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

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):

# 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):

# 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.

# 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:

# 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:

# 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

# Get current temperature
current_temp = hs_mod.current_temperature

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

Shaking Control

Basic Shaking

# 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

# 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

# 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)

# 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.

# 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

# 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

# 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

# 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

# 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:

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)

# 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:

# 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

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

Common Mistakes

❌ Shaking with open latch:

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

✅ Correct:

hs_mod.close_labware_latch()
hs_mod.set_and_wait_for_shake_speed(500)

❌ Gripper movement without opening latch:

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

✅ Correct:

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

❌ Not deactivating modules:

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

✅ Correct:

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

❌ Temperature out of range:

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

✅ Correct:

# 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)

# 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

# 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)