updates for abr1, abr2, abr3, abr4, abr8, reverted abr12

Author: rclarke0

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

@@ -5,7 +5,7 @@
     ThermocyclerContext,
     TemperatureModuleContext,
 )
-from opentrons.protocol_api import SINGLE, Well
+from opentrons.protocol_api import SINGLE, Well, ALL
 from abr_testing.protocols import helpers
 from typing import List, Dict
 
@@ -206,6 +206,7 @@ def run(ctx: ProtocolContext) -> None:
         p50.configure_nozzle_layout(style=SINGLE, start="A1", tip_racks=tiprack_50)
         mmx_pic.append(water)
     # Empty plates into liquid waste
+    p50.configure_nozzle_layout(style=ALL, tip_racks=tiprack_50)
     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/2_BMS_PCR_Protocol.py

@@ -32,110 +32,160 @@ def add_parameters(parameters: ParameterContext) -> None:
         minimum=1,
         maximum=4,
     )
+    helpers.create_channel_parameter(parameters)
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
+    # Load parameters
     number_of_plates = ctx.params.number_of_plates  # type: ignore [attr-defined]
+    channels = ctx.params.channels  # type: ignore [attr-defined]
     # Plate Reader
     plate_reader: AbsorbanceReaderContext = ctx.load_module(
         helpers.abs_mod_str, "A3"
     )  # type: ignore[assignment]
     hs: HeaterShakerContext = ctx.load_module(helpers.hs_str, "A1")  # type: ignore[assignment]
     hs_adapter = hs.load_adapter("opentrons_universal_flat_adapter")
-    tube_rack = ctx.load_labware(
-        "opentrons_10_tuberack_nest_4x50ml_6x15ml_conical", "C2", "Reagent Tube"
-    )
-    tartrazine_tube = tube_rack["A1"]
-    water_tube_1 = tube_rack["A4"]
-    water_tube_2 = tube_rack["B3"]
-    sample_plate_1 = ctx.load_labware(
-        "corning_96_wellplate_360ul_flat", "D1", "Sample Plate 1"
-    )
-    sample_plate_2 = ctx.load_labware(
-        "corning_96_wellplate_360ul_flat", "D2", "Sample Plate 2"
-    )
-    sample_plate_3 = ctx.load_labware(
-        "corning_96_wellplate_360ul_flat", "C1", "Sample Plate 3"
-    )
-    sample_plate_4 = ctx.load_labware(
-        "corning_96_wellplate_360ul_flat", "B1", "Sample Plate 4"
-    )
-
-    sample_plate_list = [sample_plate_1, sample_plate_2, sample_plate_3, sample_plate_4]
-    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")
-
+    # Load Plates based off of number_of_plates parameter
+    available_deck_slots = ["D1", "D2", "C1", "B1"]
+    sample_plate_list = []
+    for plate_num, slot in zip(range(number_of_plates), available_deck_slots):
+        plate = ctx.load_labware(
+            "corning_96_wellplate_360ul_flat", slot, f"Sample Plate {plate_num + 1}"
+        )
+        sample_plate_list.append(plate)
+    available_tip_rack_slots = ["D3", "C3", "B3", "B2"]
+    # LOAD PIPETTES AND TIP RACKS
+    # 50 CHANNEL
+    tip_racks_50 = []
+    for plate_num, slot_2 in zip(range(number_of_plates), available_tip_rack_slots):
+        tiprack_50 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", slot_2)
+        tip_racks_50.append(tiprack_50)
+    p50 = ctx.load_instrument(f"flex_{channels}_50", "left", tip_racks=tip_racks_50)
+    # 1000 CHANNEL
     tiprack_1000_1 = ctx.load_labware("opentrons_flex_96_tiprack_1000ul", "A2")
-    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]
+        f"flex_{channels}_1000", "right", tip_racks=[tiprack_1000_1]
     )
+    # DETERMINE RESERVOIR BASED OFF # OF PIPETTE CHANNELS
+    # 1 CHANNEL = TUBE RACK
+    if p50.active_channels == 1:
+        reservoir = ctx.load_labware(
+            "opentrons_10_tuberack_nest_4x50ml_6x15ml_conical", "C2", "Reservoir"
+        )
+        water_max_vol = reservoir["A3"].max_volume - 500
+        reservoir_wells = reservoir.wells()[6:]  # Skip first 4 bc they are 15ml
+    else:
+        # 8 CHANNEL = 12 WELL RESERVOIR
+        reservoir = ctx.load_labware("nest_12_reservoir_15ml", "C2", "Reservoir")
+        water_max_vol = reservoir["A1"].max_volume - 500
+        reservoir_wells = reservoir.wells()[
+            1:
+        ]  # Skip A1 as it's reserved for tartrazine
+
+    # LABEL RESERVOIR WELLS AND DETERMINE NEEDED LIQUID
+    tartrazine_well = reservoir["A1"]
+    # NEEDED TARTRAZINE
+    needed_tartrazine: float = (
+        float(number_of_plates) * 96.0
+    ) * 10.0 + 1000.0  # loading extra as a safety factor
+    # NEEDED WATER
+    needed_water: float = (
+        float(number_of_plates) * 96.0 * 250
+    )  # loading extra as a safety factor
+    # CALCULATING NEEDED # OF WATER WELLS
+    needed_wells = round(needed_water / water_max_vol)
+    water_wells = []
+    for i in range(needed_wells + 1):
+        water_wells.append(reservoir_wells[i])
 
     def _mix_tartrazine(pipette: InstrumentContext, well_to_probe: Well) -> None:
         """Mix Tartrazine."""
+        # Mix step is needed to ensure tartrazine does not settle between plates.
         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))
+            p50.dispense(1, well_to_probe.bottom(z=top_of_tartrazine + 1))
         pipette.return_tip()
 
-    # Probe wells
+    # LOAD LIQUIDS AND PROBE WELLS
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Tartrazine": [{"well": tartrazine_tube, "volume": 5.0}],
-        "Water": [{"well": [water_tube_1, water_tube_2], "volume": 45.0}],
+        "Tartrazine": [{"well": tartrazine_well, "volume": needed_tartrazine}],
+        "Water": [{"well": water_wells, "volume": water_max_vol}],
     }
     helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, p50)
-
+    tip_count = 1 * p50.active_channels  # number of 50 ul tip uses.
+    p50.reset_tipracks()
     i = 0
     all_percent_error_dict = {}
     cv_dict = {}
-    vol = 0.0
-    tip_count = 0
+    vol = 0.0  # counter to track available water volume
+    water_tip_count = 0 * p1000.active_channels  # number of 1000 ul tip uses
+    well_num = 0  # index of well being used for water
     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():
-            if vol < 45000:
-                tube_of_choice = water_tube_1
+        return_location = sample_plate.parent
+        # Mix Tartrazine to ensure no settling as occurred
+        _mix_tartrazine(p50, tartrazine_well)
+        tip_count += 1 * p50.active_channels
+        # Determine list of wells to probe
+        if p50.active_channels == 1:
+            well_list = sample_plate.wells()
+        elif p50.active_channels == 8:
+            well_list = sample_plate.rows()[0]
+        for well in well_list:
+            p1000.pick_up_tip()
+            # Determine which water well to aspirate from.
+            if vol < water_max_vol - 6000:
+                well_of_choice = water_wells[well_num]
             else:
-                tube_of_choice = water_tube_2
+                well_num += 1
+                well_of_choice = water_wells[well_num]
+                vol = 0.0
             p50.pick_up_tip()
-            p1000.aspirate(190, tube_of_choice)
+            p1000.aspirate(190, well_of_choice)
             p1000.air_gap(10)
-            p1000.dispense(5, well.top())
+            p1000.dispense(10, well.top())
             p1000.dispense(190, well)
-            vol += 190
-            height = helpers.find_liquid_height(p50, tartrazine_tube)
-            p50.aspirate(10, tartrazine_tube.bottom(z=height), rate=0.15)
+            # Two blow outs ensures water is completely removed from pipette
+            p1000.blow_out(well.top())
+            ctx.delay(minutes=0.1)
+            p1000.blow_out(well.top())
+            vol += 190 * p1000.active_channels
+            # Probe to find liquid height of tartrazine to ensure correct amount is aspirated
+            height = helpers.find_liquid_height(p50, tartrazine_well)
+            p50.aspirate(10, tartrazine_well.bottom(z=height), rate=0.15)
             p50.air_gap(5)
             p50.dispense(5, well.top())
             p50.dispense(10, well.bottom(z=0.5), rate=0.15)
             p50.blow_out()
+            ctx.delay(minutes=0.1)
+            p50.blow_out()
             p50.return_tip()
-            tip_count += 1
-            if tip_count >= (96 * 4):
+            tip_count += p50.active_channels
+            if tip_count >= (96 * len(tip_racks_50)):
                 p50.reset_tipracks()
-        p1000.return_tip()
+                tip_count = 0
+            p1000.return_tip()
+            water_tip_count += p1000.active_channels
+            if water_tip_count >= 96:
+                p1000.reset_tipracks()
+                water_tip_count = 0
+        # Move labware to heater shaker to be mixed
         helpers.move_labware_to_hs(ctx, sample_plate, hs, hs_adapter)
         helpers.set_hs_speed(ctx, hs, 1500, 2.0, True)
         hs.open_labware_latch()
+        # Initialize plate reader
         plate_reader.close_lid()
         plate_reader.initialize("single", [450])
         plate_reader.open_lid()
+        # Move sample plate into plate reader
         ctx.move_labware(sample_plate, plate_reader, use_gripper=True)
         sample_plate_name = "sample plate_" + str(i + 1)
         csv_string = sample_plate_name + "_" + str(datetime.now())
         plate_reader.close_lid()
         result = plate_reader.read(csv_string)
+        # Calculate CV and % error of expected value.
         for wavelength in result:
             dict_of_wells = result[wavelength]
             readings_and_wells = dict_of_wells.items()
@@ -163,12 +213,13 @@ def _mix_tartrazine(pipette: InstrumentContext, well_to_probe: Well) -> None:
                 "SD": standard_deviation,
                 "Avg Percent Error": avg_percent_error,
             }
-        ctx.comment(f"------plate {sample_plate}. {cv_dict[sample_plate_name]}------")
+        # Move Plate back to original location
         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)
+        ctx.comment(f"------plate {sample_plate}. {cv_dict[sample_plate_name]}------")
+        ctx.move_labware(sample_plate, return_location, use_gripper=True)
         i += 1
     # Print percent error dictionary
     ctx.comment("Percent Error: " + str(all_percent_error_dict))
     # Print cv dictionary
-    ctx.comment("Plate Reader result: " + str(cv_dict))
+    ctx.comment("Plate Reader Result: " + str(cv_dict))