diff --git a/protoBuilds/0845ab/0845ab.ot2.apiv2.py.json b/protoBuilds/0845ab/0845ab.ot2.apiv2.py.json index 30df03895..c328eb992 100644 --- a/protoBuilds/0845ab/0845ab.ot2.apiv2.py.json +++ b/protoBuilds/0845ab/0845ab.ot2.apiv2.py.json @@ -1,13 +1,10 @@ { - "content": "import math\nfrom opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'Digestion and Bead Cleanup',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.14'\n}\n\n\ndef run(ctx):\n\n [num_samp, real_mode, p20_mount, m300_mount] = get_values( # noqa: F821\n \"num_samp\", \"real_mode\", \"p20_mount\", \"m300_mount\")\n\n # num_samp = 48\n num_col = math.ceil(num_samp/8)\n #\n # m300_mount = 'left'\n # p20_mount = 'right'\n #\n # real_mode = True\n\n # labware\n mag_mod = ctx.load_module(\"magnetic module gen2\", 1)\n try:\n mag_plate = mag_mod.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt') # noqa: E501\n\n except FileNotFoundError:\n mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt') # noqa: E501\n\n try:\n old_plate = ctx.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt', 2) # noqa: E501\n except FileNotFoundError:\n old_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n 2)\n\n tuberack = ctx.load_labware('opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', 3) # noqa: E501\n\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', 6)\n trash = ctx.load_labware('nest_1_reservoir_195ml', 8).wells()[0].top()\n tmt_plate = ctx.load_labware('tmtpro18_pcr_plate', 9)\n\n if not ctx.is_simulating:\n\n hs_mod = ctx.load_module('heaterShakerModuleV1', 10)\n hs_mod.close_labware_latch()\n else:\n dummy = ctx.load_labware('nest_12_reservoir_15ml', 10)\n dummy = dummy\n\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [4, 5]]\n tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in [7, 11]]\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tips300)\n\n def slow_tip_withdrawal(pipette, well_location, to_center=False):\n pipette.default_speed = 10\n if to_center is False:\n pipette.move_to(well_location.top())\n else:\n pipette.move_to(well_location.center())\n pipette.default_speed = 400\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(f\"Replace empty tip rack for {pip}\")\n pip.reset_tipracks()\n pip.pick_up_tip()\n\n # mapping\n sample_cols = old_plate.rows()[0][:num_col]\n dest_cols = mag_plate.rows()[0][:num_col]\n dest_wells = [well for well in mag_plate.wells()[:num_samp]]\n\n pool_well1 = tuberack['B1']\n pool_well2 = tuberack['B2']\n pool_well3 = tuberack['B3']\n\n num_pools = int(num_samp/16)\n\n all_pools = [pool_well1, pool_well2, pool_well3][:num_pools]\n\n acn = reservoir['A1']\n ethanol = reservoir['A2']\n\n beads = tuberack['A1']\n mm_teab = tuberack['A2']\n ha = tuberack['A3']\n formic_acid = tuberack['A4']\n\n digestion_solution = tmt_plate['A12']\n\n # protocol\n ctx.comment('\\n---------------ADDING BEADS TO PLATES----------------\\n\\n')\n\n pick_up(p20)\n p20.mix(20, 20, beads, rate=1.5)\n for well in dest_wells:\n p20.aspirate(4, beads)\n slow_tip_withdrawal(p20, beads)\n p20.dispense(4, well)\n slow_tip_withdrawal(p20, beads)\n p20.blow_out()\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n for s, d in zip(sample_cols, dest_cols):\n pick_up(m300)\n m300.aspirate(30, s)\n m300.dispense(30, d)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.comment('\\n---------------Transferring ACN----------------\\n\\n')\n for col in dest_cols:\n pick_up(m300)\n m300.aspirate(70, acn)\n m300.dispense(70, col)\n m300.mix(3, 85, col, rate=0.7)\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.delay(minutes=2 if real_mode else 0.5)\n\n mag_mod.engage(height_from_base=1)\n\n ctx.delay(minutes=5 if real_mode else 0.5)\n\n ctx.comment('\\n---------------Removing Super----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, col, rate=0.1)\n m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n m300.dispense(110, trash)\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n for _ in range(2):\n ctx.comment('\\n---------------Adding Ethanol----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, ethanol, rate=0.1)\n slow_tip_withdrawal(m300, ethanol)\n m300.dispense(100, col.top())\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.comment('\\n---------------Removing Ethanol----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, col, rate=0.1)\n m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n m300.dispense(110, trash)\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n mag_mod.disengage()\n\n ctx.comment('\\n--------------ADDING Digestion Solution--------------\\n\\n')\n for col in dest_cols:\n pick_up(m300)\n m300.aspirate(20, digestion_solution)\n m300.dispense(20, col)\n m300.mix(2, 15, col)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n if not ctx.is_simulating:\n hs_mod.open_labware_latch()\n ctx.pause('Move plate to heater shaker')\n if not ctx.is_simulating:\n hs_mod.close_labware_latch()\n hs_mod.set_and_wait_for_temperature(37)\n ctx.pause('Overnight Digestion')\n if not ctx.is_simulating:\n hs_mod.deactivate_heater()\n hs_mod.open_labware_latch()\n ctx.pause(\"Move plate to magnetic module\")\n\n mag_mod.engage(height_from_base=1)\n ctx.delay(minutes=2 if real_mode else 0.5)\n\n ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n new_cols = mag_plate.rows()[0][num_col:num_col+num_col]\n new_wells = [well for col in mag_plate.columns()[num_col:num_col+num_col]\n for well in col]\n\n for s, d in zip(dest_cols, new_cols):\n pick_up(m300)\n m300.aspirate(20, s, rate=0.05)\n m300.dispense(20, d)\n m300.move_to(d.top())\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.touch_tip()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n tmt_wells = [well for col in tmt_plate.columns()[:num_col]\n for well in col]\n\n for well in tmt_wells:\n pick_up(p20)\n p20.aspirate(5, mm_teab)\n p20.dispense(5, well)\n p20.mix(3, 20, well)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.comment('\\n-----From TMT Wells to Sample Wells----------\\n\\n')\n for s, d in zip(tmt_wells, new_wells):\n pick_up(p20)\n p20.aspirate(9, s)\n p20.dispense(9, d)\n p20.mix(3, 20, d)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.delay(minutes=60 if real_mode else 0.5)\n\n for well in new_wells:\n pick_up(p20)\n p20.aspirate(5, ha)\n p20.dispense(5, well)\n p20.mix(1, 20, well)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.delay(minutes=15 if real_mode else 0.5)\n # WHAT IS POOL VOLUME?\n for pool in all_pools:\n pick_up(p20)\n for well in new_wells:\n for _ in range(2):\n p20.aspirate(20, well)\n p20.dispense(20, pool)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n for pool in all_pools:\n pick_up(p20)\n p20.aspirate(10, formic_acid)\n p20.dispense(10, pool)\n p20.mix(3, 20, pool)\n p20.drop_tip() if real_mode else p20.return_tip()\n", + "content": "def get_values(*names):\n import json\n _all_values = json.loads(\"\"\"{\"num_samp\":48,\"real_mode\":false,\"p20_mount\":\"right\",\"m300_mount\":\"left\"}\"\"\")\n return [_all_values[n] for n in names]\n\n\nimport math\nfrom opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'Digestion and Bead Cleanup',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.14'\n}\n\n\ndef run(ctx):\n\n [num_samp, real_mode, p20_mount, m300_mount] = get_values( # noqa: F821\n \"num_samp\", \"real_mode\", \"p20_mount\", \"m300_mount\")\n\n # num_samp = 48\n num_col = math.ceil(num_samp/8)\n #\n # m300_mount = 'left'\n # p20_mount = 'right'\n #\n # real_mode = True\n\n # labware\n mag_mod = ctx.load_module(\"magnetic module gen2\", 1)\n try:\n mag_plate = mag_mod.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt') # noqa: E501\n\n except FileNotFoundError:\n mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt') # noqa: E501\n\n try:\n old_plate = ctx.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt', 2) # noqa: E501\n except FileNotFoundError:\n old_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n 2)\n\n tuberack = ctx.load_labware('opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', 3) # noqa: E501\n\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', 6)\n trash = ctx.load_labware('nest_1_reservoir_195ml', 8).wells()[0].top()\n tmt_plate = ctx.load_labware('opentrons_96_tiprack_sarstedt_200ul', 9)\n\n if not ctx.is_simulating:\n\n hs_mod = ctx.load_module('heaterShakerModuleV1', 10)\n hs_mod.close_labware_latch()\n else:\n dummy = ctx.load_labware('nest_12_reservoir_15ml', 10)\n dummy = dummy\n\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [4, 5]]\n tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in [7, 11]]\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tips300)\n\n def slow_tip_withdrawal(pipette, well_location, to_center=False):\n pipette.default_speed = 10\n if to_center is False:\n pipette.move_to(well_location.top())\n else:\n pipette.move_to(well_location.center())\n pipette.default_speed = 400\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(f\"Replace empty tip rack for {pip}\")\n pip.reset_tipracks()\n pip.pick_up_tip()\n\n # mapping\n sample_cols = old_plate.rows()[0][:num_col]\n dest_cols = mag_plate.rows()[0][:num_col]\n dest_wells = [well for well in mag_plate.wells()[:num_samp]]\n\n pool_well1 = tuberack['B1']\n pool_well2 = tuberack['B2']\n pool_well3 = tuberack['B3']\n\n num_pools = int(num_samp/16)\n\n all_pools = [pool_well1, pool_well2, pool_well3][:num_pools]\n\n acn = reservoir['A1']\n ethanol = reservoir['A2']\n\n beads = tuberack['A1']\n mm_teab = tuberack['A2']\n ha = tuberack['A3']\n formic_acid = tuberack['A4']\n\n digestion_solution = tmt_plate['A12']\n\n # protocol\n ctx.comment('\\n---------------ADDING BEADS TO PLATES----------------\\n\\n')\n\n pick_up(p20)\n p20.mix(15, 20, beads, rate=1.5)\n for well in dest_wells:\n p20.aspirate(4, beads)\n slow_tip_withdrawal(p20, beads)\n p20.dispense(4, well)\n p20.blow_out()\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n for s, d in zip(sample_cols, dest_cols):\n pick_up(m300)\n m300.aspirate(30, s)\n m300.dispense(30, d)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.comment('\\n---------------Transferring ACN----------------\\n\\n')\n for col in dest_cols:\n pick_up(m300)\n m300.aspirate(70, acn)\n m300.dispense(70, col)\n m300.mix(3, 85, col, rate=0.7)\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.delay(minutes=2 if real_mode else 0.5)\n\n mag_mod.engage(height_from_base=1)\n\n ctx.delay(minutes=5 if real_mode else 0.5)\n\n ctx.comment('\\n---------------Removing Super----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, col, rate=0.1)\n m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n m300.dispense(110, trash)\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n for _ in range(2):\n ctx.comment('\\n---------------Adding Ethanol----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, ethanol, rate=0.5)\n slow_tip_withdrawal(m300, ethanol)\n m300.dispense(100, col.top())\n m300.drop_tip() if real_mode else m300.return_tip()\n\n ctx.comment('\\n---------------Removing Ethanol----------------\\n\\n')\n pick_up(m300)\n for col in dest_cols:\n m300.aspirate(100, col, rate=0.1)\n m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n m300.dispense(110, trash)\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n mag_mod.disengage()\n\n ctx.comment('\\n--------------ADDING Digestion Solution--------------\\n\\n')\n for col in dest_cols:\n pick_up(m300)\n m300.aspirate(20, digestion_solution)\n m300.dispense(20, col)\n m300.mix(2, 15, col)\n m300.blow_out()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n if not ctx.is_simulating:\n hs_mod.open_labware_latch()\n ctx.pause('Move plate to heater shaker')\n if not ctx.is_simulating:\n hs_mod.close_labware_latch()\n hs_mod.set_and_wait_for_temperature(37)\n ctx.pause('Overnight Digestion')\n if not ctx.is_simulating:\n hs_mod.deactivate_heater()\n hs_mod.open_labware_latch()\n ctx.pause(\"Move plate to magnetic module\")\n\n mag_mod.engage(height_from_base=1)\n ctx.delay(minutes=2 if real_mode else 0.5)\n\n ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n new_cols = mag_plate.rows()[0][num_col:num_col+num_col]\n new_wells = [well for col in mag_plate.columns()[num_col:num_col+num_col]\n for well in col]\n\n for s, d in zip(dest_cols, new_cols):\n pick_up(m300)\n m300.aspirate(20, s, rate=0.05)\n m300.dispense(20, d)\n m300.move_to(d.top())\n ctx.delay(seconds=1.5)\n m300.blow_out()\n m300.touch_tip()\n m300.drop_tip() if real_mode else m300.return_tip()\n\n tmt_wells = [well for col in tmt_plate.columns()[:num_col]\n for well in col]\n\n for well in tmt_wells:\n pick_up(p20)\n p20.aspirate(5, mm_teab)\n p20.dispense(5, well)\n p20.mix(3, 9, well)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.comment('\\n-----From TMT Wells to Sample Wells----------\\n\\n')\n for s, d in zip(tmt_wells, new_wells):\n pick_up(p20)\n p20.aspirate(9, s)\n p20.dispense(9, d)\n p20.mix(3, 20, d)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.delay(minutes=60 if real_mode else 0.5)\n\n for well in new_wells:\n pick_up(p20)\n p20.aspirate(5, ha)\n p20.dispense(5, well)\n p20.mix(1, 20, well)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n ctx.delay(minutes=15 if real_mode else 0.5)\n # WHAT IS POOL VOLUME?\n print(all_pools)\n ctx.comment('ddd')\n for pool in all_pools:\n pick_up(p20)\n for well in new_wells:\n for _ in range(2):\n p20.aspirate(20, well)\n p20.dispense(20, pool)\n p20.drop_tip() if real_mode else p20.return_tip()\n\n for pool in all_pools:\n pick_up(p20)\n p20.aspirate(10, formic_acid)\n p20.dispense(10, pool)\n p20.mix(3, 20, pool)\n p20.drop_tip() if real_mode else p20.return_tip()\n", "custom_labware_defs": [ { "brand": { - "brand": "Sarstedt, Opentrons", - "brandId": [ - "72.985.002", - "991-00076" - ] + "brand": "Opentrons", + "brandId": [] }, "cornerOffsetFromSlot": { "x": 0, @@ -17,11 +14,18 @@ "dimensions": { "xDimension": 127.76, "yDimension": 85.48, - "zDimension": 25.06 + "zDimension": 66.5 }, "groups": [ { + "brand": { + "brand": "Sarstedt", + "brandId": [ + "72.985.002" + ] + }, "metadata": { + "displayCategory": "tubeRack", "wellBottomShape": "v" }, "wells": [ @@ -125,8 +129,8 @@ } ], "metadata": { - "displayCategory": "wellPlate", - "displayName": "TMTpro18 PCR strip plate", + "displayCategory": "tubeRack", + "displayName": "Opentrons 96 tiprack with sarstedt 200ul PCR tube", "displayVolumeUnits": "\u00b5L", "tags": [] }, @@ -257,875 +261,875 @@ "format": "irregular", "isMagneticModuleCompatible": false, "isTiprack": false, - "loadName": "tmtpro18_pcr_plate", + "loadName": "opentrons_96_tiprack_sarstedt_200ul", "quirks": [] }, "schemaVersion": 2, "version": 1, "wells": { "A1": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 14.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A10": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 95.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A11": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 104.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A12": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A2": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 23.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A3": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 32.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A4": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 41.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A5": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 50.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A6": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 59.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A7": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 68.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A8": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "A9": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "B1": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 14.38, "y": 65.24, - "z": 5.43 + "z": 46.7 }, "B10": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 95.38, "y": 65.24, - "z": 5.43 + "z": 46.7 }, "B11": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 104.38, "y": 65.24, - "z": 5.43 + "z": 46.7 }, "B12": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 65.24, - "z": 5.43 + "z": 46.7 }, "B2": { - "depth": 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"z": 46.7 }, "H8": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 11.24, - "z": 5.43 + "z": 46.7 }, "H9": { - "depth": 19.63, - "diameter": 5.3, + "depth": 19.8, + "diameter": 5.4, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 11.24, - "z": 5.43 + "z": 46.7 } } } @@ -1256,10 +1260,10 @@ "type": "nest_1_reservoir_195ml" }, { - "name": "TMTpro18 PCR strip plate on 9", + "name": "Opentrons 96 tiprack with sarstedt 200ul PCR tube on 9", "share": false, "slot": "9", - "type": "tmtpro18_pcr_plate" + "type": "opentrons_96_tiprack_sarstedt_200ul" }, { "name": "NEST 12 Well Reservoir 15 mL on 10", diff --git a/protocols/0845ab/0845ab.ot2.apiv2.py b/protocols/0845ab/0845ab.ot2.apiv2.py index 0f6cf8f05..8d562bb29 100644 --- a/protocols/0845ab/0845ab.ot2.apiv2.py +++ b/protocols/0845ab/0845ab.ot2.apiv2.py @@ -1,3 +1,9 @@ +def get_values(*names): + import json + _all_values = json.loads("""{"num_samp":48,"real_mode":false,"p20_mount":"right","m300_mount":"left"}""") + return [_all_values[n] for n in names] + + import math from opentrons import protocol_api @@ -40,7 +46,7 @@ def run(ctx): reservoir = ctx.load_labware('nest_12_reservoir_15ml', 6) trash = ctx.load_labware('nest_1_reservoir_195ml', 8).wells()[0].top() - tmt_plate = ctx.load_labware('tmtpro18_pcr_plate', 9) + tmt_plate = ctx.load_labware('opentrons_96_tiprack_sarstedt_200ul', 9) if not ctx.is_simulating: @@ -103,12 +109,11 @@ def pick_up(pip): ctx.comment('\n---------------ADDING BEADS TO PLATES----------------\n\n') pick_up(p20) - p20.mix(20, 20, beads, rate=1.5) + p20.mix(15, 20, beads, rate=1.5) for well in dest_wells: p20.aspirate(4, beads) slow_tip_withdrawal(p20, beads) p20.dispense(4, well) - slow_tip_withdrawal(p20, beads) p20.blow_out() p20.drop_tip() if real_mode else p20.return_tip() @@ -148,7 +153,7 @@ def pick_up(pip): ctx.comment('\n---------------Adding Ethanol----------------\n\n') pick_up(m300) for col in dest_cols: - m300.aspirate(100, ethanol, rate=0.1) + m300.aspirate(100, ethanol, rate=0.5) slow_tip_withdrawal(m300, ethanol) m300.dispense(100, col.top()) m300.drop_tip() if real_mode else m300.return_tip() @@ -211,7 +216,7 @@ def pick_up(pip): pick_up(p20) p20.aspirate(5, mm_teab) p20.dispense(5, well) - p20.mix(3, 20, well) + p20.mix(3, 9, well) p20.drop_tip() if real_mode else p20.return_tip() ctx.comment('\n-----From TMT Wells to Sample Wells----------\n\n') @@ -233,6 +238,8 @@ def pick_up(pip): ctx.delay(minutes=15 if real_mode else 0.5) # WHAT IS POOL VOLUME? + print(all_pools) + ctx.comment('ddd') for pool in all_pools: pick_up(p20) for well in new_wells: diff --git a/protocols/0845ab/labware/tmtpro18_pcr_plate.json b/protocols/0845ab/labware/opentrons_96_tiprack_sarstedt_200ul.json similarity index 70% rename from protocols/0845ab/labware/tmtpro18_pcr_plate.json rename to protocols/0845ab/labware/opentrons_96_tiprack_sarstedt_200ul.json index c595fcea0..feadad964 100644 --- a/protocols/0845ab/labware/tmtpro18_pcr_plate.json +++ b/protocols/0845ab/labware/opentrons_96_tiprack_sarstedt_200ul.json @@ -122,893 +122,897 @@ ] ], "brand": { - "brand": "Sarstedt, Opentrons", - "brandId": [ - "72.985.002", - "991-00076" - ] + "brand": "Opentrons", + "brandId": [] }, "metadata": { - "displayName": "TMTpro18 PCR strip plate", - "displayCategory": "wellPlate", + "displayName": "Opentrons 96 tiprack with sarstedt 200ul PCR tube", + "displayCategory": "tubeRack", "displayVolumeUnits": "µL", "tags": [] }, "dimensions": { "xDimension": 127.76, "yDimension": 85.48, - "zDimension": 25.06 + "zDimension": 66.5 }, "wells": { "A1": { - "depth": 19.63, + "depth": 19.8, "totalLiquidVolume": 200, "shape": "circular", - "diameter": 5.3, + "diameter": 5.4, "x": 14.38, "y": 74.24, - "z": 5.43 + "z": 46.7 }, "B1": { - "depth": 19.63, + "depth": 19.8, "totalLiquidVolume": 200, 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