Pylabrobot

pip install pylabrobot
pip install "pylabrobot[hamilton]"   # add Hamilton USB driver
pip install "pylabrobot[opentrons]"  # add Opentrons REST driver

import asyncio
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import SimulatorBackend
from pylabrobot.resources import Deck, Cos_96_Rd, HTF_L

async def main():
    backend = SimulatorBackend(open_browser=False)
    lh = LiquidHandler(backend=backend, deck=Deck())
    await lh.setup()

    plate = Cos_96_Rd(name="plate")
    tips  = HTF_L(name="tips")
    lh.deck.assign_child_resource(plate, rails=2)
    lh.deck.assign_child_resource(tips,  rails=5)

    await lh.pick_up_tips(tips["A1"])
    await lh.aspirate(plate["A1"], vols=50)
    await lh.dispense(plate["B1"], vols=50)
    await lh.drop_tips(tips["A1"])
    await lh.stop()
    print("Transfer complete: 50 uL from A1 -> B1")

asyncio.run(main())

import asyncio
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import SimulatorBackend
from pylabrobot.resources import Deck

async def main():
    backend = SimulatorBackend(open_browser=False)
    lh = LiquidHandler(backend=backend, deck=Deck())
    await lh.setup()      # connect to hardware / start simulator
    print("LiquidHandler ready:", lh)
    await lh.stop()       # disconnect cleanly

asyncio.run(main())

# Connecting to a real Hamilton STAR
from pylabrobot.liquid_handling.backends.hamilton import STAR

async def main():
    backend = STAR()
    lh = LiquidHandler(backend=backend, deck=Deck())
    await lh.setup()
    # lh is now connected to physical hardware
    await lh.stop()

from pylabrobot.resources import (
    Deck,
    Cos_96_Rd,                  # Corning 96-well round-bottom plate
    Cos_384_Sq,                 # Corning 384-well plate
    HTF_L,                      # Hamilton tip rack (filtered, large)
    Trough_1_Row_1_Col_4,       # 4-channel reservoir
)

deck = Deck()
plate_96  = Cos_96_Rd(name="sample_plate")
plate_384 = Cos_384_Sq(name="assay_plate")
tips      = HTF_L(name="tip_rack")
reservoir = Trough_1_Row_1_Col_4(name="buffer")

deck.assign_child_resource(plate_96,  rails=1)
deck.assign_child_resource(plate_384, rails=4)
deck.assign_child_resource(tips,      rails=8)
deck.assign_child_resource(reservoir, rails=11)

print("Deck resources:", [r.name for r in deck.children])

# Pick up tips from the first column of the tip rack
await lh.pick_up_tips(tips["A1:H1"])   # all 8 tips in column 1

# After liquid operations, drop tips back
await lh.drop_tips(tips["A1:H1"])

# Single tip
await lh.pick_up_tips(tips["A1"])
await lh.drop_tips(tips["A1"])
print("Tip operations complete")

# Aspirate 100 uL from a single well
await lh.aspirate(plate["A1"], vols=100)

# Aspirate different volumes from multiple wells simultaneously
await lh.aspirate(
    plate["A1:A4"],
    vols=[50, 75, 100, 125],
)
print("Aspiration complete")

from pylabrobot.resources import Coordinate

# Aspirate with flow rate and liquid height control
await lh.aspirate(
    plate["A1"],
    vols=50,
    flow_rates=100,                    # uL/s
    offsets=Coordinate(0, 0, 1),       # 1 mm above well bottom
)

# Dispense 100 uL into a single well
await lh.dispense(plate["B1"], vols=100)

# Multi-well dispense with different volumes
await lh.dispense(
    plate["B1:B4"],
    vols=[50, 75, 100, 125],
)
print("Dispense complete")

# Transfer 50 uL from A1 -> B1
await lh.transfer(plate["A1"], plate["B1"], transfer_volume=50)

# Multi-well pairwise transfer
sources      = plate["A1:A8"]
destinations = plate["B1:B8"]
await lh.transfer(sources, destinations, transfer_volume=75)
print("Transfer complete")

from pylabrobot.liquid_handling.backends import SimulatorBackend

# With visual browser (default — opens http://localhost:2121)
backend = SimulatorBackend(open_browser=True)

# Headless simulation (CI/testing)
backend = SimulatorBackend(open_browser=False)

# After setup(), liquid movements are visualized in real time
await lh.setup()
# Check browser for visual confirmation before running on real hardware
print("Simulator running at http://localhost:2121")

import asyncio

async def run_protocol(lh, plate, tips):
    await lh.pick_up_tips(tips["A1"])
    await lh.aspirate(plate["A1"], vols=50)
    await lh.dispense(plate["B1"], vols=50)
    await lh.drop_tips(tips["A1"])
    print("Protocol complete")

asyncio.run(run_protocol(lh, plate, tips))

well    = plate["A1"]             # single well
col1    = plate["A1:H1"]          # 8 wells in column 1
row_a   = plate["A1:A12"]         # 12 wells in row A
print(f"Single: {well.name}")
print(f"Column: {len(col1)} wells")
print(f"Row:    {len(row_a)} wells")

import asyncio
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import SimulatorBackend
from pylabrobot.resources import Deck, Cos_96_Rd, HTF_L, Trough_1_Row_1_Col_4

async def serial_dilution():
    backend = SimulatorBackend(open_browser=False)
    lh = LiquidHandler(backend=backend, deck=Deck())
    await lh.setup()

    plate   = Cos_96_Rd(name="plate")
    tips    = HTF_L(name="tips")
    diluent = Trough_1_Row_1_Col_4(name="diluent")
    lh.deck.assign_child_resource(plate,   rails=1)
    lh.deck.assign_child_resource(tips,    rails=5)
    lh.deck.assign_child_resource(diluent, rails=9)

    # Add 100 uL diluent to columns 2-12
    for col in range(2, 13):
        col_label = f"A{col}:H{col}"
        await lh.pick_up_tips(tips[f"A{col}:H{col}"])
        await lh.aspirate(diluent["A1:H1"], vols=100)
        await lh.dispense(plate[col_label], vols=100)
        await lh.drop_tips(tips[f"A{col}:H{col}"])

    # Serial transfer: col 1 -> 2 -> ... -> 11
    for col in range(1, 12):
        src = f"A{col}:H{col}"
        dst = f"A{col+1}:H{col+1}"
        await lh.pick_up_tips(tips[f"A{col}:H{col}"])
        await lh.aspirate(plate[src], vols=100)
        await lh.dispense(plate[dst], vols=100)
        await lh.drop_tips(tips[f"A{col}:H{col}"])

    print("Serial dilution complete: 12 columns, 2-fold steps")
    await lh.stop()

asyncio.run(serial_dilution())

import asyncio
import pandas as pd
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import SimulatorBackend
from pylabrobot.resources import Deck, Cos_96_Rd, HTF_L

async def cherry_pick(hit_list_csv: str, volume: float = 50.0):
    # CSV must have columns: source_well, dest_well
    hits = pd.read_csv(hit_list_csv)
    print(f"Cherry-picking {len(hits)} hits at {volume} uL each")

    backend = SimulatorBackend(open_browser=False)
    lh = LiquidHandler(backend=backend, deck=Deck())
    await lh.setup()

    src  = Cos_96_Rd(name="source")
    dst  = Cos_96_Rd(name="destination")
    tips = HTF_L(name="tips")
    lh.deck.assign_child_resource(src,  rails=1)
    lh.deck.assign_child_resource(dst,  rails=4)
    lh.deck.assign_child_resource(tips, rails=8)

    # Get all well names from tip rack
    tip_wells = [w.name for w in tips.wells]
    for i, row in hits.iterrows():
        await lh.pick_up_tips(tips[tip_wells[i]])
        await lh.transfer(src[row["source_well"]], dst[row["dest_well"]],
                          transfer_volume=volume)
        await lh.drop_tips(tips[tip_wells[i]])

    print(f"Cherry-pick complete: {len(hits)} transfers done")
    await lh.stop()

# asyncio.run(cherry_pick("hits.csv", volume=50))