clean up plate function, longer pvt1abr9

Author: rclarke0

abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py

@@ -114,7 +114,7 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     magblock: MagneticBlockContext = ctx.load_module(
         helpers.mag_str, "C1"
     )  # type: ignore[assignment]
-    waste_reservoir = ctx.load_labware("nest_1_reservoir_195ml", "B3", "Liquid Waste")
+    waste_reservoir = ctx.load_labware("nest_1_reservoir_290ml", "B3", "Liquid Waste")
     waste = waste_reservoir.wells()[0].top()
     res1 = ctx.load_labware(res_type, "D2", "reagent reservoir 1")
     res2 = ctx.load_labware(res_type, "C2", "reagent reservoir 2")

abr-testing/abr_testing/protocols/active_protocols/12_KAPA HyperPlus Library Prep.py

@@ -143,7 +143,7 @@ def run(ctx: ProtocolContext) -> None:
     )
     samples_2 = sample_plate_2.rows()[0][:num_cols]
     samples = sample_plate.rows()[0][:num_cols]
-    reservoir = ctx.load_labware("nest_96_wellplate_2ml_deep", "C2")
+    reservoir = ctx.load_labware("nest_96_wellplate_2ml_deep", "C2", "Liquid Waste")
     # Load tipracks
     tiprack_50_1 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "A3")
     tiprack_50_2 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "A2")
@@ -205,8 +205,8 @@ def run(ctx: ProtocolContext) -> None:
         "Adapters": [{"well": adapters, "volume": adapter_vol * 2.0}],
         "End Repair Mix": [
             {
-                "well": end_repair_cols,
-                "volume": (end_repair_vol * num_cols) + (0.1 * end_repair_vol),
+                "well": temp_plate.wells()[: 8 * num_cols],
+                "volume": 10.0,
             }
         ],
         "Fragmentation Mix": [
@@ -981,7 +981,6 @@ def lib_cleanup_2() -> None:
     lib_cleanup_2()
 
     # Probe liquid waste
-    reservoir.label = "Liquid Waste"  # type: ignore[attr-defined]
     waste1 = reservoir.columns()[6]
     waste1_res = waste1[0]
 

abr-testing/abr_testing/protocols/active_protocols/1_Simple Normalize Long Right.py

@@ -23,8 +23,8 @@
 def add_parameters(parameters: ParameterContext) -> None:
     """Parameters."""
     helpers.create_single_pipette_mount_parameter(parameters)
-    helpers.create_tip_size_parameter(parameters)
     helpers.create_csv_parameter(parameters)
+    helpers.create_dot_bottom_parameter(parameters)
 
 
 def get_next_tip_by_row(tip_rack: Labware, pipette: InstrumentContext) -> Well | None:
@@ -79,15 +79,15 @@ def get_next_tip_by_row(tip_rack: Labware, pipette: InstrumentContext) -> Well |
 
 def run(protocol: ProtocolContext) -> None:
     """Protocol."""
-    tip_type = protocol.params.tip_size  # type: ignore[attr-defined]
+    dot_bottom = protocol.params.dot_bottom  # type: ignore[attr-defined]
     mount_pos = protocol.params.pipette_mount  # type: ignore[attr-defined]
     all_data = protocol.params.parameters_csv.parse_as_csv()  # type: ignore[attr-defined]
     data = all_data[1:]
     # DECK SETUP AND LABWARE
     protocol.comment("THIS IS A NO MODULE RUN")
-    tiprack_x_1 = protocol.load_labware(tip_type, "D1")
-    tiprack_x_2 = protocol.load_labware(tip_type, "D2")
-    tiprack_x_3 = protocol.load_labware(tip_type, "A1")
+    tiprack_x_1 = protocol.load_labware("opentrons_flex_96_tiprack_200ul", "D1")
+    tiprack_x_2 = protocol.load_labware("opentrons_flex_96_tiprack_200ul", "D2")
+    tiprack_x_3 = protocol.load_labware("opentrons_flex_96_tiprack_200ul", "A1")
     sample_plate_1 = protocol.load_labware(
         "armadillo_96_wellplate_200ul_pcr_full_skirt", "D3"
     )
@@ -178,7 +178,7 @@ def run(protocol: ProtocolContext) -> None:
             if DilutionVol != 0 and DilutionVol < 100:
                 well = get_next_tip_by_row(current_rack, p1000)
                 p1000.pick_up_tip(well)
-                p1000.aspirate(DilutionVol, Diluent_1.bottom(z=2))
+                p1000.aspirate(DilutionVol, Diluent_1.bottom(z=dot_bottom))
                 p1000.dispense(
                     DilutionVol, sample_plate_1.wells_by_name()[CurrentWell].top(z=0.2)
                 )
@@ -223,7 +223,7 @@ def run(protocol: ProtocolContext) -> None:
             DilutionVol = float(data[current][2])
             if DilutionVol != 0 and DilutionVol < 100:
                 p1000_single.pick_up_tip()
-                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=2))
+                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=dot_bottom))
                 p1000_single.dispense(
                     DilutionVol, sample_plate_2.wells_by_name()[CurrentWell].top(z=0.2)
                 )
@@ -269,7 +269,7 @@ def run(protocol: ProtocolContext) -> None:
             DilutionVol = float(data[current][2])
             if DilutionVol != 0 and DilutionVol < 100:
                 p1000_single.pick_up_tip()
-                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=2))
+                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=dot_bottom))
                 p1000_single.dispense(
                     DilutionVol, sample_plate_3.wells_by_name()[CurrentWell].top(z=0.2)
                 )
@@ -315,7 +315,7 @@ def run(protocol: ProtocolContext) -> None:
             DilutionVol = float(data[current][2])
             if DilutionVol != 0 and DilutionVol < 100:
                 p1000_single.pick_up_tip()
-                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=2))
+                p1000_single.aspirate(DilutionVol, Diluent_2.bottom(z=dot_bottom))
                 p1000_single.dispense(
                     DilutionVol, sample_plate_4.wells_by_name()[CurrentWell].top(z=0.2)
                 )
@@ -327,5 +327,14 @@ def run(protocol: ProtocolContext) -> None:
             current += 1
 
         current = 0
-        # Probe heights
-        helpers.find_liquid_height_of_all_wells(protocol, p1000_single, wells)
+    # Probe heights
+    p1000.configure_nozzle_layout(style=ALL, tip_racks=[tiprack_x_3])
+    helpers.clean_up_plates(
+        p1000,
+        [sample_plate_1, sample_plate_2, sample_plate_3, sample_plate_4],
+        waste_reservoir["A1"],
+        200,
+    )
+    helpers.find_liquid_height_of_all_wells(
+        protocol, p1000_single, [waste_reservoir["A1"]]
+    )

abr-testing/abr_testing/protocols/active_protocols/2_BMS_PCR_Protocol.py

@@ -5,7 +5,7 @@
     ThermocyclerContext,
     TemperatureModuleContext,
 )
-from opentrons.protocol_api import SINGLE, Well, ALL
+from opentrons.protocol_api import SINGLE, Well
 from abr_testing.protocols import helpers
 from typing import List, Dict
 
@@ -83,9 +83,9 @@ def run(ctx: ProtocolContext) -> None:
     mmx_pic: List[Well] = reagent_rack.rows()[0]
     dna_pic: List[Well] = source_plate_1.wells()
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Water": [{"well": water, "volume": 1500.0}],
-        "Mastermix": [{"well": mmx_pic, "volume": 1500.0}],
-        "DNA": [{"well": dna_pic, "volume": 50.0}],
+        "Water": [{"well": water, "volume": 500.0}],
+        "Mastermix": [{"well": mmx_pic, "volume": 500.0}],
+        "DNA": [{"well": dna_pic, "volume": 100.0}],
     }
     helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, p50)
     # adding water
@@ -205,33 +205,7 @@ def run(ctx: ProtocolContext) -> None:
         p50.drop_tip()
         p50.configure_nozzle_layout(style=SINGLE, start="A1", tip_racks=tiprack_50)
         mmx_pic.append(water)
-        helpers.find_liquid_height_of_all_wells(ctx, p50, mmx_pic)
-    # Empty Destination plate
-    p50.configure_nozzle_layout(ALL, tip_racks=[tiprack_50[1]])
-    first_row = [
-        "A1",
-        "A2",
-        "A3",
-        "A4",
-        "A5",
-        "A6",
-        "A7",
-        "A8",
-        "A9",
-        "A10",
-        "A11",
-        "A12",
-    ]
-    p50.pick_up_tip()
-    for row in first_row:
-        p50.aspirate(50, dest_plate_1[row])
-        p50.dispense(50, liquid_waste.top())
-        p50.aspirate(50, dest_plate_1[row])
-        p50.dispense(50, liquid_waste.top())
-        p50.aspirate(50, dest_plate_1[row])
-        p50.dispense(50, liquid_waste.top())
-        p50.aspirate(50, dest_plate_1[row])
-        p50.dispense(50, liquid_waste.top())
-    p50.return_tip()
-
+    # Empty plates into liquid waste
+    helpers.clean_up_plates(p50, [source_plate_1, dest_plate_1], liquid_waste, 50)
+    # Probe liquid waste
     helpers.find_liquid_height_of_all_wells(ctx, p50, [liquid_waste])

abr-testing/abr_testing/protocols/active_protocols/3_Tartrazine Protocol.py

@@ -1,5 +1,10 @@
 """Tartrazine Protocol."""
-from opentrons.protocol_api import ProtocolContext, ParameterContext, Well
+from opentrons.protocol_api import (
+    ProtocolContext,
+    ParameterContext,
+    Well,
+    InstrumentContext,
+)
 from abr_testing.protocols import helpers
 from opentrons.protocol_api.module_contexts import (
     AbsorbanceReaderContext,
@@ -41,7 +46,7 @@ def run(ctx: ProtocolContext) -> None:
     tube_rack = ctx.load_labware(
         "opentrons_10_tuberack_nest_4x50ml_6x15ml_conical", "C2", "Reagent Tube"
     )
-    tartrazine_tube = tube_rack["A3"]
+    tartrazine_tube = tube_rack["A1"]
     water_tube_1 = tube_rack["A4"]
     water_tube_2 = tube_rack["B3"]
     sample_plate_1 = ctx.load_labware(
@@ -61,18 +66,29 @@ def run(ctx: ProtocolContext) -> None:
     tiprack_50_1 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "D3")
     tiprack_50_2 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "C3")
     tiprack_50_3 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "B3")
+    tiprack_50_4 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "B2")
+
     tiprack_1000_1 = ctx.load_labware("opentrons_flex_96_tiprack_1000ul", "A2")
-    tip_racks = [tiprack_50_1, tiprack_50_2, tiprack_50_3]
+    tip_racks = [tiprack_50_1, tiprack_50_2, tiprack_50_3, tiprack_50_4]
 
     # Pipette
     p50 = ctx.load_instrument("flex_1channel_50", "left", tip_racks=tip_racks)
     p1000 = ctx.load_instrument(
         "flex_1channel_1000", "right", tip_racks=[tiprack_1000_1]
     )
 
+    def _mix_tartrazine(pipette: InstrumentContext, well_to_probe: Well) -> None:
+        """Mix Tartrazine."""
+        pipette.pick_up_tip()
+        top_of_tartrazine = helpers.find_liquid_height(pipette, well_to_probe)
+        for i in range(20):
+            p50.aspirate(1, well_to_probe.bottom(z=1))
+            p50.dispense(1, well_to_probe.bottom(z=top_of_tartrazine - 2))
+        pipette.return_tip()
+
     # Probe wells
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Tartrazine": [{"well": tartrazine_tube, "volume": 45.0}],
+        "Tartrazine": [{"well": tartrazine_tube, "volume": 5.0}],
         "Water": [{"well": [water_tube_1, water_tube_2], "volume": 45.0}],
     }
     helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, p50)
@@ -83,6 +99,8 @@ def run(ctx: ProtocolContext) -> None:
     vol = 0.0
     tip_count = 0
     for sample_plate in sample_plate_list[:number_of_plates]:
+        _mix_tartrazine(p50, tartrazine_tube)
+        tip_count += 1
         deck_locations = ["D1", "D2", "C1", "B1"]
         p1000.pick_up_tip()
         for well in sample_plate.wells():
@@ -92,19 +110,19 @@ def run(ctx: ProtocolContext) -> None:
                 tube_of_choice = water_tube_2
             p50.pick_up_tip()
             p1000.aspirate(190, tube_of_choice)
-            p1000.air_gap(5)
+            p1000.air_gap(10)
             p1000.dispense(5, well.top())
             p1000.dispense(190, well)
             vol += 190
             height = helpers.find_liquid_height(p50, tartrazine_tube)
-            p50.aspirate(10, tartrazine_tube.bottom(z=height))
+            p50.aspirate(10, tartrazine_tube.bottom(z=height), rate=0.15)
             p50.air_gap(5)
             p50.dispense(5, well.top())
-            p50.dispense(10, well.bottom(z=0.5))
+            p50.dispense(10, well.bottom(z=0.5), rate=0.15)
             p50.blow_out()
             p50.return_tip()
             tip_count += 1
-            if tip_count >= (96 * 3):
+            if tip_count >= (96 * 4):
                 p50.reset_tipracks()
         p1000.return_tip()
         helpers.move_labware_to_hs(ctx, sample_plate, hs, hs_adapter)
@@ -145,6 +163,7 @@ def run(ctx: ProtocolContext) -> None:
                 "SD": standard_deviation,
                 "Avg Percent Error": avg_percent_error,
             }
+        ctx.comment(f"------plate {sample_plate}. {cv_dict[sample_plate_name]}------")
         all_percent_error_dict[sample_plate_name] = percent_error_dict
         plate_reader.open_lid()
         ctx.move_labware(sample_plate, deck_locations[i], use_gripper=True)

abr-testing/abr_testing/protocols/active_protocols/5_96ch complex protocol with single tip Pick Up.py

@@ -79,9 +79,7 @@ def run(ctx: ProtocolContext) -> None:
     dest_pcr_plate = ctx.load_labware(PCR_PLATE_96_NAME, "C2")
     liquid_waste = ctx.load_labware("nest_1_reservoir_290ml", "B2", "Liquid Waste")
 
-    tip_rack_1 = ctx.load_labware(
-        TIPRACK_96_NAME, "A4"
-    )
+    tip_rack_1 = ctx.load_labware(TIPRACK_96_NAME, "A4")
 
     tip_rack_2 = ctx.load_labware(TIPRACK_96_NAME, "C3")
     tip_rack_3 = ctx.load_labware(TIPRACK_96_NAME, "C4")
@@ -293,28 +291,34 @@ def test_single_tip_pickup_usage() -> None:
             ctx.move_labware(tip_rack_2, waste_chute, use_gripper=USING_GRIPPER)
 
         def test_column_tip_rack_usage() -> None:
-            """Full Tip Pick Up."""
-            list_of_columns = list(range(1,13))
-            not_reversed = list(range(1,13))
-            list_of_columns.reverse()
+            """Column Tip Pick Up."""
+            list_of_columns = list(range(1, 13))
             i = 0
             column_racks = [tip_rack_1, tip_rack_3]
+            pipette_96_channel.configure_nozzle_layout(
+                style=COLUMN, start="A12", tip_racks=column_racks
+            )
+            ctx.comment("------------------------------")
+            ctx.comment(f"channels {pipette_96_channel.active_channels}")
             for rack in column_racks:
-                ctx.move_labware(rack, "C3", use_gripper = USING_GRIPPER)
-                for (column,well) in zip(list_of_columns, not_reversed):
-                    tiprack_well = "A" + str(column)
+                ctx.move_labware(rack, "C3", use_gripper=USING_GRIPPER)
+                for well in list_of_columns:
+                    tiprack_well = "A" + str(well)
                     well_name = "A" + str(well)
-                    pipette_96_channel.configure_nozzle_layout(style=COLUMN, start="A12")
+
                     pipette_96_channel.liquid_presence_detection = True
                     pipette_96_channel.pick_up_tip(rack[tiprack_well])
                     pipette_96_channel.aspirate(45, source_reservoir[well_name])
                     pipette_96_channel.liquid_presence_detection = False
                     pipette_96_channel.air_gap(5)
-                    pipette_96_channel.dispense(25, dest_pcr_plate[tiprack_well].bottom(b))
+                    pipette_96_channel.dispense(
+                        25, dest_pcr_plate[tiprack_well].bottom(b)
+                    )
                     pipette_96_channel.blow_out(location=liquid_waste["A1"])
                     pipette_96_channel.drop_tip()
                 ctx.move_labware(rack, waste_chute, use_gripper=USING_GRIPPER)
-                i +=1
+                i += 1
+
         test_single_tip_pickup_usage()
         test_column_tip_rack_usage()
 

abr-testing/abr_testing/protocols/active_protocols/7_HDQ_DNA_Bacteria_Flex.py

@@ -170,7 +170,6 @@ def tiptrack(tipbox: List[Well]) -> None:
         drop_count = drop_count + 8
         if drop_count >= 150:
             drop_count = 0
-            ctx.pause("Empty Waste Bin.")
 
     def remove_supernatant(vol: float) -> None:
         """Remove supernatants."""
@@ -503,7 +502,5 @@ def elute(vol: float) -> None:
     # Probe wells
     end_wells_with_liquid = [
         waste_reservoir.wells()[0],
-        res1.wells()[0],
-        elutionplate.wells()[0],
     ]
     helpers.find_liquid_height_of_all_wells(ctx, m1000, end_wells_with_liquid)

abr-testing/abr_testing/protocols/active_protocols/8_Illumina and Plate Reader.py

@@ -116,7 +116,9 @@ def run(protocol: ProtocolContext) -> None:
     tiprack_50_2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "A3")
     # MODULES + LABWARE
     # Reservoir
-    reservoir = protocol.load_labware("nest_96_wellplate_2ml_deep", "D2")
+    reservoir = protocol.load_labware(
+        "nest_96_wellplate_2ml_deep", "D2", "Liquid Waste"
+    )
     # Heatershaker
     heatershaker: HeaterShakerContext = protocol.load_module(
         helpers.hs_str, "D1"
@@ -971,7 +973,6 @@ def tipcheck() -> None:
                 p200_tips += 1
                 tipcheck()
 
-        reservoir.label = "Liquid Waste"  # type: ignore[attr-defined]
         Liquid_trash_well_1 = reservoir["A9"]
         Liquid_trash_well_2 = reservoir["A10"]
         Liquid_trash_well_4 = reservoir["A12"]