zhongwei/gh-k-dense-ai-claude-scientific-skills-scientific-skills

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Zhongwei Li f0bd18fb4e Initial commit

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Material Handling Equipment in PyLabRobot

Overview

PyLabRobot integrates with material handling equipment including heater shakers, incubators, centrifuges, and pumps. These devices enable environmental control, sample preparation, and automated workflows beyond basic liquid handling.

Heater Shakers

Hamilton HeaterShaker

The Hamilton HeaterShaker provides temperature control and orbital shaking for microplates.

Setup

from pylabrobot.heating_shaking import HeaterShaker
from pylabrobot.heating_shaking.hamilton import HamiltonHeaterShakerBackend

# Create heater shaker
hs = HeaterShaker(
    name="heater_shaker_1",
    backend=HamiltonHeaterShakerBackend(),
    size_x=156.0,
    size_y=  156.0,
    size_z=18.0
)

await hs.setup()

Operations

Temperature Control:

# Set temperature (Celsius)
await hs.set_temperature(37)

# Get current temperature
temp = await hs.get_temperature()
print(f"Current temperature: {temp}°C")

# Turn off heating
await hs.set_temperature(None)

Shaking Control:

# Start shaking (RPM)
await hs.set_shake_rate(300)  # 300 RPM

# Stop shaking
await hs.set_shake_rate(0)

Plate Operations:

# Lock plate in position
await hs.lock_plate()

# Unlock plate
await hs.unlock_plate()

Integration with Liquid Handler

from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import STAR
from pylabrobot.resources import STARLetDeck

# Initialize devices
lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
hs = HeaterShaker(name="hs", backend=HamiltonHeaterShakerBackend())

await lh.setup()
await hs.setup()

try:
    # Assign heater shaker to deck
    lh.deck.assign_child_resource(hs, rails=8)

    # Prepare samples
    tip_rack = TIP_CAR_480_A00(name="tips")
    plate = Cos_96_DW_1mL(name="plate")

    lh.deck.assign_child_resource(tip_rack, rails=1)

    # Place plate on heater shaker
    hs.assign_child_resource(plate, location=(0, 0, 0))

    # Transfer reagents to plate on heater shaker
    await lh.pick_up_tips(tip_rack["A1:H1"])
    await lh.transfer(reagent["A1:H1"], plate["A1:H1"], vols=100)
    await lh.drop_tips()

    # Lock plate and start incubation
    await hs.lock_plate()
    await hs.set_temperature(37)
    await hs.set_shake_rate(300)

    # Incubate
    import asyncio
    await asyncio.sleep(600)  # 10 minutes

    # Stop shaking and heating
    await hs.set_shake_rate(0)
    await hs.set_temperature(None)
    await hs.unlock_plate()

finally:
    await lh.stop()
    await hs.stop()

Multiple Heater Shakers

The HamiltonHeaterShakerBackend handles multiple units:

# Backend automatically manages multiple heater shakers
hs1 = HeaterShaker(name="hs1", backend=HamiltonHeaterShakerBackend())
hs2 = HeaterShaker(name="hs2", backend=HamiltonHeaterShakerBackend())

await hs1.setup()
await hs2.setup()

# Assign to different deck positions
lh.deck.assign_child_resource(hs1, rails=8)
lh.deck.assign_child_resource(hs2, rails=12)

# Control independently
await hs1.set_temperature(37)
await hs2.set_temperature(42)

Inheco ThermoShake

The Inheco ThermoShake provides temperature control and shaking.

Setup

from pylabrobot.heating_shaking import HeaterShaker
from pylabrobot.heating_shaking.inheco import InhecoThermoShakeBackend

hs = HeaterShaker(
    name="thermoshake",
    backend=InhecoThermoShakeBackend(),
    size_x=156.0,
    size_y=156.0,
    size_z=18.0
)

await hs.setup()

Operations

Similar to Hamilton HeaterShaker:

# Temperature control
await hs.set_temperature(37)
temp = await hs.get_temperature()

# Shaking control
await hs.set_shake_rate(300)

# Plate locking
await hs.lock_plate()
await hs.unlock_plate()

Incubators

Inheco Incubators

PyLabRobot supports various Inheco incubator models for temperature-controlled plate storage.

Supported Models

Inheco Single Plate Incubator
Inheco Multi-Plate Incubators
Other Inheco temperature controllers

Setup

from pylabrobot.temperature_control import TemperatureController
from pylabrobot.temperature_control.inheco import InhecoBackend

# Create incubator
incubator = TemperatureController(
    name="incubator",
    backend=InhecoBackend(),
    size_x=156.0,
    size_y=156.0,
    size_z=50.0
)

await incubator.setup()

Operations

# Set temperature
await incubator.set_temperature(37)

# Get temperature
temp = await incubator.get_temperature()
print(f"Incubator temperature: {temp}°C")

# Turn off
await incubator.set_temperature(None)

Thermo Fisher Cytomat Incubators

Cytomat incubators provide automated plate storage with temperature and CO2 control.

Setup

from pylabrobot.incubation import Incubator
from pylabrobot.incubation.cytomat_backend import CytomatBackend

incubator = Incubator(
    name="cytomat",
    backend=CytomatBackend()
)

await incubator.setup()

Operations

# Store plate
await incubator.store_plate(plate_id="plate_001", position=1)

# Retrieve plate
await incubator.retrieve_plate(position=1)

# Set environmental conditions
await incubator.set_temperature(37)
await incubator.set_co2(5.0)  # 5% CO2

Centrifuges

Agilent VSpin

The Agilent VSpin is a vacuum-assisted centrifuge for plate processing.

Setup

from pylabrobot.centrifuge import Centrifuge
from pylabrobot.centrifuge.vspin import VSpinBackend

centrifuge = Centrifuge(
    name="vspin",
    backend=VSpinBackend()
)

await centrifuge.setup()

Operations

Door Control:

# Open door
await centrifuge.open_door()

# Close door
await centrifuge.close_door()

# Lock door
await centrifuge.lock_door()

# Unlock door
await centrifuge.unlock_door()

Bucket Positioning:

# Move bucket to loading position
await centrifuge.move_bucket_to_loading()

# Move bucket to home position
await centrifuge.move_bucket_to_home()

Spinning:

# Run centrifuge
await centrifuge.spin(
    speed=2000,      # RPM
    duration=300     # seconds
)

# Stop spinning
await centrifuge.stop_spin()

Integration Example

async def centrifuge_workflow():
    """Complete centrifugation workflow"""

    lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
    centrifuge = Centrifuge(name="vspin", backend=VSpinBackend())

    await lh.setup()
    await centrifuge.setup()

    try:
        # Prepare samples
        await lh.pick_up_tips(tip_rack["A1:H1"])
        await lh.transfer(samples["A1:H12"], plate["A1:H12"], vols=200)
        await lh.drop_tips()

        # Load into centrifuge
        print("Move plate to centrifuge")
        await centrifuge.open_door()
        await centrifuge.move_bucket_to_loading()
        input("Press Enter when plate is loaded...")

        await centrifuge.move_bucket_to_home()
        await centrifuge.close_door()
        await centrifuge.lock_door()

        # Centrifuge
        await centrifuge.spin(speed=2000, duration=300)

        # Unload
        await centrifuge.unlock_door()
        await centrifuge.open_door()
        await centrifuge.move_bucket_to_loading()
        input("Press Enter when plate is removed...")

        await centrifuge.move_bucket_to_home()
        await centrifuge.close_door()

    finally:
        await lh.stop()
        await centrifuge.stop()

Pumps

Cole Parmer Masterflex

PyLabRobot supports Cole Parmer Masterflex peristaltic pumps for fluid transfer.

Setup

from pylabrobot.pumps import Pump
from pylabrobot.pumps.cole_parmer import ColeParmerMasterflexBackend

pump = Pump(
    name="masterflex",
    backend=ColeParmerMasterflexBackend()
)

await pump.setup()

Operations

Running Pump:

# Run for duration
await pump.run_for_duration(
    duration=10,      # seconds
    speed=50          # % of maximum
)

# Run continuously
await pump.start(speed=50)

# Stop pump
await pump.stop()

Volume-Based Pumping:

# Pump specific volume (requires calibration)
await pump.pump_volume(
    volume=10,        # mL
    speed=50          # % of maximum
)

Calibration

# Calibrate pump for volume accuracy
# (requires known volume measurement)
await pump.run_for_duration(duration=60, speed=50)
actual_volume = 25.3  # mL measured

pump.calibrate(duration=60, speed=50, volume=actual_volume)

Agrowtek Pump Array

Support for Agrowtek pump arrays for multiple simultaneous fluid transfers.

Setup

from pylabrobot.pumps import PumpArray
from pylabrobot.pumps.agrowtek import AgrowtekBackend

pump_array = PumpArray(
    name="agrowtek",
    backend=AgrowtekBackend(),
    num_pumps=8
)

await pump_array.setup()

Operations

# Run specific pump
await pump_array.run_pump(
    pump_number=1,
    duration=10,
    speed=50
)

# Run multiple pumps simultaneously
await pump_array.run_pumps(
    pump_numbers=[1, 2, 3],
    duration=10,
    speed=50
)

Multi-Device Protocols

Complex Workflow Example

async def complex_workflow():
    """Multi-device automated workflow"""

    # Initialize all devices
    lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
    hs = HeaterShaker(name="hs", backend=HamiltonHeaterShakerBackend())
    centrifuge = Centrifuge(name="vspin", backend=VSpinBackend())
    pump = Pump(name="pump", backend=ColeParmerMasterflexBackend())

    await lh.setup()
    await hs.setup()
    await centrifuge.setup()
    await pump.setup()

    try:
        # 1. Sample preparation
        await lh.pick_up_tips(tip_rack["A1:H1"])
        await lh.transfer(samples["A1:H12"], plate["A1:H12"], vols=100)
        await lh.drop_tips()

        # 2. Add reagent via pump
        await pump.pump_volume(volume=50, speed=50)

        # 3. Mix on heater shaker
        await hs.lock_plate()
        await hs.set_temperature(37)
        await hs.set_shake_rate(300)
        await asyncio.sleep(600)  # 10 min incubation
        await hs.set_shake_rate(0)
        await hs.set_temperature(None)
        await hs.unlock_plate()

        # 4. Centrifuge
        await centrifuge.open_door()
        # (load plate)
        await centrifuge.close_door()
        await centrifuge.spin(speed=2000, duration=180)
        await centrifuge.open_door()
        # (unload plate)

        # 5. Transfer supernatant
        await lh.pick_up_tips(tip_rack["A2:H2"])
        await lh.transfer(
            plate["A1:H12"],
            output_plate["A1:H12"],
            vols=80
        )
        await lh.drop_tips()

    finally:
        await lh.stop()
        await hs.stop()
        await centrifuge.stop()
        await pump.stop()

Best Practices

Device Initialization: Setup all devices at protocol start
Sequential Operations: Material handling often requires sequential steps
Safety: Always unlock/open doors before manual plate handling
Temperature Equilibration: Allow time for devices to reach temperature
Error Handling: Handle device errors gracefully with try/finally
State Verification: Check device state before operations
Timing: Account for device-specific delays (heating, centrifugation)
Maintenance: Follow manufacturer maintenance schedules
Calibration: Regularly calibrate pumps and temperature controllers
Documentation: Record all device settings and parameters

Common Patterns

Temperature-Controlled Incubation

async def incubate_with_shaking(
    plate,
    temperature: float,
    shake_rate: int,
    duration: int
):
    """Incubate plate with temperature and shaking"""

    hs = HeaterShaker(name="hs", backend=HamiltonHeaterShakerBackend())
    await hs.setup()

    try:
        # Assign plate to heater shaker
        hs.assign_child_resource(plate, location=(0, 0, 0))

        # Start incubation
        await hs.lock_plate()
        await hs.set_temperature(temperature)
        await hs.set_shake_rate(shake_rate)

        # Wait
        await asyncio.sleep(duration)

        # Stop
        await hs.set_shake_rate(0)
        await hs.set_temperature(None)
        await hs.unlock_plate()

    finally:
        await hs.stop()

# Use in protocol
await incubate_with_shaking(
    plate=assay_plate,
    temperature=37,
    shake_rate=300,
    duration=600  # 10 minutes
)

Automated Plate Processing

async def process_plates(plate_list: list):
    """Process multiple plates through workflow"""

    lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
    hs = HeaterShaker(name="hs", backend=HamiltonHeaterShakerBackend())

    await lh.setup()
    await hs.setup()

    try:
        for i, plate in enumerate(plate_list):
            print(f"Processing plate {i+1}/{len(plate_list)}")

            # Transfer samples
            await lh.pick_up_tips(tip_rack[f"A{i+1}:H{i+1}"])
            await lh.transfer(
                source[f"A{i+1}:H{i+1}"],
                plate["A1:H1"],
                vols=100
            )
            await lh.drop_tips()

            # Incubate
            hs.assign_child_resource(plate, location=(0, 0, 0))
            await hs.lock_plate()
            await hs.set_temperature(37)
            await hs.set_shake_rate(300)
            await asyncio.sleep(300)  # 5 min
            await hs.set_shake_rate(0)
            await hs.set_temperature(None)
            await hs.unlock_plate()
            hs.unassign_child_resource(plate)

    finally:
        await lh.stop()
        await hs.stop()

Additional Resources

Material Handling Documentation: https://docs.pylabrobot.org/user_guide/01_material-handling/
Heater Shakers: https://docs.pylabrobot.org/user_guide/01_material-handling/heating_shaking/
API Reference: https://docs.pylabrobot.org/api/
Supported Equipment: https://docs.pylabrobot.org/user_guide/machines.html

14 KiB Raw Blame History

Material Handling Equipment in PyLabRobot

Overview

Heater Shakers

Hamilton HeaterShaker

Setup

Operations

Integration with Liquid Handler

Multiple Heater Shakers

Inheco ThermoShake

Setup

Operations

Incubators

Inheco Incubators

Supported Models

Setup

Operations

Thermo Fisher Cytomat Incubators

Setup

Operations

Centrifuges

Agilent VSpin

Setup

Operations

Integration Example

Pumps

Cole Parmer Masterflex

Setup

Operations

Calibration

Agrowtek Pump Array

Setup

Operations

Multi-Device Protocols

Complex Workflow Example

Best Practices

Common Patterns

Temperature-Controlled Incubation

Automated Plate Processing

Additional Resources

14 KiB

Raw Blame History