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fix
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“ramifarawi” committed Jan 25, 2024
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2 changes: 1 addition & 1 deletion protoBuilds/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py.json
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{
"content": "metadata = {\n 'protocolName': 'Kapa Bead Clean Up',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_col, bead_dry_time, m300_mount] = get_values( # noqa: F821\n \"num_col\", \"bead_dry_time\", \"m300_mount\")\n\n # num_col = 2\n # bead_dry_time = 3\n # m300_mount = 'left'\n\n # labware\n # mag_mod = ctx.load_module('magnetic module gen2', 1)\n mag_stand = ctx.load_labware('genericmagnet_96_wellplate_1500ul', 1)\n mag_plate = ctx.load_labware('generic_96_wellplate_1500ul', 4)\n # mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', 3)\n elute_plate = ctx.load_labware('agilent_96_wellplate_270ul', 2)\n tips = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in [7, 8]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n # mapping\n beads = reservoir['A1']\n ethanol = reservoir['A2']\n eb = reservoir['A3']\n trash = reservoir['A12'].top()\n\n sample_cols = mag_plate.rows()[0][:num_col]\n sample_cols_stand = mag_stand.rows()[0][:num_col]\n\n def slow_tip_withdrawal(pipette, well_location, to_center=False):\n if pipette.mount == 'right':\n axis = 'A'\n else:\n axis = 'Z'\n ctx.max_speeds[axis] = 10\n if to_center is False:\n pipette.move_to(well_location.top())\n else:\n pipette.move_to(well_location.center())\n ctx.max_speeds[axis] = None\n\n # protocol\n m300.pick_up_tip()\n m300.mix(20, 200, beads)\n ctx.comment('\\n---------------ADDING BEADS TO PLATE----------------\\n\\n')\n for col in sample_cols:\n if not m300.has_tip:\n m300.pick_up_tip()\n m300.aspirate(90, beads)\n slow_tip_withdrawal(m300, col)\n m300.dispense(90, col)\n m300.mix(10, 110, col)\n m300.drop_tip()\n\n ctx.delay(minutes=5)\n\n ctx.pause('Move plate to magnetic stand, then select resume')\n\n ctx.delay(minutes=3)\n\n ctx.comment('\\n---------------REMOVING SUPER----------------\\n\\n')\n for col in sample_cols_stand:\n m300.pick_up_tip()\n m300.aspirate(140, col, rate=0.1)\n m300.aspirate(20, col.bottom(z=0.6), rate=0.1)\n m300.dispense(160, trash)\n m300.drop_tip()\n\n ctx.comment('\\n---------------TWO ETHANOL WASHES----------------\\n\\n')\n for _ in range(2):\n\n m300.pick_up_tip()\n for col in sample_cols_stand:\n m300.aspirate(200, ethanol)\n slow_tip_withdrawal(m300, ethanol)\n m300.dispense(200, col.top())\n ctx.delay(seconds=2)\n m300.blow_out()\n\n ctx.delay(seconds=30)\n\n for col in sample_cols_stand:\n if not m300.has_tip:\n m300.pick_up_tip()\n m300.aspirate(180, col, rate=0.1)\n m300.aspirate(20, col.bottom(z=0.6), rate=0.1)\n m300.dispense(200, trash)\n ctx.delay(seconds=2)\n m300.blow_out()\n m300.drop_tip()\n\n ctx.delay(minutes=bead_dry_time)\n\n ctx.pause('Move magplate to slot 4, then select resume')\n\n ctx.comment('\\n---------------Resuspend----------------\\n\\n')\n for col in sample_cols:\n m300.pick_up_tip()\n m300.aspirate(23, eb)\n m300.dispense(23, col)\n m300.mix(15, 19, col.bottom(z=0.7))\n m300.drop_tip()\n\n ctx.pause('Move plate to magnetic stand, then select resume')\n ctx.delay(minutes=3)\n\n ctx.comment('\\n---------------Transfer Elute----------------\\n\\n')\n for s, d in zip(sample_cols, elute_plate.rows()[0]):\n m300.pick_up_tip()\n m300.aspirate(20, s.bottom(z=0.7), rate=0.1)\n m300.dispense(20, d)\n m300.blow_out(d.top())\n m300.touch_tip()\n m300.drop_tip()\n",
"content": "metadata = {\n 'protocolName': 'Kapa Bead Clean Up',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_col, bead_dry_time, m300_mount] = get_values( # noqa: F821\n \"num_col\", \"bead_dry_time\", \"m300_mount\")\n\n # num_col = 2\n # bead_dry_time = 3\n # m300_mount = 'left'\n\n # labware\n # mag_mod = ctx.load_module('magnetic module gen2', 1)\n mag_stand = ctx.load_labware('genericmagnet_96_wellplate_1500ul', 1)\n mag_plate = ctx.load_labware('generic_96_wellplate_1500ul', 4)\n # mag_plate = mag_mod.load_labware('nest_wellplate_100ul_pcr_full_skirt')\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', 3)\n elute_plate = ctx.load_labware('agilent_96_wellplate_270ul', 2)\n tips = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in [7, 8]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)\n\n # mapping\n beads = reservoir['A1']\n ethanol = reservoir['A2']\n eb = reservoir['A3']\n trash = reservoir['A12'].top()\n\n sample_cols = mag_plate.rows()[0][:num_col]\n sample_cols_stand = mag_stand.rows()[0][:num_col]\n\n def slow_tip_withdrawal(pipette, well_location, to_center=False):\n if pipette.mount == 'right':\n axis = 'A'\n else:\n axis = 'Z'\n ctx.max_speeds[axis] = 10\n if to_center is False:\n pipette.move_to(well_location.top())\n else:\n pipette.move_to(well_location.center())\n ctx.max_speeds[axis] = None\n\n # protocol\n m300.pick_up_tip()\n m300.mix(20, 200, beads)\n ctx.comment('\\n---------------ADDING BEADS TO PLATE----------------\\n\\n')\n for col in sample_cols:\n if not m300.has_tip:\n m300.pick_up_tip()\n m300.aspirate(90, beads)\n slow_tip_withdrawal(m300, col)\n m300.dispense(90, col)\n m300.mix(10, 110, col)\n m300.drop_tip()\n\n ctx.delay(minutes=5)\n\n ctx.pause('Move plate to magnetic stand, then select resume')\n\n ctx.delay(minutes=3)\n\n ctx.comment('\\n---------------REMOVING SUPER----------------\\n\\n')\n for col in sample_cols_stand:\n m300.pick_up_tip()\n m300.aspirate(140, col, rate=0.1)\n m300.aspirate(20, col.bottom(z=0.6), rate=0.1)\n m300.dispense(160, trash)\n m300.drop_tip()\n\n ctx.comment('\\n---------------TWO ETHANOL WASHES----------------\\n\\n')\n for _ in range(2):\n\n m300.pick_up_tip()\n for col in sample_cols_stand:\n m300.aspirate(200, ethanol)\n slow_tip_withdrawal(m300, ethanol)\n m300.dispense(200, col.top())\n ctx.delay(seconds=2)\n m300.blow_out()\n\n ctx.delay(seconds=30)\n\n for col in sample_cols_stand:\n if not m300.has_tip:\n m300.pick_up_tip()\n m300.aspirate(180, col, rate=0.1)\n m300.aspirate(20, col.bottom(z=0.6), rate=0.1)\n m300.dispense(200, trash)\n ctx.delay(seconds=2)\n m300.blow_out()\n m300.drop_tip()\n\n ctx.delay(minutes=bead_dry_time)\n\n ctx.pause('Move magplate to slot 4, then select resume')\n\n ctx.comment('\\n---------------Resuspend----------------\\n\\n')\n for col in sample_cols:\n m300.pick_up_tip()\n m300.aspirate(23, eb)\n m300.dispense(23, col)\n m300.mix(15, 19, col.bottom(z=0.7))\n m300.drop_tip()\n\n ctx.pause('Move plate to magnetic stand, then select resume')\n ctx.delay(minutes=3)\n\n ctx.comment('\\n---------------Transfer Elute----------------\\n\\n')\n for s, d in zip(sample_cols, elute_plate.rows()[0]):\n m300.pick_up_tip()\n m300.aspirate(20, s.bottom(z=0.7), rate=0.1)\n m300.dispense(20, d)\n m300.blow_out(d.top())\n m300.touch_tip()\n m300.drop_tip()\n",
"custom_labware_defs": [
{
"brand": {
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2 changes: 1 addition & 1 deletion protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ def run(ctx):
# 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')
# mag_plate = mag_mod.load_labware('nest_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)
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