PyLabRobot 1.0.0b1

What is PyLabRobot?

PyLabRobot is a hardware agnostic, pure Python library for liquid handling robots, plate readers, pumps, scales, heater shakers, and other lab automation equipment. Read the paper in Device.

Advantages over proprietary software:

• Cross-platform: PyLabRobot works on Windows, macOS, and Linux. Many other interfaces are Windows-only.
• Universal: PyLabRobot works with any supported liquid handling robot, plate reader, pump, scale, heater shaker, etc. through a single interface.
• Fast iteration: PyLabRobot enables rapid development of protocols using atomic commands run interactively in Jupyter notebooks or the Python REPL. This decreases iteration time from minutes to seconds.
• Open-source: PyLabRobot is open-source and free to use.
• Control: With Python, you have ultimate flexibility to control your lab automation equipment. You can write Turing-complete protocols that include feedback loops.
• Modern: PyLabRobot is built on modern Python 3.9+ features and async/await syntax.
• Fast support: PyLabRobot has an active community forum for support and discussion, and most pull requests are merged within a day.

Liquid handling robots (docs)

PyLabRobot enables the use of any liquid handling robot through a single universal interface, that works on any modern operating system (Windows, macOS, Linux). We currently support Hamilton STAR, Hamilton Vantage, Tecan Freedom EVO, and Opentrons OT-2 robots, but we will soon support many more.

Here's a quick example showing how to move 100uL of liquid from well A1 to A2 using firmware on Hamilton STAR (this will work on any operating system!):

from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import STARBackend
from pylabrobot.resources import Deck

deck = Deck.load_from_json_file("hamilton-layout.json")
lh = LiquidHandler(backend=STARBackend(), deck=deck)
await lh.setup()

await lh.pick_up_tips(lh.deck.get_resource("tip_rack")["A1"])
await lh.aspirate(lh.deck.get_resource("plate")["A1"], vols=100)
await lh.dispense(lh.deck.get_resource("plate")["A2"], vols=100)
await lh.return_tips()

To run the same protocol on an Opentrons, use the following:

from pylabrobot.liquid_handling.backends import OpentronsOT2Backend
deck = Deck.load_from_json_file("opentrons-layout.json")
lh = LiquidHandler(backend=OpentronsOT2Backend(host="x.x.x.x"), deck=deck)

Or Tecan (also works on any operating system!):

from pylabrobot.liquid_handling.backends import EVOBackend
deck = Deck.load_from_json_file("tecan-layout.json")
lh = LiquidHandler(backend=EVOBackend(), deck=deck)

We also provide a browser-based Visualizer which can visualize the state of the deck during a run, and can be used to develop and test protocols without a physical robot.

Plate readers (docs)

Moving a plate to a ClarioStar using a liquid handler, and reading luminescence:

from pylabrobot.plate_reading import PlateReader, CLARIOstarBackend

pr = PlateReader(name="plate reader", backend=CLARIOstarBackend(), size_x=1, size_y=1, size_z=1)
await pr.setup()

# Use in combination with a liquid handler
lh.assign_child_resource(pr, location=Coordinate(x, y, z))
lh.move_plate(lh.deck.get_resource("plate"), pr)

data = await pr.read_luminescence()

For Cytation5, use the Cytation5 backend.

Centrifuges (docs)

Centrifugation at 800g for 60 seconds with an Agilent VSpin:

from pylabrobot.centrifuge import Centrifuge, VSpinBackend

vspin_backend = VSpinBackend(device_id="YOUR_FTDI_ID_HERE")
cf = Centrifuge(name="centrifuge", backend=vspin_backend, size_x=1, size_y=1, size_z=1)
await cf.setup()

await cf.spin(g=800, duration=60)

For a HighRes Biosolutions MicroSpin, use the MicroSpin factory:

from pylabrobot.centrifuge import MicroSpin

cf = MicroSpin(name="microspin", host="192.168.127.60")
await cf.setup()
await cf.backend.home()

await cf.spin(g=800, duration=60)

Pumps (docs)

Pumping at 100 rpm for 30 seconds using a Masterflex pump:

from pylabrobot.pumps import Pump
from pylabrobot.pumps.cole_parmer.masterflex import Masterflex

p = Pump(backend=Masterflex())
await p.setup()
await p.run_for_duration(speed=100, duration=30)

Scales (docs)

Taking a measurement from a Mettler Toledo scale:

from pylabrobot.mettler_toledo import MTSICSDriver

scale = MTSICSDriver(port="/dev/cu.usbserial-110")
await scale.setup()

weight = await scale.read_weight()

Heater shakers (docs)

Setting the temperature of a heater shaker to 37°C:

from pylabrobot.heating_shaking import HeaterShaker, InhecoThermoShakeBackend

backend = InhecoThermoShakeBackend()
hs = HeaterShaker(backend=backend, name="HeaterShaker", size_x=0, size_y=0, size_z=0)
await hs.setup()
await hs.set_temperature(37)

Fans (docs)

Running a fan at 100% intensity for one minute:

from pylabrobot.only_fans import Fan
from pylabrobot.only_fans import HamiltonHepaFanBackend

fan = Fan(backend=HamiltonHepaFanBackend(), name="my fan")
await fan.setup()
await fan.turn_on(intensity=100, duration=60)

Thermocyclers (docs)

Running a thermocycler with a simple protocol:

await tc.run_pcr_profile(
  denaturation_temp=98.0,
  denaturation_time=10.0,
  annealing_temp=55.0,
  annealing_time=30.0,
  extension_temp=72.0,
  extension_time=60.0,
  num_cycles=2,
  block_max_volume=25.0,
  lid_temperature=105.0,
  pre_denaturation_temp=95.0,
  pre_denaturation_time=180.0,
  final_extension_temp=72.0,
  final_extension_time=300.0,
  storage_temp=4.0,
  storage_time=600.0,
)

Resources

Documentation

docs.pylabrobot.org

• Installation
• Getting Started
• Contributing
• API Reference

Support

• discuss.pylabrobot.org for questions and discussions.
• GitHub Issues for bug reports and feature requests.

Citing

If you use PyLabRobot in your research, please cite the following:

@article{WIERENGA2023100111,
  title = {PyLabRobot: An open-source, hardware-agnostic interface for liquid-handling robots and accessories},
  journal = {Device},
  volume = {1},
  number = {4},
  pages = {100111},
  year = {2023},
  issn = {2666-9986},
  doi = {https://doi.org/10.1016/j.device.2023.100111},
  url = {https://www.sciencedirect.com/science/article/pii/S2666998623001709},
  author = {Rick P. Wierenga and Stefan M. Golas and Wilson Ho and Connor W. Coley and Kevin M. Esvelt},
  keywords = {laboratory automation, open source, standardization, liquid-handling robots},
}

Disclaimer: PyLabRobot is officially endorsed and supported by an increasing number of robot manufacturers (https://docs.pylabrobot.org/stable/#supported-by), but not all. If you use a firmware driver, such as the STAR driver provided here, you do so at your own risk. Whether it affects your warranty is between you and your vendor. Please contact us with any questions.

Developed for the Sculpting Evolution Group at the MIT Media Lab