Merge branch 'edge' into pd_refactor-toolbox-layouts

abr-testing/abr_testing/protocols/active_protocols/6_Omega_HDQ_DNA_Cells-Flex_96_channel.py

@@ -0,0 +1,351 @@
+"""Omega Bio-tek Mag-Bind Blood & Tissue DNA HDQ - Bacteria."""
+from typing import List, Dict
+from abr_testing.protocols import helpers
+from opentrons.protocol_api import (
+    ProtocolContext,
+    ParameterContext,
+    Well,
+    InstrumentContext,
+)
+from opentrons.protocol_api.module_contexts import (
+    HeaterShakerContext,
+    MagneticBlockContext,
+    TemperatureModuleContext,
+)
+from opentrons import types
+import numpy as np
+
+metadata = {
+    "author": "Zach Galluzzo <[email protected]>",
+    "protocolName": "Omega Bio-tek Mag-Bind Blood & Tissue DNA HDQ - Bacteria",
+}
+
+requirements = {
+    "robotType": "Flex",
+    "apiLevel": "2.21",
+}
+
+
+def add_parameters(parameters: ParameterContext) -> None:
+    """Parameters."""
+    helpers.create_dot_bottom_parameter(parameters)
+
+
+# Start protocol
+def run(ctx: ProtocolContext) -> None:
+    """Protocol."""
+    dot_bottom = ctx.params.dot_bottom  # type: ignore[attr-defined]
+
+    dry_run = False
+    tip_mixing = False
+
+    wash_vol = 600.0
+    AL_vol = 230.0
+    bind_vol = 320.0
+    sample_vol = 180.0
+    elution_vol = 100.0
+
+    # Same for all HDQ Extractions
+    deepwell_type = "nest_96_wellplate_2ml_deep"
+    if not dry_run:
+        settling_time = 2.0
+        num_washes = 3
+    if dry_run:
+        settling_time = 0.5
+        num_washes = 1
+    bead_vol = PK_vol = 20.0
+    inc_temp = 55.0
+    AL_total_vol = AL_vol + PK_vol
+    binding_buffer_vol = bead_vol + bind_vol
+    starting_vol = AL_total_vol + sample_vol
+
+    h_s: HeaterShakerContext = ctx.load_module(helpers.hs_str, "D1")  # type: ignore[assignment]
+    sample_plate, h_s_adapter = helpers.load_hs_adapter_and_labware(
+        deepwell_type, h_s, "Sample Plate"
+    )
+    h_s.close_labware_latch()
+    samples_m = sample_plate.wells()[0]
+
+    # NOTE: MAG BLOCK will be on slot 6
+
+    temp: TemperatureModuleContext = ctx.load_module(
+        helpers.temp_str, "A3"
+    )  # type: ignore[assignment]
+    elutionplate, tempblock = helpers.load_temp_adapter_and_labware(
+        "armadillo_96_wellplate_200ul_pcr_full_skirt", temp, "Elution Plate/Reservoir"
+    )
+
+    magblock: MagneticBlockContext = ctx.load_module(
+        "magneticBlockV1", "C1"
+    )  # type: ignore[assignment]
+    liquid_waste = ctx.load_labware("nest_1_reservoir_195ml", "B3", "Liquid Waste")
+    waste = liquid_waste.wells()[0].top()
+
+    lysis_reservoir = ctx.load_labware(deepwell_type, "D2", "Lysis reservoir")
+    lysis_res = lysis_reservoir.wells()[0]
+    bind_reservoir = ctx.load_labware(
+        deepwell_type, "C2", "Beads and binding reservoir"
+    )
+    bind_res = bind_reservoir.wells()[0]
+    wash1_reservoir = ctx.load_labware(deepwell_type, "C3", "Wash 1 reservoir")
+    wash1_res = wash1_reservoir.wells()[0]
+    wash2_reservoir = ctx.load_labware(deepwell_type, "B1", "Wash 2 reservoir")
+    wash2_res = wash2_reservoir.wells()[0]
+    elution_res = elutionplate.wells()[0]
+    # Load Pipette and tip racks
+    # Load tips
+    tiprack_1 = ctx.load_labware(
+        "opentrons_flex_96_tiprack_1000ul",
+        "A1",
+        adapter="opentrons_flex_96_tiprack_adapter",
+    )
+    tips = tiprack_1.wells()[0]
+
+    tiprack_2 = ctx.load_labware(
+        "opentrons_flex_96_tiprack_1000ul",
+        "A2",
+        adapter="opentrons_flex_96_tiprack_adapter",
+    )
+    tips1 = tiprack_2.wells()[0]
+    # load 96 channel pipette
+    pip: InstrumentContext = ctx.load_instrument(
+        "flex_96channel_1000", mount="left", tip_racks=[tiprack_1, tiprack_2]
+    )
+    # Load Liquids and probe
+    liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
+        "Lysis Buffer": [{"well": lysis_reservoir.wells(), "volume": AL_vol + 92.0}],
+        "PK Buffer": [{"well": lysis_reservoir.wells(), "volume": PK_vol + 8.0}],
+        "Binding Buffer": [{"well": bind_reservoir.wells(), "volume": bind_vol + 91.5}],
+        "Magnetic Beads": [{"well": bind_reservoir.wells(), "volume": bead_vol + 8.5}],
+        "Wash 1 and 2 Buffer": [
+            {"well": wash1_reservoir.wells(), "volume": (wash_vol * 2.0) + 100.0}
+        ],
+        "Wash 3 Buffer": [
+            {"well": wash2_reservoir.wells(), "volume": wash_vol + 100.0}
+        ],
+        "Elution Buffer": [{"well": elutionplate.wells(), "volume": elution_vol + 5}],
+        "Samples": [{"well": sample_plate.wells(), "volume": sample_vol}],
+    }
+
+    helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, pip)
+
+    pip.flow_rate.aspirate = 50
+    pip.flow_rate.dispense = 150
+    pip.flow_rate.blow_out = 300
+
+    def resuspend_pellet(vol: float, plate: Well, reps: int = 3) -> None:
+        """Re-suspend pellets."""
+        pip.flow_rate.aspirate = 200
+        pip.flow_rate.dispense = 300
+
+        loc1 = plate.bottom().move(types.Point(x=1, y=0, z=1))
+        loc2 = plate.bottom().move(types.Point(x=0.75, y=0.75, z=1))
+        loc3 = plate.bottom().move(types.Point(x=0, y=1, z=1))
+        loc4 = plate.bottom().move(types.Point(x=-0.75, y=0.75, z=1))
+        loc5 = plate.bottom().move(types.Point(x=-1, y=0, z=1))
+        loc6 = plate.bottom().move(types.Point(x=-0.75, y=0 - 0.75, z=1))
+        loc7 = plate.bottom().move(types.Point(x=0, y=-1, z=1))
+        loc8 = plate.bottom().move(types.Point(x=0.75, y=-0.75, z=1))
+
+        if vol > 1000:
+            vol = 1000
+
+        mixvol = vol * 0.9
+
+        for _ in range(reps):
+            pip.aspirate(mixvol, loc1)
+            pip.dispense(mixvol, loc1)
+            pip.aspirate(mixvol, loc2)
+            pip.dispense(mixvol, loc2)
+            pip.aspirate(mixvol, loc3)
+            pip.dispense(mixvol, loc3)
+            pip.aspirate(mixvol, loc4)
+            pip.dispense(mixvol, loc4)
+            pip.aspirate(mixvol, loc5)
+            pip.dispense(mixvol, loc5)
+            pip.aspirate(mixvol, loc6)
+            pip.dispense(mixvol, loc6)
+            pip.aspirate(mixvol, loc7)
+            pip.dispense(mixvol, loc7)
+            pip.aspirate(mixvol, loc8)
+            pip.dispense(mixvol, loc8)
+            if _ == reps - 1:
+                pip.flow_rate.aspirate = 50
+                pip.flow_rate.dispense = 30
+                pip.aspirate(mixvol, loc8)
+                pip.dispense(mixvol, loc8)
+
+        pip.flow_rate.aspirate = 150
+        pip.flow_rate.dispense = 200
+
+    def bead_mix(vol: float, plate: Well, reps: int = 5) -> None:
+        """Bead mix."""
+        pip.flow_rate.aspirate = 200
+        pip.flow_rate.dispense = 300
+
+        loc1 = plate.bottom().move(types.Point(x=0, y=0, z=1))
+        loc2 = plate.bottom().move(types.Point(x=0, y=0, z=8))
+        loc3 = plate.bottom().move(types.Point(x=0, y=0, z=16))
+        loc4 = plate.bottom().move(types.Point(x=0, y=0, z=24))
+
+        if vol > 1000:
+            vol = 1000
+
+        mixvol = vol * 0.9
+
+        for _ in range(reps):
+            pip.aspirate(mixvol, loc1)
+            pip.dispense(mixvol, loc1)
+            pip.aspirate(mixvol, loc1)
+            pip.dispense(mixvol, loc2)
+            pip.aspirate(mixvol, loc1)
+            pip.dispense(mixvol, loc3)
+            pip.aspirate(mixvol, loc1)
+            pip.dispense(mixvol, loc4)
+            if _ == reps - 1:
+                pip.flow_rate.aspirate = 50
+                pip.flow_rate.dispense = 30
+                pip.aspirate(mixvol, loc1)
+                pip.dispense(mixvol, loc1)
+
+        pip.flow_rate.aspirate = 150
+        pip.flow_rate.dispense = 200
+
+    # Start Protocol
+    temp.set_temperature(inc_temp)
+    # Transfer and mix lysis
+    pip.pick_up_tip(tips)
+    pip.aspirate(AL_total_vol, lysis_res)
+    pip.dispense(AL_total_vol, samples_m)
+    resuspend_pellet(400, samples_m, reps=4 if not dry_run else 1)
+    if not tip_mixing:
+        pip.return_tip()
+
+    # Mix, then heat
+    ctx.comment("Lysis Mixing")
+    helpers.set_hs_speed(ctx, h_s, 1800, 10, False)
+    if not dry_run:
+        h_s.set_and_wait_for_temperature(55)
+    ctx.delay(
+        minutes=10 if not dry_run else 0.25,
+        msg="Please allow another 10 minutes of 55C incubation to complete lysis.",
+    )
+    h_s.deactivate_shaker()
+
+    # Transfer and mix bind&beads
+    pip.pick_up_tip(tips)
+    bead_mix(binding_buffer_vol, bind_res, reps=4 if not dry_run else 1)
+    pip.aspirate(binding_buffer_vol, bind_res)
+    pip.dispense(binding_buffer_vol, samples_m)
+    bead_mix(binding_buffer_vol + starting_vol, samples_m, reps=4 if not dry_run else 1)
+    if not tip_mixing:
+        pip.return_tip()
+        pip.home()
+
+    # Shake for binding incubation
+    ctx.comment("Binding incubation")
+    helpers.set_hs_speed(ctx, h_s, 1800, 10, True)
+
+    # Transfer plate to magnet
+    helpers.move_labware_from_hs_to_destination(ctx, sample_plate, h_s, magblock)
+
+    ctx.delay(
+        minutes=settling_time,
+        msg="Please wait " + str(settling_time) + " minute(s) for beads to pellet.",
+    )
+
+    # Remove Supernatant and move off magnet
+    pip.pick_up_tip(tips)
+    pip.aspirate(1000, samples_m.bottom(dot_bottom))
+    pip.dispense(1000, waste)
+    if starting_vol + binding_buffer_vol > 1000:
+        pip.aspirate(1000, samples_m.bottom(dot_bottom))
+        pip.dispense(1000, waste)
+    pip.return_tip()
+
+    # Transfer plate from magnet to H/S
+    helpers.move_labware_to_hs(ctx, sample_plate, h_s, h_s_adapter)
+
+    # Washes
+    for i in range(num_washes if not dry_run else 1):
+        if i == 0 or i == 1:
+            wash_res = wash1_res
+        else:
+            wash_res = wash2_res
+
+        pip.pick_up_tip(tips)
+        pip.aspirate(wash_vol, wash_res)
+        pip.dispense(wash_vol, samples_m)
+        if not tip_mixing:
+            pip.return_tip()
+        helpers.set_hs_speed(ctx, h_s, 1800, 5, True)
+
+        # Transfer plate to magnet
+        helpers.move_labware_from_hs_to_destination(ctx, sample_plate, h_s, magblock)
+
+        ctx.delay(
+            minutes=settling_time,
+            msg="Please wait " + str(settling_time) + " minute(s) for beads to pellet.",
+        )
+
+        # Remove Supernatant and move off magnet
+        pip.pick_up_tip(tips)
+        pip.aspirate(1000, samples_m.bottom(dot_bottom))
+        pip.dispense(1000, bind_res.top())
+        if wash_vol > 1000:
+            pip.aspirate(1000, samples_m.bottom(dot_bottom))
+            pip.dispense(1000, bind_res.top())
+        pip.return_tip()
+
+        # Transfer plate from magnet to H/S
+        helpers.move_labware_to_hs(ctx, sample_plate, h_s, h_s_adapter)
+
+    # Dry beads
+    if dry_run:
+        drybeads = 0.5
+    else:
+        drybeads = 10
+    # Number of minutes you want to dry for
+    for beaddry in np.arange(drybeads, 0, -0.5):
+        ctx.delay(
+            minutes=0.5,
+            msg="There are " + str(beaddry) + " minutes left in the drying step.",
+        )
+
+    # Elution
+    pip.pick_up_tip(tips1)
+    pip.aspirate(elution_vol, elution_res)
+    pip.dispense(elution_vol, samples_m)
+    resuspend_pellet(elution_vol, samples_m, reps=3 if not dry_run else 1)
+    if not tip_mixing:
+        pip.return_tip()
+        pip.home()
+
+    helpers.set_hs_speed(ctx, h_s, 2000, 5, True)
+
+    # Transfer plate to magnet
+    helpers.move_labware_from_hs_to_destination(ctx, sample_plate, h_s, magblock)
+
+    ctx.delay(
+        minutes=settling_time,
+        msg="Please wait " + str(settling_time) + " minute(s) for beads to pellet.",
+    )
+
+    pip.pick_up_tip(tips1)
+    pip.aspirate(elution_vol, samples_m)
+    pip.dispense(elution_vol, elutionplate.wells()[0])
+    pip.return_tip()
+
+    pip.home()
+    pip.reset_tipracks()
+
+    # Empty Plates
+    pip.pick_up_tip()
+    pip.aspirate(1000, samples_m)
+    pip.dispense(1000, liquid_waste["A1"].top())
+    pip.aspirate(1000, wash1_res)
+    pip.dispense(1000, liquid_waste["A1"].top())
+    pip.aspirate(1000, wash2_res)
+    pip.dispense(1000, liquid_waste["A1"].top())
+    pip.return_tip()
+    helpers.find_liquid_height_of_all_wells(ctx, pip, [liquid_waste["A1"]])