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“ramifarawi” committed Aug 8, 2023
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2 changes: 1 addition & 1 deletion protoBuilds/076f67/076f67.ot2.apiv2.py.json
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{
"content": "from opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'SARS-COV2 (VSV) Neutralization Assay',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n # [num_plates, plate_type, serum_vol, m300_mount] = get_values( # noqa: F821\n # \"num_plates\", \"plate_type\", \"serum_vol\", \"m300_mount\")\n\n num_plates = 3\n plate_type = 'corning_96_wellplate_360ul_flat'\n serum_vol = 70\n m300_mount = 'left'\n\n # labware\n serum_res = ctx.load_labware('agilent_1_reservoir_290ml', 7)\n virus_res = ctx.load_labware('nest_12_reservoir_15ml', 8)\n source_plates = [ctx.load_labware(plate_type, slot)\n for slot in [1, 2, 3]][:num_plates]\n dest_plates = [ctx.load_labware(plate_type, slot)\n for slot in [4, 5, 6]][:num_plates]\n tips = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [9, 10, 11]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n def pick_up():\n try:\n m300.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks\")\n m300.reset_tipracks()\n m300.pick_up_tip()\n\n def slow_tip_withdrawal(current_pipette, well_location, to_center=False):\n if current_pipette.mount == 'right':\n axis = 'A'\n else:\n axis = 'Z'\n ctx.max_speeds[axis] = 10\n if to_center is False:\n current_pipette.move_to(well_location.top())\n else:\n current_pipette.move_to(well_location.center())\n ctx.max_speeds[axis] = None\n\n # mapping\n virus = virus_res.wells()[0]\n overlay = virus_res.wells()[1:4][:num_plates]\n serum = serum_res.wells()[0]\n trash = virus_res.wells()[11]\n\n # protocol\n ctx.comment('\\n---------------ADDING SERUM TO PLATES----------------\\n\\n')\n pick_up()\n for plate in source_plates:\n m300.distribute(40, serum, plate.rows()[0][1:7], new_tip='never')\n ctx.comment('\\n\\n')\n\n for plate in source_plates:\n m300.aspirate(80, serum)\n m300.dispense(80, plate.rows()[0][7])\n ctx.comment('\\n\\n')\n\n for plate in source_plates:\n m300.aspirate(serum_vol, serum)\n m300.dispense(serum_vol, plate.rows()[0][0])\n\n m300.drop_tip()\n ctx.comment('\\n\\n')\n\n ctx.pause(f'''Please add {80-serum_vol}ul of media and appropriate amount\n of sample to column 1''')\n\n ctx.comment('\\n---------------SERIALLY DILUTING----------------\\n\\n')\n for plate in source_plates:\n for i in range(len(plate.rows()[0][:6])):\n pick_up()\n m300.mix(3, 40, plate.rows()[0][i])\n m300.aspirate(40, plate.rows()[0][i])\n if i < 5:\n m300.dispense(40, plate.rows()[0][i+1])\n if i == 5:\n m300.dispense(40, trash)\n\n m300.drop_tip()\n ctx.comment('\\n')\n ctx.comment('\\n\\n\\n\\n \u02da')\n\n ctx.comment('\\n---------------ADDING VIRUS----------------\\n\\n')\n m300.pick_up_tip()\n for plate in source_plates:\n for col in plate.rows()[0][:7]:\n m300.aspirate(40, virus)\n m300.dispense(40, col.top())\n ctx.delay(seconds=2)\n m300.blow_out(col.top())\n m300.drop_tip()\n\n ctx.pause('Place plate in incubator at 37C for one hour')\n\n ctx.comment('\\n------DISCARDING MEDIA & TRANSFER TO NEW PLATE-------\\n\\n')\n\n for s_plate, d_plate in zip(source_plates, dest_plates):\n for s, d in zip(s_plate.rows()[0][:8], d_plate.rows()[0][:8]):\n pick_up()\n m300.aspirate(100, d, rate=0.1)\n m300.dispense(100, trash)\n m300.aspirate(60, s)\n m300.dispense(60, d)\n m300.drop_tip()\n\n ctx.pause('Place plate in incubator at 37C for one hour')\n\n ctx.comment('\\n------------TRANSFERRING OVERLAY-------------\\n\\n')\n for res_well, plate in zip(overlay, dest_plates):\n for col in plate.rows()[0][:8]:\n pick_up()\n m300.aspirate(140, res_well, rate=0.2)\n ctx.delay(seconds=1)\n slow_tip_withdrawal(m300, col)\n m300.dispense(140, col, rate=0.2)\n slow_tip_withdrawal(m300, col)\n m300.drop_tip()\n ctx.comment('\\n')\n",
"content": "from opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'SARS-COV2 (VSV) Neutralization Assay',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_plates, plate_type, serum_vol, m300_mount] = get_values( # noqa: F821\n \"num_plates\", \"plate_type\", \"serum_vol\", \"m300_mount\")\n\n # labware\n serum_res = ctx.load_labware('agilent_1_reservoir_290ml', 7)\n virus_res = ctx.load_labware('nest_12_reservoir_15ml', 8)\n source_plates = [ctx.load_labware(plate_type, slot)\n for slot in [1, 2, 3]][:num_plates]\n dest_plates = [ctx.load_labware(plate_type, slot)\n for slot in [4, 5, 6]][:num_plates]\n tips = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [9, 10, 11]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n def pick_up():\n try:\n m300.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks\")\n m300.reset_tipracks()\n m300.pick_up_tip()\n\n def slow_tip_withdrawal(current_pipette, well_location, to_center=False):\n if current_pipette.mount == 'right':\n axis = 'A'\n else:\n axis = 'Z'\n ctx.max_speeds[axis] = 10\n if to_center is False:\n current_pipette.move_to(well_location.top())\n else:\n current_pipette.move_to(well_location.center())\n ctx.max_speeds[axis] = None\n\n # mapping\n virus = virus_res.wells()[0]\n overlay = virus_res.wells()[1:4][:num_plates]\n serum = serum_res.wells()[0]\n trash = virus_res.wells()[11]\n\n # protocol\n ctx.comment('\\n---------------ADDING SERUM TO PLATES----------------\\n\\n')\n pick_up()\n for plate in source_plates:\n m300.distribute(40, serum, plate.rows()[0][1:7], new_tip='never')\n ctx.comment('\\n\\n')\n\n for plate in source_plates:\n m300.aspirate(80, serum)\n m300.dispense(80, plate.rows()[0][7])\n ctx.comment('\\n\\n')\n\n for plate in source_plates:\n m300.aspirate(serum_vol, serum)\n m300.dispense(serum_vol, plate.rows()[0][0])\n\n m300.drop_tip()\n ctx.comment('\\n\\n')\n\n ctx.pause(f'''Please add {80-serum_vol}ul of media and appropriate amount\n of sample to column 1''')\n\n ctx.comment('\\n---------------SERIALLY DILUTING----------------\\n\\n')\n for plate in source_plates:\n for i in range(len(plate.rows()[0][:6])):\n pick_up()\n m300.mix(3, 40, plate.rows()[0][i])\n m300.aspirate(40, plate.rows()[0][i])\n if i < 5:\n m300.dispense(40, plate.rows()[0][i+1])\n if i == 5:\n m300.dispense(40, trash)\n\n m300.drop_tip()\n ctx.comment('\\n')\n ctx.comment('\\n\\n\\n\\n \u02da')\n\n ctx.comment('\\n---------------ADDING VIRUS----------------\\n\\n')\n m300.pick_up_tip()\n for plate in source_plates:\n for col in plate.rows()[0][:7]:\n m300.aspirate(40, virus)\n m300.dispense(40, col.top())\n ctx.delay(seconds=2)\n m300.blow_out(col.top())\n m300.drop_tip()\n\n ctx.pause('Place plate in incubator at 37C for one hour')\n\n ctx.comment('\\n------DISCARDING MEDIA & TRANSFER TO NEW PLATE-------\\n\\n')\n\n for s_plate, d_plate in zip(source_plates, dest_plates):\n for s, d in zip(s_plate.rows()[0][:8], d_plate.rows()[0][:8]):\n pick_up()\n m300.aspirate(100, d, rate=0.1)\n m300.dispense(100, trash)\n m300.aspirate(60, s)\n m300.dispense(60, d)\n m300.drop_tip()\n\n ctx.pause('Place plate in incubator at 37C for one hour')\n\n ctx.comment('\\n------------TRANSFERRING OVERLAY-------------\\n\\n')\n for res_well, plate in zip(overlay, dest_plates):\n for col in plate.rows()[0][:8]:\n pick_up()\n m300.aspirate(140, res_well, rate=0.2)\n ctx.delay(seconds=1)\n slow_tip_withdrawal(m300, col)\n m300.dispense(140, col, rate=0.2)\n slow_tip_withdrawal(m300, col)\n m300.drop_tip()\n ctx.comment('\\n')\n",
"custom_labware_defs": [
{
"brand": {
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9 changes: 2 additions & 7 deletions protocols/076f67/076f67.ot2.apiv2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,8 @@

def run(ctx):

# [num_plates, plate_type, serum_vol, m300_mount] = get_values( # noqa: F821
# "num_plates", "plate_type", "serum_vol", "m300_mount")

num_plates = 3
plate_type = 'corning_96_wellplate_360ul_flat'
serum_vol = 70
m300_mount = 'left'
[num_plates, plate_type, serum_vol, m300_mount] = get_values( # noqa: F821
"num_plates", "plate_type", "serum_vol", "m300_mount")

# labware
serum_res = ctx.load_labware('agilent_1_reservoir_290ml', 7)
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