LabGPT

Your task is to set up an assay that will allow the IC50 of a malaria drug to be calculated.

You have these reagents:

• drug: the drug in a reservoir

• media: malaria culture media in a reservoir for diluting the drug

• parasites: packed RBCs infected with malaria parasites

You can ask the user to set these up as you want (as long as there is one item per slot). You can request whatever extra empty labware you want.

Task: Set up an assay that will allow the IC50 of a malaria drug to be calculated.

Thought: First, I need to ask the user to set up the labware and reagents in the appropriate positions on the OT2 robot deck.

Thought: I should request labware for the drug, media, parasites, a tip rack, an empty 96-well plate for the serial dilutions and assay, and an extra reservoir for waste.

Request: Please set up the following labware on the OT2 robot deck:

Place the drug reservoir in slot 1.

Place the media reservoir in slot 2.

Place the parasite reservoir in slot 3.

Place a P300 tip rack in slot 5.

Place an empty 96-well plate in slot 6 for the serial dilutions and assay.

Place an empty reservoir in slot 7 for waste disposal.

That’s done

Thought: Great, the labware is set up. Now I can start preparing the serial dilutions of the drug in the 96-well plate.

Thought: I’ll begin by adding 100 µL of media to columns 1-11 of the 96-well plate. This will create a base for the serial dilutions.

ExecuteRobotScript:

from opentrons import protocol_api
metadata = {'apiLevel': '2.11'}
def run(protocol: protocol_api.ProtocolContext):
    # Labware
    tip_rack = protocol.load_labware('opentrons_96_tiprack_300ul', 5)
    media_reservoir = protocol.load_labware('nest_12_reservoir_15ml', 2)
    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 6)
    # Pipettes
    p300_multi = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[tip_rack])
    # Add 100 µL of media to columns 1-11 of the 96-well plate
    p300_multi.pick_up_tip()
    for column in plate.columns()[0:11]:
        p300_multi.aspirate(100, media_reservoir['A1'])
        p300_multi.dispense(100, column[0])
    p300_multi.drop_tip()

Thought: Once the media is added to the plate, I can proceed with the serial dilutions.

That’s done

Thought: Now that the media is in the 96-well plate, I can start preparing the serial dilutions by adding the drug to column 1 and then performing the dilutions across columns 2-11.

Thought: First, I’ll add 100 µL of the drug to column 1, which will result in a 1:1 dilution.

ExecuteRobotScript:

from opentrons import protocol_api

metadata = {'apiLevel': '2.11'}

def run(protocol: protocol_api.ProtocolContext):
    # Labware
    tip_rack = protocol.load_labware('opentrons_96_tiprack_300ul', 5)
    drug_reservoir = protocol.load_labware('nest_12_reservoir_15ml', 1)
    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 6)

    # Pipettes
    p300_multi = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[tip_rack])

    # Add 100 µL of the drug to column 1 of the 96-well plate
    p300_multi.pick_up_tip()
    p300_multi.aspirate(100, drug_reservoir['A1'])
    p300_multi.dispense(100, plate['A1'])
    p300_multi.drop_tip()

Thought: After adding the drug to column 1, I can perform the serial dilutions across columns 2-11.

That’s done too :)

Thought: The drug has been added to column 1. Now I can perform the serial dilutions across columns 2-11 by transferring 100 µL from one column to the next and mixing.

ExecuteRobotScript:

from opentrons import protocol_api

metadata = {'apiLevel': '2.11'}

def run(protocol: protocol_api.ProtocolContext):
    # Labware
    tip_rack = protocol.load_labware('opentrons_96_tiprack_300ul', 5)
    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 6)

    # Pipettes
    p300_multi = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[tip_rack])

    # Perform serial dilutions across columns 2-11
    for source_col, dest_col in zip(plate.columns()[0:10], plate.columns()[1:11]):
        p300_multi.pick_up_tip()
        p300_multi.aspirate(100, source_col[0])
        p300_multi.dispense(100, dest_col[0])
        p300_multi.mix(5, 100, dest_col[0])
        p300_multi.blow_out(dest_col[0].top())
        p300_multi.drop_tip()

Thought: Once the serial dilutions are complete, I can add the parasites to each well and set up the assay.

That’s done

Thought: The serial dilutions are ready. Now, I can add 100 µL of the parasite suspension to each well in columns 1-11 of the 96-well plate to set up the assay.

ExecuteRobotScript:

from opentrons import protocol_api

metadata = {'apiLevel': '2.11'}

def run(protocol: protocol_api.ProtocolContext):
    # Labware
    tip_rack = protocol.load_labware('opentrons_96_tiprack_300ul', 5)
    parasite_reservoir = protocol.load_labware('nest_12_reservoir_15ml', 3)
    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 6)

    # Pipettes
    p300_multi = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[tip_rack])

    # Add 100 µL of parasite suspension to each well in columns 1-11 of the 96-well plate
    p300_multi.pick_up_tip()
    for column in plate.columns()[0:11]:
        p300_multi.aspirate(100, parasite_reservoir['A1'])
        p300_multi.dispense(100, column[0])
        p300_multi.mix(5, 100, column[0])
    p300_multi.drop_tip()

Thought: With the parasites added to the wells, the assay is set up and ready for incubation and further analysis.

Fantastic – thanks! I’ll stick them in the incubator