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:
from pylabrobot.centrifuge import Centrifuge, VSpin cf = Centrifuge(backend=VSpin(bucket_1_position=0), name="centrifuge", size_x=1, size_y=1, size_z=1) await cf.setup() await cf.start_spin_cycle(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
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