PyLabRobot 0.2.2

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.scales import Scale
from pylabrobot.scales.mettler_toledo import MettlerToledoWXS205SDU

backend = MettlerToledoWXS205SDU(port="/dev/cu.usbserial-110")
scale = Scale(backend=backend, size_x=0, size_y=0, size_z=0)
await scale.setup()

weight = await scale.get_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 not officially endorsed or supported by any robot manufacturer. If you use a firmware driver such as the STAR driver provided here, you do so at your own risk. Usage of a firmware driver such as STAR may invalidate your warranty. Please contact us with any questions.

Developed for the Sculpting Evolution Group at the MIT Media Lab