diff --git a/protoBuilds/010d6c/010d6c.ot2.apiv2.py.json b/protoBuilds/010d6c/010d6c.ot2.apiv2.py.json index 530ecf523..a1bb3e851 100644 --- a/protoBuilds/010d6c/010d6c.ot2.apiv2.py.json +++ b/protoBuilds/010d6c/010d6c.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "def get_values(*names):\n import json\n _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,\"m300_mount\":\"left\",\"p300_mount\":\"right\"}\"\"\")\n return [_all_values[n] for n in names]\n\n\n# flake8: noqa\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [csv_samp, plate_standard, diluent_buff_col,\n duplicate_plating, m300_mount, p300_mount] = get_values( # noqa: F821\n \"csv_samp\", \"plate_standard\", \"diluent_buff_col\",\n \"duplicate_plating\", \"m300_mount\", \"p300_mount\")\n\n # p300_mount = 'left'\n # m300_mount = 'right'\n # plate_standard = True\n # diluent_buff_col = 4\n # duplicate_plating = False\n # csv_samp = \"\"\"\n #\n # source slot, source well, dest well\n # 7, A1, A1\n # 8, A1, A2\n # 7, A3, A3\n #\n # \"\"\"\n\n def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):\n # Split transfer up to allow for more control over touch tip height\n ## p300.transfer(vol, matrix_buff, well, new_tip='never')\n\n # Loop is used if volume is more than pipette max\n current_vol = Vol\n while current_vol > Pipette.max_volume:\n # Aspirate max volume\n Pipette.aspirate(Pipette.max_volume, Source.bottom(z = 4))\n # Touch tip\n Pipette.move_to(Source.top(z = -3))\n Pipette.touch_tip()\n\n # Dispense max volume\n if not Dispense_Top:\n Pipette.dispense(Pipette.max_volume, Destination.bottom(z = 3)) # With z offset\n else:\n Pipette.dispense(Pipette.max_volume, Destination.top())\n\n # Touch tip\n Pipette.move_to(Destination.top(z = -3))\n Pipette.touch_tip()\n\n # Update current volume\n current_vol -= Pipette.max_volume\n\n # If volume to transfer is 0, do nothing\n if current_vol == 0:\n return()\n\n # If volume more than 0 but less than or equal to max\n\n # Aspirate volume\n Pipette.aspirate(current_vol, Source.bottom(z = 4))\n # Touch tip\n Pipette.move_to(Source.top(z = -3))\n Pipette.touch_tip()\n\n # Dispense volume\n if not Dispense_Top:\n Pipette.dispense(current_vol, Destination.bottom(z = 3)) # With z offset\n else:\n Pipette.dispense(current_vol, Destination.top())\n # Touch tip\n Pipette.move_to(Destination.top(z = -3))\n Pipette.touch_tip()\n\n\n # labware\n reservoir = ctx.load_labware('corning_12_reservoir', 2)\n try:\n heater_shaker = ctx.load_module('heaterShakerModuleV1', 6)\n heater_shaker.close_labware_latch()\n hs_plate = heater_shaker.load_labware('nunc_96_wellplate_400ul')\n except ValueError:\n hs_plate = ctx.load_labware('nunc_96_wellplate_400ul', 6)\n\n deep_plate = ctx.load_labware('pyramid_96_wellplate_2000ul', 4)\n tuberack_15 = ctx.load_labware('opentrons_15_tuberack_5000ul', 7)\n tuberack_24 = ctx.load_labware('opentrons_24_tuberack_nest_2ml_snapcap', 8)\n tuberack_24 = tuberack_24\n\n tips = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [1]]\n\n # pipettes\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount, tip_racks=tips)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # mapping\n matrix_buff = reservoir.wells_by_name()['A1']\n\n triton = reservoir.wells_by_name()['A3']\n\n te = reservoir.wells_by_name()['A5']\n\n dye = reservoir.wells_by_name()['A7']\n\n calibration_solution = tuberack_15.wells()[0]\n\n\n # protocol\n diluent_buff_col = deep_plate.columns()[diluent_buff_col-1]\n if plate_standard:\n ctx.comment('\\n------------ADDING BUFFER TO PLATE------------\\n\\n')\n buffer_vols = [0, 250, 500, 750, 900, 950, 980, 1000]\n\n p300.pick_up_tip()\n p300.mix(1, 300, matrix_buff)\n\n for vol, well in zip(buffer_vols, diluent_buff_col):\n\n Transfer_With_TT(\n Pipette = p300,\n Source = matrix_buff,\n Destination = well,\n Vol = vol,\n Dispense_Top = False\n )\n\n p300.drop_tip()\n\n ctx.comment('\\n------------ADDING CALIBRATION------------\\n\\n')\n calibration_vols = [1000, 750, 500, 250, 100, 50, 20, 0]\n\n p300.pick_up_tip() # Moved to outside of loop\n p300.mix(1, 300, calibration_solution.bottom(z=4)) # Moved to outside of loop\n\n for vol, well in zip(calibration_vols, diluent_buff_col):\n if vol == 0:\n continue\n\n Transfer_With_TT(\n Pipette = p300,\n Source = calibration_solution,\n Destination = well,\n Vol = vol,\n Dispense_Top = True\n )\n\n p300.drop_tip() # Moved to outside of loop\n\n if duplicate_plating:\n ctx.comment('\\n------------DUPLICATE PLATING------------\\n\\n')\n dispense_wells = [hs_plate.wells_by_name()[well]\n for well in ['A1', 'A2', 'A11', 'A12']]\n source_col = diluent_buff_col[0]\n m300.pick_up_tip()\n m300.mix(1, 220, source_col.bottom(z = 3)) # Added in pre-wet\n m300.aspirate(220, source_col.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(source_col.top(z = -3))\n m300.touch_tip()\n\n for well in dispense_wells:\n m300.dispense(50, well.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(well.top(z = -3))\n m300.touch_tip()\n\n m300.drop_tip()\n\n else:\n ctx.comment('\\n------------TRIPLICATE PLATING------------\\n\\n')\n dispense_wells = [hs_plate.wells_by_name()[well]\n for well in ['A1', 'A2', 'A3', 'A10', 'A11', 'A12']]\n source_col = diluent_buff_col[0]\n m300.pick_up_tip()\n m300.mix(1, 300, source_col.bottom(z = 3)) # Added in pre-wet\n m300.aspirate(300, source_col.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(source_col.top(z = -3))\n m300.touch_tip()\n\n for well in dispense_wells:\n m300.dispense(50, well.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(well.top(z = -3))\n m300.touch_tip()\n\n m300.drop_tip()\n\n ctx.comment('\\n------------ADDING SAMPLE------------\\n\\n')\n\n # Modified for faster sample addition with less tip wastage\n if duplicate_plating:\n reps = 2 * 2\n else:\n reps = 3 * 2\n\n for index, line in enumerate(csv_lines):\n csv_slot = int(line[0])\n\n csv_well = line[1]\n source_well = ctx.loaded_labwares[csv_slot].wells_by_name()[csv_well]\n dest_well = line[2]\n\n # Only pick up tip and aspirate if start of new replicate batch\n if index%reps == 0:\n p300.pick_up_tip()\n p300.mix(1, 50*reps, source_well.bottom(z = 3)) # Added in pre-wet\n p300.aspirate(50*reps, source_well.bottom(z = 3))\n p300.move_to(source_well.top(-3))\n p300.touch_tip()\n\n p300.dispense(50, hs_plate.wells_by_name()[dest_well].bottom(z = 3)) # Set z offset\n p300.move_to(hs_plate.wells_by_name()[dest_well].top(-3))\n p300.touch_tip()\n\n # Only drop up tip if end of new replicate batch\n if index%reps == reps - 1:\n p300.drop_tip()\n\n ctx.comment('\\n------------PLATING TRITON------------\\n\\n')\n\n # Slow down aspirate and dispense rate\n m300.flow_rate.dispense *= 2\n m300.flow_rate.aspirate *= 2\n\n dispense_wells = hs_plate.rows()[0][:6]\n m300.pick_up_tip()\n m300.mix(1, 300, triton.bottom(z = 3))\n m300.aspirate(300, triton.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(triton.top(z = -3))\n m300.touch_tip()\n\n\n for well in dispense_wells:\n m300.dispense(50, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n m300.drop_tip()\n\n ctx.comment('\\n------------PLATING TE------------\\n\\n')\n dispense_wells = hs_plate.rows()[0][6:]\n m300.pick_up_tip()\n m300.mix(1, 300, te.bottom(z = 3))\n m300.aspirate(300, te.bottom(z = 3))\n for well in dispense_wells:\n m300.dispense(50, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n m300.drop_tip()\n\n try:\n heater_shaker.set_and_wait_for_temperature(37)\n ctx.delay(minutes=10)\n heater_shaker.deactivate_heater()\n except:\n ctx.delay(minutes=10)\n\n ctx.comment('\\n------------PLATING DYE------------\\n\\n')\n\n m300.pick_up_tip()\n m300.mix(1, 300, dye.bottom(z = 3))\n\n # Changed how dye is dispensed so that each well only has one transfer action to preserve accuracy\n for i in range(0, 12, 3):\n wells = [well for well in hs_plate.rows()[0][i : i+3]]\n m300.aspirate(300, dye.bottom(z = 3))\n m300.touch_tip()\n\n for well in wells:\n m300.dispense(100, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n# for _ in range(2):\n# m300.distribute(50, dye, [well.top() for well in hs_plate.rows()[0]],\n# new_tip='never')\n\n m300.drop_tip()\n\n ctx.pause('''\n Plate is ready! Please remove, seal, and transport to the plate reader for\n analysis. Please remember to tidy the robot deck and dispose of any waste.\n ''')\n", + "content": "# flake8: noqa\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [csv_samp, plate_standard, diluent_buff_col,\n duplicate_plating, m300_mount, p300_mount] = get_values( # noqa: F821\n \"csv_samp\", \"plate_standard\", \"diluent_buff_col\",\n \"duplicate_plating\", \"m300_mount\", \"p300_mount\")\n\n # p300_mount = 'left'\n # m300_mount = 'right'\n # plate_standard = True\n # diluent_buff_col = 4\n # duplicate_plating = False\n # csv_samp = \"\"\"\n #\n # source slot, source well, dest well\n # 7, A1, A1\n # 8, A1, A2\n # 7, A3, A3\n #\n # \"\"\"\n\n def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):\n # Split transfer up to allow for more control over touch tip height\n ## p300.transfer(vol, matrix_buff, well, new_tip='never')\n\n # Loop is used if volume is more than pipette max\n current_vol = Vol\n while current_vol > Pipette.max_volume:\n # Aspirate max volume\n Pipette.aspirate(Pipette.max_volume, Source.bottom(z = 4))\n # Touch tip\n Pipette.move_to(Source.top(z = -3))\n Pipette.touch_tip()\n\n # Dispense max volume\n if not Dispense_Top:\n Pipette.dispense(Pipette.max_volume, Destination.bottom(z = 3)) # With z offset\n else:\n Pipette.dispense(Pipette.max_volume, Destination.top())\n\n # Touch tip\n Pipette.move_to(Destination.top(z = -3))\n Pipette.touch_tip()\n\n # Update current volume\n current_vol -= Pipette.max_volume\n\n # If volume to transfer is 0, do nothing\n if current_vol == 0:\n return()\n\n # If volume more than 0 but less than or equal to max\n\n # Aspirate volume\n Pipette.aspirate(current_vol, Source.bottom(z = 4))\n # Touch tip\n Pipette.move_to(Source.top(z = -3))\n Pipette.touch_tip()\n\n # Dispense volume\n if not Dispense_Top:\n Pipette.dispense(current_vol, Destination.bottom(z = 3)) # With z offset\n else:\n Pipette.dispense(current_vol, Destination.top())\n # Touch tip\n Pipette.move_to(Destination.top(z = -3))\n Pipette.touch_tip()\n\n\n # labware\n reservoir = ctx.load_labware('corning_12_reservoir', 2)\n try:\n heater_shaker = ctx.load_module('heaterShakerModuleV1', 6)\n heater_shaker.close_labware_latch()\n hs_plate = heater_shaker.load_labware('nunc_96_wellplate_400ul')\n except ValueError:\n hs_plate = ctx.load_labware('nunc_96_wellplate_400ul', 6)\n\n deep_plate = ctx.load_labware('pyramid_96_wellplate_2000ul', 4)\n tuberack_15 = ctx.load_labware('opentrons_15_tuberack_5000ul', 7)\n tuberack_24 = ctx.load_labware('opentrons_24_tuberack_nest_2ml_snapcap', 8)\n tuberack_24 = tuberack_24\n\n tips = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [1]]\n\n # pipettes\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount, tip_racks=tips)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # mapping\n matrix_buff = reservoir.wells_by_name()['A1']\n\n triton = reservoir.wells_by_name()['A3']\n\n te = reservoir.wells_by_name()['A5']\n\n dye = reservoir.wells_by_name()['A7']\n\n calibration_solution = tuberack_15.wells()[0]\n\n\n # protocol\n diluent_buff_col = deep_plate.columns()[diluent_buff_col-1]\n if plate_standard:\n ctx.comment('\\n------------ADDING BUFFER TO PLATE------------\\n\\n')\n buffer_vols = [0, 250, 500, 750, 900, 950, 980, 1000]\n\n p300.pick_up_tip()\n p300.mix(1, 300, matrix_buff)\n\n for vol, well in zip(buffer_vols, diluent_buff_col):\n\n Transfer_With_TT(\n Pipette = p300,\n Source = matrix_buff,\n Destination = well,\n Vol = vol,\n Dispense_Top = False\n )\n\n p300.drop_tip()\n\n ctx.comment('\\n------------ADDING CALIBRATION------------\\n\\n')\n calibration_vols = [1000, 750, 500, 250, 100, 50, 20, 0]\n\n p300.pick_up_tip() # Moved to outside of loop\n p300.mix(1, 300, calibration_solution.bottom(z=4)) # Moved to outside of loop\n\n for vol, well in zip(calibration_vols, diluent_buff_col):\n if vol == 0:\n continue\n\n Transfer_With_TT(\n Pipette = p300,\n Source = calibration_solution,\n Destination = well,\n Vol = vol,\n Dispense_Top = True\n )\n\n p300.drop_tip() # Moved to outside of loop\n\n if duplicate_plating:\n ctx.comment('\\n------------DUPLICATE PLATING------------\\n\\n')\n dispense_wells = [hs_plate.wells_by_name()[well]\n for well in ['A1', 'A2', 'A11', 'A12']]\n source_col = diluent_buff_col[0]\n m300.pick_up_tip()\n m300.mix(1, 220, source_col.bottom(z = 3)) # Added in pre-wet\n m300.aspirate(220, source_col.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(source_col.top(z = -3))\n m300.touch_tip()\n\n for well in dispense_wells:\n m300.dispense(50, well.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(well.top(z = -3))\n m300.touch_tip()\n\n m300.drop_tip()\n\n else:\n ctx.comment('\\n------------TRIPLICATE PLATING------------\\n\\n')\n dispense_wells = [hs_plate.wells_by_name()[well]\n for well in ['A1', 'A2', 'A3', 'A10', 'A11', 'A12']]\n source_col = diluent_buff_col[0]\n m300.pick_up_tip()\n m300.mix(1, 300, source_col.bottom(z = 3)) # Added in pre-wet\n m300.aspirate(300, source_col.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(source_col.top(z = -3))\n m300.touch_tip()\n\n for well in dispense_wells:\n m300.dispense(50, well.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(well.top(z = -3))\n m300.touch_tip()\n\n m300.drop_tip()\n\n ctx.comment('\\n------------ADDING SAMPLE------------\\n\\n')\n\n # Modified for faster sample addition with less tip wastage\n if duplicate_plating:\n reps = 2 * 2\n else:\n reps = 3 * 2\n\n for index, line in enumerate(csv_lines):\n csv_slot = int(line[0])\n\n csv_well = line[1]\n source_well = ctx.loaded_labwares[csv_slot].wells_by_name()[csv_well]\n dest_well = line[2]\n\n # Only pick up tip and aspirate if start of new replicate batch\n if index%reps == 0:\n p300.pick_up_tip()\n p300.mix(1, 50*reps, source_well.bottom(z = 3)) # Added in pre-wet\n p300.aspirate(50*reps, source_well.bottom(z = 3))\n p300.move_to(source_well.top(-3))\n p300.touch_tip()\n\n p300.dispense(50, hs_plate.wells_by_name()[dest_well].bottom(z = 3)) # Set z offset\n p300.move_to(hs_plate.wells_by_name()[dest_well].top(-3))\n p300.touch_tip()\n\n # Only drop up tip if end of new replicate batch\n if index%reps == reps - 1:\n p300.drop_tip()\n\n ctx.comment('\\n------------PLATING TRITON------------\\n\\n')\n\n # Slow down aspirate and dispense rate\n m300.flow_rate.dispense *= 2\n m300.flow_rate.aspirate *= 2\n\n dispense_wells = hs_plate.rows()[0][:6]\n m300.pick_up_tip()\n m300.mix(1, 300, triton.bottom(z = 3))\n m300.aspirate(300, triton.bottom(z = 3))\n\n # Added in touch tip\n m300.move_to(triton.top(z = -3))\n m300.touch_tip()\n\n\n for well in dispense_wells:\n m300.dispense(50, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n m300.drop_tip()\n\n ctx.comment('\\n------------PLATING TE------------\\n\\n')\n dispense_wells = hs_plate.rows()[0][6:]\n m300.pick_up_tip()\n m300.mix(1, 300, te.bottom(z = 3))\n m300.aspirate(300, te.bottom(z = 3))\n for well in dispense_wells:\n m300.dispense(50, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n m300.drop_tip()\n\n try:\n heater_shaker.set_and_wait_for_temperature(37)\n ctx.delay(minutes=10)\n heater_shaker.deactivate_heater()\n except:\n ctx.delay(minutes=10)\n\n ctx.comment('\\n------------PLATING DYE------------\\n\\n')\n\n m300.pick_up_tip()\n m300.mix(1, 300, dye.bottom(z = 3))\n\n # Changed how dye is dispensed so that each well only has one transfer action to preserve accuracy\n for i in range(0, 12, 3):\n wells = [well for well in hs_plate.rows()[0][i : i+3]]\n m300.aspirate(300, dye.bottom(z = 3))\n m300.touch_tip()\n\n for well in wells:\n m300.dispense(100, well.top())\n ctx.delay(seconds = 1)\n m300.move_to(well.top(z = 0))\n m300.touch_tip()\n ctx.delay(seconds = 1)\n\n# for _ in range(2):\n# m300.distribute(50, dye, [well.top() for well in hs_plate.rows()[0]],\n# new_tip='never')\n\n m300.drop_tip()\n\n ctx.pause('''\n Plate is ready! Please remove, seal, and transport to the plate reader for\n analysis. Please remember to tidy the robot deck and dispose of any waste.\n ''')\n", "custom_labware_defs": [ { "brand": { @@ -2881,13 +2881,13 @@ "label": "P300 Multi-Channel Mount", "name": "m300_mount", "options": [ - { - "label": "Left", - "value": "left" - }, { "label": "Right", "value": "right" + }, + { + "label": "Left", + "value": "left" } ], "type": "dropDown" @@ -2896,13 +2896,13 @@ "label": "P300 Single-Channel Mount", "name": "p300_mount", "options": [ - { - "label": "Right", - "value": "right" - }, { "label": "Left", "value": "left" + }, + { + "label": "Right", + "value": "right" } ], "type": "dropDown" @@ -2911,11 +2911,11 @@ "instruments": [ { "mount": "left", - "name": "p300_multi_gen2" + "name": "p300_single_gen2" }, { "mount": "right", - "name": "p300_single_gen2" + "name": "p300_multi_gen2" } ], "labware": [ diff --git a/protocols/010d6c/010d6c.ot2.apiv2.py b/protocols/010d6c/010d6c.ot2.apiv2.py index 05fb15ac0..ecc4ff0af 100644 --- a/protocols/010d6c/010d6c.ot2.apiv2.py +++ b/protocols/010d6c/010d6c.ot2.apiv2.py @@ -1,9 +1,3 @@ -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,"m300_mount":"left","p300_mount":"right"}""") - return [_all_values[n] for n in names] - - # flake8: noqa metadata = { diff --git a/protocols/010d6c/fields.json b/protocols/010d6c/fields.json index 9dceee839..28d6b7357 100644 --- a/protocols/010d6c/fields.json +++ b/protocols/010d6c/fields.json @@ -49,8 +49,8 @@ "label": "P300 Multi-Channel Mount", "name": "m300_mount", "options": [ - {"label": "Left", "value": "left"}, - {"label": "Right", "value": "right"} + {"label": "Right", "value": "right"}, + {"label": "Left", "value": "left"} ] }, { @@ -58,9 +58,8 @@ "label": "P300 Single-Channel Mount", "name": "p300_mount", "options": [ - - {"label": "Right", "value": "right"}, - {"label": "Left", "value": "left"} + {"label": "Left", "value": "left"}, + {"label": "Right", "value": "right"} ] } ]