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 protected]>',
    '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(