opentrons-integration - Agent Skills

Opentrons Integration

Overview

Opentrons is a Python-based lab automation platform for Flex and OT-2 robots. Write Protocol API v2 protocols for liquid handling, control hardware modules (heater-shaker, thermocycler), manage labware, for automated pipetting workflows.

When to Use This Skill

This skill should be used when:

Writing Opentrons Protocol API v2 protocols in Python

Automating liquid handling workflows on Flex or OT-2 robots

Controlling hardware modules (temperature, magnetic, heater-shaker, thermocycler)

Setting up labware configurations and deck layouts

Implementing complex pipetting operations (serial dilutions, plate replication, PCR setup)

Managing tip usage and optimizing protocol efficiency

Working with multi-channel pipettes for 96-well plate operations

Simulating and testing protocols before robot execution

Core Capabilities

1. Protocol Structure and Metadata

Every Opentrons protocol follows a standard structure:

from opentrons import protocol_api
Metadata

metadata = {
    'protocolName': 'My Protocol',
    'author': 'Name <email@example.com>',
    'description': 'Protocol description',
    'apiLevel': '2.19'  # Use latest available API version
}
Requirements (optional)

requirements = {
    'robotType': 'Flex',  # or 'OT-2'
    'apiLevel': '2.19'
}
Run function

def run(protocol: protocol_api.ProtocolContext):
    # Protocol commands go here
    pass

Key elements:

Import protocol_api from opentrons

Define metadata dict with protocolName, author, description, apiLevel

Optional requirements dict for robot type and API version

Implement run() function receiving ProtocolContext as parameter

All protocol logic goes inside the run() function

2. Loading Hardware

Loading Instruments (Pipettes):

def run(protocol: protocol_api.ProtocolContext):
    # Load pipette on specific mount
    left_pipette = protocol.load_instrument(
        'p1000_single_flex',  # Instrument name
        'left',               # Mount: 'left' or 'right'
        tip_racks=[tip_rack]  # List of tip rack labware objects
    )

Common pipette names:

Flex: p50_single_flex, p1000_single_flex, p50_multi_flex, p1000_multi_flex

OT-2: p20_single_gen2, p300_single_gen2, p1000_single_gen2, p20_multi_gen2, p300_multi_gen2

Loading Labware:

# Load labware directly on deck
plate = protocol.load_labware(
    'corning_96_wellplate_360ul_flat',  # Labware API name
    'D1',                                # Deck slot (Flex: A1-D3, OT-2: 1-11)
    label='Sample Plate'                 # Optional display label
)
Load tip rack

tip_rack = protocol.load_labware('opentrons_flex_96_tiprack_1000ul', 'C1')
Load labware on adapter

adapter = protocol.load_adapter('opentrons_flex_96_tiprack_adapter', 'B1')
tips = adapter.load_labware('opentrons_flex_96_tiprack_200ul')

Loading Modules:

# Temperature module
temp_module = protocol.load_module('temperature module gen2', 'D3')
temp_plate = temp_module.load_labware('corning_96_wellplate_360ul_flat')
Magnetic module

mag_module = protocol.load_module('magnetic module gen2', 'C2')
mag_plate = mag_module.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')
Heater-Shaker module

hs_module = protocol.load_module('heaterShakerModuleV1', 'D1')
hs_plate = hs_module.load_labware('corning_96_wellplate_360ul_flat')
Thermocycler module (takes up specific slots automatically)

tc_module = protocol.load_module('thermocyclerModuleV2')
tc_plate = tc_module.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')

3. Liquid Handling Operations

Basic Operations:

# Pick up tip
pipette.pick_up_tip()
Aspirate (draw liquid in)

pipette.aspirate(
    volume=100,           # Volume in µL
    location=source['A1'] # Well or location object
)
Dispense (expel liquid)

pipette.dispense(
    volume=100,
    location=dest['B1']
)
Drop tip

pipette.drop_tip()
Return tip to rack

pipette.return_tip()

Complex Operations:

# Transfer (combines pick_up, aspirate, dispense, drop_tip)
pipette.transfer(
    volume=100,
    source=source_plate['A1'],
    dest=dest_plate['B1'],
    new_tip='always'  # 'always', 'once', or 'never'
)
Distribute (one source to multiple destinations)

pipette.distribute(
    volume=50,
    source=reservoir['A1'],
    dest=[plate['A1'], plate['A2'], plate['A3']],
    new_tip='once'
)
Consolidate (multiple sources to one destination)

pipette.consolidate(
    volume=50,
    source=[plate['A1'], plate['A2'], plate['A3']],
    dest=reservoir['A1'],
    new_tip='once'
)

Advanced Techniques:

# Mix (aspirate and dispense in same location)
pipette.mix(
    repetitions=3,
    volume=50,
    location=plate['A1']
)
Air gap (prevent dripping)

pipette.aspirate(100, source['A1'])
pipette.air_gap(20)  # 20µL air gap
pipette.dispense(120, dest['A1'])
Blow out (expel remaining liquid)

pipette.blow_out(location=dest['A1'].top())
Touch tip (remove droplets on tip exterior)

pipette.touch_tip(location=plate['A1'])

Flow Rate Control:

# Set flow rates (µL/s)
pipette.flow_rate.aspirate = 150
pipette.flow_rate.dispense = 300
pipette.flow_rate.blow_out = 400

4. Accessing Wells and Locations

Well Access Methods:

# By name
well_a1 = plate['A1']
By index

first_well = plate.wells()[0]
All wells

all_wells = plate.wells()  # Returns list
By rows

rows = plate.rows()  # Returns list of lists
row_a = plate.rows()[0]  # All wells in row A
By columns

columns = plate.columns()  # Returns list of lists
column_1 = plate.columns()[0]  # All wells in column 1
Wells by name (dictionary)

wells_dict = plate.wells_by_name()  # {'A1': Well, 'A2': Well, ...}

Location Methods:

# Top of well (default: 1mm below top)
pipette.aspirate(100, well.top())
pipette.aspirate(100, well.top(z=5))  # 5mm above top
Bottom of well (default: 1mm above bottom)

pipette.aspirate(100, well.bottom())
pipette.aspirate(100, well.bottom(z=2))  # 2mm above bottom
Center of well

pipette.aspirate(100, well.center())

5. Hardware Module Control

Temperature Module:

# Set temperature
temp_module.set_temperature(celsius=4)
Wait for temperature

temp_module.await_temperature(celsius=4)
Deactivate

temp_module.deactivate()
Check status

current_temp = temp_module.temperature  # Current temperature
target_temp = temp_module.target  # Target temperature

Magnetic Module:

# Engage (raise magnets)
mag_module.engage(height_from_base=10)  # mm from labware base
Disengage (lower magnets)

mag_module.disengage()
Check status

is_engaged = mag_module.status  # 'engaged' or 'disengaged'

Heater-Shaker Module:

# Set temperature
hs_module.set_target_temperature(celsius=37)
Wait for temperature

hs_module.wait_for_temperature()
Set shake speed

hs_module.set_and_wait_for_shake_speed(rpm=500)
Close labware latch

hs_module.close_labware_latch()
Open labware latch

hs_module.open_labware_latch()
Deactivate heater

hs_module.deactivate_heater()
Deactivate shaker

hs_module.deactivate_shaker()

Thermocycler Module:

# Open lid
tc_module.open_lid()
Close lid

tc_module.close_lid()
Set lid temperature

tc_module.set_lid_temperature(celsius=105)
Set block temperature

tc_module.set_block_temperature(
    temperature=95,
    hold_time_seconds=30,
    hold_time_minutes=0.5,
    block_max_volume=50  # µL per well
)
Execute profile (PCR cycling)

profile = [
    {'temperature': 95, 'hold_time_seconds': 30},
    {'temperature': 57, 'hold_time_seconds': 30},
    {'temperature': 72, 'hold_time_seconds': 60}
]
tc_module.execute_profile(
    steps=profile,
    repetitions=30,
    block_max_volume=50
)
Deactivate

tc_module.deactivate_lid()
tc_module.deactivate_block()

Absorbance Plate Reader:

# Initialize and read
result = plate_reader.read(wavelengths=[450, 650])
Access readings

absorbance_data = result  # Dict with wavelength keys

6. Liquid Tracking and Labeling

Define Liquids:

# Define liquid types
water = protocol.define_liquid(
    name='Water',
    description='Ultrapure water',
    display_color='#0000FF'  # Hex color code
)sample = protocol.define_liquid(
    name='Sample',
    description='Cell lysate sample',
    display_color='#FF0000'
)

Load Liquids into Wells:

# Load liquid into specific wells
reservoir['A1'].load_liquid(liquid=water, volume=50000)  # µL
plate['A1'].load_liquid(liquid=sample, volume=100)
Mark wells as empty

plate['B1'].load_empty()

7. Protocol Control and Utilities

Execution Control:

# Pause protocol
protocol.pause(msg='Replace tip box and resume')
Delay

protocol.delay(seconds=60)
protocol.delay(minutes=5)
Comment (appears in logs)

protocol.comment('Starting serial dilution')
Home robot

protocol.home()

Conditional Logic:

# Check if simulating
if protocol.is_simulating():
    protocol.comment('Running in simulation mode')
else:
    protocol.comment('Running on actual robot')

Rail Lights (Flex only):

# Turn lights on
protocol.set_rail_lights(on=True)
Turn lights off

protocol.set_rail_lights(on=False)

8. Multi-Channel and 8-Channel Pipetting

When using multi-channel pipettes:

# Load 8-channel pipette
multi_pipette = protocol.load_instrument(
    'p300_multi_gen2',
    'left',
    tip_racks=[tips]
)
Access entire column with single well reference

multi_pipette.transfer(
    volume=100,
    source=source_plate['A1'],  # Accesses entire column 1
    dest=dest_plate['A1']       # Dispenses to entire column 1
)
Use rows() for row-wise operations

for row in plate.rows():
    multi_pipette.transfer(100, reservoir['A1'], row[0])

9. Common Protocol Patterns

Serial Dilution:

def run(protocol: protocol_api.ProtocolContext):
    # Load labware
    tips = protocol.load_labware('opentrons_flex_96_tiprack_200ul', 'D1')
    reservoir = protocol.load_labware('nest_12_reservoir_15ml', 'D2')
    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 'D3')
    # Load pipette
    p300 = protocol.load_instrument('p300_single_flex', 'left', tip_racks=[tips])
    # Add diluent to all wells except first
    p300.transfer(100, reservoir['A1'], plate.rows()[0][1:])    # Serial dilution across row
    p300.transfer(
        100,
        plate.rows()[0][:11],  # Source: wells 0-10
        plate.rows()[0][1:],   # Dest: wells 1-11
        mix_after=(3, 50),     # Mix 3x with 50µL after dispense
        new_tip='always'
    )

Plate Replication:

def run(protocol: protocol_api.ProtocolContext):
    # Load labware
    tips = protocol.load_labware('opentrons_flex_96_tiprack_1000ul', 'C1')
    source = protocol.load_labware('corning_96_wellplate_360ul_flat', 'D1')
    dest = protocol.load_labware('corning_96_wellplate_360ul_flat', 'D2')
    # Load pipette
    p1000 = protocol.load_instrument('p1000_single_flex', 'left', tip_racks=[tips])    # Transfer from all wells in source to dest
    p1000.transfer(
        100,
        source.wells(),
        dest.wells(),
        new_tip='always'
    )

PCR Setup:

def run(protocol: protocol_api.ProtocolContext):
    # Load thermocycler
    tc_mod = protocol.load_module('thermocyclerModuleV2')
    tc_plate = tc_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')
    # Load tips and reagents
    tips = protocol.load_labware('opentrons_flex_96_tiprack_200ul', 'C1')
    reagents = protocol.load_labware('opentrons_24_tuberack_nest_1.5ml_snapcap', 'D1')
    # Load pipette
    p300 = protocol.load_instrument('p300_single_flex', 'left', tip_racks=[tips])
    # Open thermocycler lid
    tc_mod.open_lid()
    # Distribute master mix
    p300.distribute(
        20,
        reagents['A1'],
        tc_plate.wells(),
        new_tip='once'
    )
    # Add samples (example for first 8 wells)
    for i, well in enumerate(tc_plate.wells()[:8]):
        p300.transfer(5, reagents.wells()[i+1], well, new_tip='always')
    # Run PCR
    tc_mod.close_lid()
    tc_mod.set_lid_temperature(105)
    # PCR profile
    tc_mod.set_block_temperature(95, hold_time_seconds=180)
    profile = [
        {'temperature': 95, 'hold_time_seconds': 15},
        {'temperature': 60, 'hold_time_seconds': 30},
        {'temperature': 72, 'hold_time_seconds': 30}
    ]
    tc_mod.execute_profile(steps=profile, repetitions=35, block_max_volume=25)
    tc_mod.set_block_temperature(72, hold_time_minutes=5)
    tc_mod.set_block_temperature(4)    tc_mod.deactivate_lid()
    tc_mod.open_lid()

Best Practices

Always specify API level: Use the latest stable API version in metadata

Use meaningful labels: Label labware for easier identification in logs

Check tip availability: Ensure sufficient tips for protocol completion

Add comments: Use protocol.comment() for debugging and logging

Simulate first: Always test protocols in simulation before running on robot

Handle errors gracefully: Add pauses for manual intervention when needed

Consider timing: Use delays when protocols require incubation periods

Track liquids: Use liquid tracking for better setup validation

Optimize tip usage: Use new_tip='once' when appropriate to save tips

Control flow rates: Adjust flow rates for viscous or volatile liquids

Troubleshooting

Common Issues:

Out of tips: Verify tip rack capacity matches protocol requirements

Labware collisions: Check deck layout for spatial conflicts

Volume errors: Ensure volumes don't exceed well or pipette capacities

Module not responding: Verify module is properly connected and firmware is updated

Inaccurate volumes: Calibrate pipettes and check for air bubbles

Protocol fails in simulation: Check API version compatibility and labware definitions

Resources

For detailed API documentation, see references/api_reference.md in this skill directory.

For example protocol templates, see scripts/ directory.

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