Opentrons Heater-Shaker Module

Overview

The Heater-Shaker Module combines precise temperature control (37-95°C) with orbital shaking (200-3000 rpm) for automated protocols requiring simultaneous heating and mixing. Ideal for cell culture incubation, enzymatic reactions, bacterial transformations, and any workflow needing temperature-controlled agitation.

Core value: Automate temperature-sensitive mixing protocols with reproducible timing and conditions. Replace manual incubator transfers with on-deck temperature control.

When to Use

Use the Heater-Shaker skill when:

•Performing enzymatic reactions requiring temperature control and mixing
•Incubating cell cultures or bacterial transformations
•Conducting ELISA washing steps with temperature control
•Running temperature-sensitive binding or hybridization reactions
•Protocols requiring precise timing of heating + mixing cycles
•Resuspending beads or particles with controlled agitation

Don't use when:

•Only temperature control needed (use Temperature Module instead)
•Only mixing needed (consider manual shaking or alternative approaches)
•Temperature outside 37-95°C range (or <1.5°C above ambient)

Quick Reference

Operation	Method	Key Parameters
Load module	`protocol.load_module()`	`"heaterShakerModuleV1"`, location
Set temperature (blocking)	`set_and_wait_for_temperature()`	celsius (37-95)
Set temperature (non-blocking)	`set_target_temperature()`	celsius
Wait for temperature	`wait_for_temperature()`	-
Start shaking (blocking)	`set_and_wait_for_shake_speed()`	rpm (200-3000)
Stop shaking	`deactivate_shaker()`	-
Stop heating	`deactivate_heater()`	-
Open latch	`open_labware_latch()`	-
Close latch	`close_labware_latch()`	-
Check status	`.current_temperature`, `.current_speed`	-

Platform Compatibility

Opentrons Flex

•Allowed slots: Column 1 or Column 3 (A1, B1, C1, D1, A3, B3, C3, D3)
•No adjacent restrictions - Full deck flexibility

OT-2

•Allowed slots: 1, 3, 4, 6, 7, or 10
•
Adjacent slot restrictions:
- •Keep adjacent slots clear or use only low-profile labware (<53mm height)
- •8-channel pipettes cannot pipette in adjacent slots (tip racks OK if front/back)

Loading the Module

Basic Loading

python

from opentrons import protocol_api

metadata = {'apiLevel': '2.19'}

def run(protocol: protocol_api.ProtocolContext):
    # Load Heater-Shaker in deck slot
    hs_mod = protocol.load_module("heaterShakerModuleV1", location="D1")  # Flex
    # hs_mod = protocol.load_module("heaterShakerModuleV1", location="1")  # OT-2

Loading Labware with Adapters

Two-step approach (recommended):

python

# Load adapter first, then labware
hs_adapter = hs_mod.load_adapter("opentrons_96_flat_bottom_adapter")
hs_plate = hs_adapter.load_labware("nest_96_wellplate_200ul_flat")

Available adapters:

•opentrons_96_flat_bottom_adapter - Universal flat-bottom plates
•opentrons_96_pcr_adapter - PCR plates and strips
•opentrons_96_deep_well_adapter - Deep-well plates
•opentrons_universal_flat_adapter - Custom flat-bottom labware

Pre-configured combinations (legacy):

python

# Load labware directly (adapter implicit)
hs_plate = hs_mod.load_labware("nest_96_wellplate_200ul_flat")

Latch Control

The labware latch MUST be closed for shaking operations.

python

# Close latch before shaking
hs_mod.close_labware_latch()

# Open latch for pipetting or gripper access
hs_mod.open_labware_latch()

Important:

•Pipetting is possible with latch open or closed
•Shaking requires latch closed (method will error if open)
•Gripper access requires latch open
•Always open latch before gripper operations

Temperature Control

Blocking Temperature Control

Protocol waits until temperature is reached before continuing:

python

# Set temperature and wait
hs_mod.set_and_wait_for_temperature(celsius=37)

# Perform operations at target temperature
protocol.delay(minutes=10)

# Turn off heater
hs_mod.deactivate_heater()

Temperature range:

•Minimum: The greater of 37°C or ambient temperature + 1.5°C (the Heater-Shaker cannot actively cool)
•Maximum: 95°C
•Resolution: 1°C

Non-Blocking Temperature Control

Set target temperature and continue with other operations while heating:

python

# Start heating (non-blocking)
hs_mod.set_target_temperature(celsius=75)

# Perform pipetting while heating
pipette.transfer(100, source, hs_plate.columns()[0])

# Wait for temperature before critical step
hs_mod.wait_for_temperature()

# Now at target temperature
protocol.delay(minutes=5)

Use case: Parallel pipetting during heating to save time.

Checking Temperature Status

python

# Get current temperature
current_temp = hs_mod.current_temperature

# Log temperature
protocol.comment(f"Heater-Shaker at {current_temp}°C")

Shaking Control

Basic Shaking

python

# Close latch first (required)
hs_mod.close_labware_latch()

# Start shaking and wait to reach speed
hs_mod.set_and_wait_for_shake_speed(rpm=500)

# Shake for specific duration
protocol.delay(minutes=5)

# Stop shaking
hs_mod.deactivate_shaker()

# Open latch for pipetting access
hs_mod.open_labware_latch()

Speed range:

•Minimum: 200 rpm
•Maximum: 3000 rpm

Checking Shake Speed

python

# Get current speed
current_speed = hs_mod.current_speed

if current_speed > 0:
    protocol.comment(f"Shaking at {current_speed} rpm")

Shake Speed Guidelines

Recommended speeds by application:

•Gentle mixing: 200-500 rpm
•Cell culture: 300-600 rpm
•Enzymatic reactions: 400-800 rpm
•Vigorous mixing: 800-1500 rpm
•Aggressive agitation: 1500-3000 rpm

Note: Higher speeds increase risk of splashing and cross-contamination.

Combined Heating and Shaking

Sequential Approach

python

# Set temperature first
hs_mod.set_and_wait_for_temperature(celsius=37)

# Then start shaking
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=400)

# Incubate with heating and shaking
protocol.delay(minutes=30)

# Stop shaking, then heating
hs_mod.deactivate_shaker()
hs_mod.open_labware_latch()
hs_mod.deactivate_heater()

Parallel Approach (Time-Optimized)

python

# Start heating (non-blocking)
hs_mod.set_target_temperature(celsius=42)

# Prepare samples while heating
pipette.transfer(100, samples, hs_plate.wells())

# Wait for temperature
hs_mod.wait_for_temperature()

# Start shaking
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=600)

# Incubate
protocol.delay(minutes=20)

# Cleanup
hs_mod.deactivate_shaker()
hs_mod.open_labware_latch()
hs_mod.deactivate_heater()

Common Patterns

Bacterial Transformation

Note: The Heater-Shaker cannot cool below 37C. Use a Temperature Module for ice incubation and heat shock steps, then transfer to the Heater-Shaker for the 37C recovery with shaking.

python

# Ice incubation and heat shock on Temperature Module
temp_mod.set_temperature(celsius=4)
protocol.delay(minutes=20)  # Ice incubation
temp_mod.set_temperature(celsius=42)
protocol.delay(seconds=45)  # Heat shock

# Transfer plate to Heater-Shaker for recovery
temp_mod.deactivate()
protocol.move_labware(plate, hs_mod, use_gripper=True)

# Recovery at 37C with shaking
hs_mod.set_and_wait_for_temperature(celsius=37)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=300)
protocol.delay(minutes=60)

hs_mod.deactivate_shaker()
hs_mod.deactivate_heater()
hs_mod.open_labware_latch()

Enzymatic Reaction

python

# Pre-warm to reaction temperature
hs_mod.set_and_wait_for_temperature(celsius=37)

# Add enzyme while at temperature
hs_mod.open_labware_latch()
pipette.transfer(10, enzyme, hs_plate.wells(), mix_after=(3, 50))

# Incubate with gentle mixing
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=300)
protocol.delay(minutes=30)

# Stop reaction - transfer to Temperature Module for cooling
hs_mod.deactivate_shaker()
hs_mod.deactivate_heater()
hs_mod.open_labware_latch()

# Use Temperature Module for cooling below 37C
# protocol.move_labware(hs_plate, temp_mod, use_gripper=True)
# temp_mod.set_temperature(celsius=4)

ELISA Wash with Incubation

python

# Incubate with antibody
hs_mod.set_and_wait_for_temperature(celsius=37)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=400)
protocol.delay(minutes=60)

# Stop for washing
hs_mod.deactivate_shaker()
hs_mod.open_labware_latch()

# Wash steps
for _ in range(3):
    # Remove liquid
    pipette.transfer(200, hs_plate.wells(), waste, new_tip="always")
    # Add wash buffer
    pipette.transfer(200, wash_buffer, hs_plate.wells())
    # Mix
    hs_mod.close_labware_latch()
    hs_mod.set_and_wait_for_shake_speed(rpm=500)
    protocol.delay(seconds=30)
    hs_mod.deactivate_shaker()
    hs_mod.open_labware_latch()

hs_mod.deactivate_heater()

Bead Resuspension

python

# Resuspend magnetic beads
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=1200)
protocol.delay(minutes=2)
hs_mod.deactivate_shaker()
hs_mod.open_labware_latch()

# Transfer to magnetic module for separation
protocol.move_labware(hs_plate, mag_block, use_gripper=True)

Advanced Techniques

Temperature Ramping

python

# Gradual temperature increase
for temp in [25, 35, 45, 55, 65]:
    hs_mod.set_and_wait_for_temperature(temp)
    protocol.delay(minutes=5)

hs_mod.deactivate_heater()

Precise Timing with Manual Tracking

For holds requiring exact elapsed time:

python

import time

# Set conditions
hs_mod.set_and_wait_for_temperature(celsius=37)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=500)

# Track elapsed time
start_time = time.monotonic()

# Perform operations
# ... your protocol steps ...

# Calculate remaining time
elapsed = time.monotonic() - start_time
remaining = max(0, (10 * 60) - elapsed)  # 10 minutes total

# Complete the hold
protocol.delay(seconds=remaining)

hs_mod.deactivate_shaker()
hs_mod.deactivate_heater()
hs_mod.open_labware_latch()

Integration with Gripper (Flex)

python

# Heat/shake on Heater-Shaker
hs_mod.set_and_wait_for_temperature(celsius=37)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(rpm=400)
protocol.delay(minutes=30)
hs_mod.deactivate_shaker()
hs_mod.deactivate_heater()

# Open latch BEFORE gripper operation
hs_mod.open_labware_latch()

# Move plate to next module
protocol.move_labware(hs_plate, magnetic_block, use_gripper=True)

OT-2 Specific Considerations

Deck Layout Restrictions

Height restrictions:

•Adjacent slots must be empty OR contain labware <53mm tall
•Tall labware (>53mm) in adjacent slots interferes with module

8-channel pipette restrictions:

•Cannot pipette in slots adjacent to Heater-Shaker
•Exception: Tip racks allowed if oriented front-to-back (not left-to-right)

Example valid OT-2 layout:

python

# Heater-Shaker in slot 4
hs_mod = protocol.load_module("heaterShakerModuleV1", "4")

# Adjacent slots 1, 5, 7 - keep empty or use tip racks
tips_1 = protocol.load_labware("opentrons_96_tiprack_300ul", "1")  # OK
tips_5 = protocol.load_labware("opentrons_96_tiprack_300ul", "5")  # OK

# Use non-adjacent slots for plates
plate_2 = protocol.load_labware("corning_96_wellplate_360ul_flat", "2")
plate_3 = protocol.load_labware("corning_96_wellplate_360ul_flat", "3")

Best Practices

•Always open latch before gripper operations - Prevents gripper errors
•Deactivate shaker before heater - Safer shutdown sequence
•Use non-blocking temperature for parallel operations - Saves protocol time
•Close latch before shaking - Required for operation
•Allow temperature stabilization - Add brief delay after reaching target
•Monitor shake speed selection - Higher speeds risk splashing/contamination
•Consider ambient temperature - Affects minimum achievable temperature
•Plan deck layout (OT-2) - Account for adjacent slot restrictions
•Add protocol comments - Document temperature/shake conditions for reproducibility
•Deactivate at protocol end - Prevents equipment running indefinitely

Common Mistakes

❌ Shaking with open latch:

python

hs_mod.open_labware_latch()
hs_mod.set_and_wait_for_shake_speed(500)  # Error: latch must be closed

✅ Correct:

python

hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(500)

❌ Gripper movement without opening latch:

python

protocol.move_labware(hs_plate, "C1", use_gripper=True)  # Error: latch closed

✅ Correct:

python

hs_mod.open_labware_latch()
protocol.move_labware(hs_plate, "C1", use_gripper=True)

❌ Not deactivating modules:

python

hs_mod.set_and_wait_for_temperature(37)
# Protocol ends - heater stays on!

✅ Correct:

python

hs_mod.set_and_wait_for_temperature(37)
# ... operations ...
hs_mod.deactivate_heater()

❌ Temperature out of range:

python

hs_mod.set_and_wait_for_temperature(celsius=25)  # May error if ambient is >23.5°C

✅ Correct:

python

# Use Temperature Module for temperatures <37°C
temp_mod.set_temperature(celsius=25)

Troubleshooting

Module won't heat below 37°C:

•Check ambient temperature - minimum is 1.5°C above ambient
•Consider using Temperature Module for lower temperatures

Shaking command errors:

•Verify latch is closed
•Check shake speed is within 200-3000 rpm range

Pipette collisions (OT-2):

•Check adjacent slots for tall labware
•Move tall labware to non-adjacent slots
•Use only tip racks in adjacent slots for 8-channel pipetting

Temperature not stable:

•Allow additional time for equilibration
•Verify module is not in high-airflow environment
•Check labware is properly seated on adapter

Gripper cannot access:

•Ensure latch is open
•Verify module is in allowed deck slot (columns 1 or 3 for Flex)

Integration with Other Modules

With Magnetic Block (Flex)

python

# Incubate with beads on Heater-Shaker
hs_mod.set_and_wait_for_temperature(37)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(400)
protocol.delay(minutes=10)
hs_mod.deactivate_shaker()
hs_mod.deactivate_heater()
hs_mod.open_labware_latch()

# Move to Magnetic Block for separation
protocol.move_labware(hs_plate, mag_block, use_gripper=True)
protocol.delay(minutes=3)  # Bead separation

# Pipette supernatant
pipette.transfer(150, hs_plate.wells(), waste.wells())

# Return to Heater-Shaker for resuspension
protocol.move_labware(hs_plate, hs_mod, use_gripper=True)

With Temperature Module

python

# Cool samples on Temperature Module
temp_mod.set_temperature(4)
protocol.move_labware(cold_plate, temp_mod, use_gripper=True)

# Heat and shake on Heater-Shaker
hs_mod.set_and_wait_for_temperature(65)
hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(600)
protocol.delay(minutes=15)

API Version Requirements

•Minimum API version: 2.13
•Recommended: 2.19 or later for full feature support
•Flex compatibility: API 2.15+ with robotType: "Flex"

Additional Resources

•Module Documentation: https://docs.opentrons.com/v2/modules/heater_shaker.html
•Opentrons Support: https://support.opentrons.com/
•Protocol Examples: https://protocols.opentrons.com/

Related Skills

•opentrons - Main Opentrons Python API skill
•opentrons-temperature-module - Temperature-only control (4-95°C)
•opentrons-thermocycler - PCR thermal cycling
•opentrons-magnetic-block - Magnetic bead separation (Flex)
•opentrons-gripper - Automated labware movement (Flex)