diff --git a/protocols/010d6c/010d6c.ot2.apiv2.py b/protocols/010d6c/010d6c.ot2.apiv2.py index da882fa7e..639cca5e1 100644 --- a/protocols/010d6c/010d6c.ot2.apiv2.py +++ b/protocols/010d6c/010d6c.ot2.apiv2.py @@ -1,5 +1,10 @@ # flake8: noqa +def get_values(*names): + import json + _all_values = json.loads("""{"csv_samp":"source slot,source well,dest well\\n8,A1,A4\\n8,A1,A5","plate_standard":true,"diluent_buff_col":1,"duplicate_plating":true,"user_input_pause":true,"m300_mount":"right","p300_mount":"left"}""") + return [_all_values[n] for n in names] + metadata = { 'protocolName': 'Ribogreen Assay', 'author': 'Rami Farawi ', @@ -10,24 +15,28 @@ def run(ctx): - [csv_samp, plate_standard, diluent_buff_col, - duplicate_plating, m300_mount, p300_mount] = get_values( # noqa: F821 - "csv_samp", "plate_standard", "diluent_buff_col", - "duplicate_plating", "m300_mount", "p300_mount") - - # p300_mount = 'left' - # m300_mount = 'right' - # plate_standard = True - # diluent_buff_col = 4 - # duplicate_plating = False - # csv_samp = """ - # - # source slot, source well, dest well - # 7, A1, A1 - # 8, A1, A2 - # 7, A3, A3 - # - # """ + # [csv_samp, plate_standard, diluent_buff_col, + # duplicate_plating, user_input_pause, m300_mount, p300_mount] = get_values( # noqa: F821 + # "csv_samp", "plate_standard", "diluent_buff_col", + # "duplicate_plating", "user_input_pause", "m300_mount", "p300_mount") + + p300_mount = 'left' + m300_mount = 'right' + plate_standard = True + diluent_buff_col = 4 + duplicate_plating = False + csv_samp = """ + + + + source slot, source well, dest well + 7, A1, A1 + 8, A1, A2 + 7, A3, A3 + + """ + + user_input_pause = True def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): # Split transfer up to allow for more control over touch tip height @@ -169,7 +178,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): m300.touch_tip(v_offset=1) for well in dispense_wells: - m300.dispense(50, well.bottom(z = 3)) + m300.dispense(50, well.bottom(z = 4)) # Added in touch tip m300.move_to(well.top(z = -3)) @@ -191,7 +200,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): m300.touch_tip(v_offset=1) for well in dispense_wells: - m300.dispense(50, well.bottom(z = 3)) + m300.dispense(50, well.bottom(z = 4)) # Added in touch tip m300.move_to(well.top(z = -3)) @@ -199,6 +208,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): m300.drop_tip() + ctx.comment('\n------------ADDING SAMPLE------------\n\n') # Modified for faster sample addition with less tip wastage @@ -216,11 +226,19 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): # Only pick up tip and aspirate if start of new replicate batch if index%reps == 0: - p300.pick_up_tip() - p300.mix(1, 50*reps, source_well.bottom(z = 4)) # Added in pre-wet - p300.aspirate(50*reps, source_well.bottom(z = 4)) - p300.move_to(source_well.top(-3)) - p300.touch_tip(v_offset=1) + if csv_slot == 8: # DIFFERENT Z HEIGHTS DEPENDING ON SLOT + print('going to 2mL on 8') + p300.pick_up_tip() + p300.mix(1, 50*reps, source_well.bottom(z = 4)) + p300.aspirate(50*reps, source_well.bottom(z = 4)) + p300.move_to(source_well.top(-3)) + p300.touch_tip(v_offset=1) + elif csv_slot == 7: + print('going to 5mL on 7') + p300.mix(1, 50*reps, source_well.bottom(z=1)) # CHANGED ASPIRATION HEIGHT BACK TO DEFAULT FOR 5ML TUBES + p300.aspirate(50*reps, source_well.bottom(z=1)) + p300.move_to(source_well.top(-3)) + p300.touch_tip(v_offset=1) p300.dispense(50, hs_plate.wells_by_name()[dest_well].bottom(z = 3)) # Set z offset p300.move_to(hs_plate.wells_by_name()[dest_well].top(-3)) @@ -284,7 +302,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top): ctx.delay(minutes=5) except: - ctx.delay(minutes=10) + ctx.pause('The protocol did not do the heater shaker steps - please cancel') ctx.comment('\n------------PLATING DYE------------\n\n') diff --git a/protocols/kapa-amp-cleanup/README.md b/protocols/kapa-amp-cleanup/README.md index 396e364e9..749e82046 100644 --- a/protocols/kapa-amp-cleanup/README.md +++ b/protocols/kapa-amp-cleanup/README.md @@ -30,7 +30,7 @@ This protocol performs a post-amplification 1X Purification using AMPure Beads. ### Deck Setup -![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/kapa-qubit/CLEANUP.png) +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/kapa-amp/Screen+Shot+2024-01-25+at+11.44.39+AM.png) diff --git a/protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py b/protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py index 2d2a7b693..029dc4a6b 100644 --- a/protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py +++ b/protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py @@ -16,8 +16,10 @@ def run(ctx): # m300_mount = 'left' # labware - mag_mod = ctx.load_module('magnetic module gen2', 1) - mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt') + # mag_mod = ctx.load_module('magnetic module gen2', 1) + mag_stand = ctx.load_labware('genericmagnet_96_wellplate_1500ul', 1) + mag_plate = ctx.load_labware('generic_96_wellplate_1500ul', 4) + # mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt') reservoir = ctx.load_labware('nest_12_reservoir_15ml', 3) elute_plate = ctx.load_labware('agilent_96_wellplate_270ul', 2) tips = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot) @@ -33,6 +35,7 @@ def run(ctx): trash = reservoir['A12'].top() sample_cols = mag_plate.rows()[0][:num_col] + sample_cols_stand = mag_stand.rows()[0][:num_col] def slow_tip_withdrawal(pipette, well_location, to_center=False): if pipette.mount == 'right': @@ -61,12 +64,12 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False): ctx.delay(minutes=5) - mag_mod.engage() + ctx.pause('Move plate to magnetic stand, then select resume') ctx.delay(minutes=3) ctx.comment('\n---------------REMOVING SUPER----------------\n\n') - for col in sample_cols: + for col in sample_cols_stand: m300.pick_up_tip() m300.aspirate(140, col, rate=0.1) m300.aspirate(20, col.bottom(z=0.6), rate=0.1) @@ -77,7 +80,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False): for _ in range(2): m300.pick_up_tip() - for col in sample_cols: + for col in sample_cols_stand: m300.aspirate(200, ethanol) slow_tip_withdrawal(m300, ethanol) m300.dispense(200, col.top()) @@ -86,7 +89,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False): ctx.delay(seconds=30) - for col in sample_cols: + for col in sample_cols_stand: if not m300.has_tip: m300.pick_up_tip() m300.aspirate(180, col, rate=0.1) @@ -98,7 +101,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False): ctx.delay(minutes=bead_dry_time) - mag_mod.disengage() + ctx.pause('Move magplate to slot 4, then select resume') ctx.comment('\n---------------Resuspend----------------\n\n') for col in sample_cols: @@ -108,10 +111,10 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False): m300.mix(15, 19, col.bottom(z=0.7)) m300.drop_tip() - mag_mod.engage() + ctx.pause('Move plate to magnetic stand, then select resume') ctx.delay(minutes=3) - ctx.comment('\n---------------REMOVING SUPER----------------\n\n') + ctx.comment('\n---------------Transfer Elute----------------\n\n') for s, d in zip(sample_cols, elute_plate.rows()[0]): m300.pick_up_tip() m300.aspirate(20, s.bottom(z=0.7), rate=0.1) diff --git a/protocols/kapa-amp-cleanup/labware/generic_96_wellplate_1500ul.json b/protocols/kapa-amp-cleanup/labware/generic_96_wellplate_1500ul.json new file mode 100644 index 000000000..03d4c6d02 --- /dev/null +++ b/protocols/kapa-amp-cleanup/labware/generic_96_wellplate_1500ul.json @@ -0,0 +1,1221 @@ +{ + "ordering": [ + [ + "A1", + "B1", + "C1", + "D1", + "E1", + "F1", + "G1", + "H1" + ], + [ + "A2", + "B2", + "C2", + "D2", + "E2", + "F2", + "G2", + "H2" + ], + [ + "A3", + "B3", + "C3", + "D3", + "E3", + "F3", + "G3", + "H3" + ], + [ + "A4", + "B4", + "C4", + "D4", + "E4", + "F4", + "G4", + "H4" + ], + [ + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5" + ], + [ + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6" + ], + [ + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7" + ], + [ + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8" + ], + [ + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9" + ], + [ + "A10", + "B10", + "C10", + "D10", + "E10", + "F10", + "G10", + "H10" + ], + [ + "A11", + "B11", + "C11", + "D11", + "E11", + "F11", + "G11", + "H11" + ], + [ + "A12", + "B12", + "C12", + "D12", + "E12", + "F12", + "G12", + "H12" + ] + ], + "brand": { + "brand": "generic", + "brandId": [] + }, + "metadata": { + "displayName": "Generic 96 Well Plate 1500 µL", + "displayCategory": "wellPlate", + "displayVolumeUnits": "µL", + "tags": [] + }, + "dimensions": { + "xDimension": 128.2, + "yDimension": 85.5, + "zDimension": 23.78 + }, + "wells": { + "A1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + "yDimension": 8.4, + "x": 14.18, + "y": 74.37, + "z": 2.88 + }, + "B1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + "yDimension": 8.4, + "x": 14.18, + "y": 65.17, + "z": 2.88 + }, + "C1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + "yDimension": 8.4, + "x": 14.18, + "y": 55.97, + "z": 2.88 + }, + "D1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + "yDimension": 8.4, + "x": 14.18, + "y": 46.77, + "z": 2.88 + }, + "E1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + "yDimension": 8.4, + "x": 14.18, + "y": 37.57, + "z": 2.88 + }, + "F1": { + "depth": 20.9, + "totalLiquidVolume": 1500, + "shape": "rectangular", + "xDimension": 8.4, + 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