASH:
pipette.drop_tip()
else:
pipette.return_tip()Post-Lab Questions
- Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
Example Paper: Automated Cell Culture Splitter (ACCS) Using the Opentrons OT‑2 An example of a novel usage of automation workflow is the Automated Cell Culture Splitter (ACCS), described in a 2024 bioRxiv preprint. The ACCS uses the Opentrons OT‑2 liquid‑handling robot to automate the passaging of both adherent and suspension cells in 96‑well plates. The system:
- Integrated on‑deck imaging‑based cell counting The ACCS incorporates a custom imaging module directly on the OT‑2 deck. This module captures images of each well and quantifies cell density using image‑analysis algorithms. In theory, this allows the robot to adjust seeding volumes dynamically through numerical controls, enabling adaptive decision‑making rather than fixed pipetting steps.
- Adaptive, per‑well control of cell numbers Using the quantitative data from the imaging module, the ACCS performs error‑aware adaptive pipetting. Instead of applying uniform dilutions, the system adjusts transfer volumes to compensate for biological variability, pipetting imprecision, and uneven growth. This reduces error propagation across passages and ensures each well reaches a consistent target cell density.
- 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.
For my final project, I plan to use lab‑automation tools to streamline the experimental workflow for testing copper‑uptake efficiency in genetically modified Lemna minor. The biological goal is to compare wild‑type plants with engineered lines expressing COPT1, PCS, and an RFP. The automation component focuses on standardizing liquid handling, exposure conditions, and measurement steps to ensure reproducibility and high‑throughput data collection.