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Update 4e4c0c.ot2.apiv2.py.json #4941

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4 changes: 2 additions & 2 deletions protoBuilds/4e4c0c/4e4c0c.ot2.apiv2.py.json
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Original file line number Diff line number Diff line change
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{
"content": "import math\n\nmetadata = {\n 'protocolName': 'KingFisher Flex Plate Set Up',\n 'author': 'Steve Plonk <[email protected]>',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n # get parameter values from json\n [num_cols, labware_processing_plate, labware_reservoir_12well,\n labware_reservoir_1well,\n m300_mount, m20_mount] = get_values( # noqa: F821\n \"num_cols\", \"labware_processing_plate\", \"labware_reservoir_12well\",\n \"labware_reservoir_1well\", \"m300_mount\", \"m20_mount\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=5)\n if not 1 <= num_cols <= 12:\n raise Exception('Invalid number of columns (must be 1-12).')\n\n # tips, p300 and p20 multi\n tips300 = [ctx.load_labware(\n \"opentrons_96_filtertiprack_200ul\", str(slot)) for slot in [11]]\n p300m = ctx.load_instrument(\n \"p300_multi_gen2\", m300_mount, tip_racks=tips300)\n\n tips20 = [ctx.load_labware(\n \"opentrons_96_filtertiprack_20ul\", str(slot)) for slot in [10]]\n p20m = ctx.load_instrument(\n \"p20_multi_gen2\", m20_mount, tip_racks=tips20)\n\n # yield list chunks of size n\n def create_chunks(list_name, n):\n for i in range(0, len(list_name), n):\n yield list_name[i:i+n]\n\n # return liquid height in a well\n def liq_height(well, effective_diameter=None):\n if well.diameter:\n if effective_diameter:\n radius = effective_diameter / 2\n else:\n radius = well.diameter / 2\n csa = math.pi*(radius**2)\n else:\n csa = well.length*well.width\n return well.liq_vol / csa\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\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 # to extend aspirate\n def extended1(func):\n \"\"\"\n Extend aspirate method.\n\n For viscous liquids.\n Half default flow rate.\n Delay after aspiration.\n Slow departure of tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs, rate=0.5)\n ctx.delay(seconds=1)\n slow_tip_withdrawal(func.__self__, [*args][1].labware.object)\n return wrapper\n\n # to extend aspirate\n def extended2(func):\n \"\"\"\n Extend aspirate method.\n\n For volatile liquids.\n Post-aspirate air gap.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.air_gap(20)\n return wrapper\n\n # to extend dispense\n def extended3(func):\n \"\"\"\n Extend dispense method.\n\n For viscous liquids.\n Half default flow rate.\n Delay after dispense.\n Blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs, rate=0.5)\n ctx.delay(seconds=1)\n func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n # to extend dispense\n def extended4(func):\n \"\"\"\n Extend dispense method.\n\n For volatile liquids.\n Delayed blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.move_to([*args][1].labware.object.top())\n ctx.delay(seconds=0.5)\n func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n # to extend dispense\n def extended5(func):\n \"\"\"\n Extend dispense method.\n\n For aqueous liquids.\n Blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n washreservoir = ctx.load_labware(\n labware_reservoir_1well, '8', 'Wash Buffer')\n\n etohreservoir = ctx.load_labware(\n labware_reservoir_1well, '9', '80 Percent EtOH')\n\n twelvewellreservoir = ctx.load_labware(\n labware_reservoir_12well, '7', '12-Well Reservoir')\n\n source_dict = {\n 'Proteinase K Solution': twelvewellreservoir.wells_by_name()['A1'],\n 'Wash Buffer': washreservoir.wells()[0],\n '80 Percent EtOH': etohreservoir.wells()[0],\n 'Elution Solution': twelvewellreservoir.wells_by_name()['A12']}\n\n processingplates = [\n ctx.load_labware(\n labware_processing_plate, str(slot+1), name) for name, slot in zip(\n ['Sample Plate',\n 'Wash Plate 1',\n 'Wash Plate 2',\n 'Wash Plate 3',\n 'Elution Plate 4'],\n [*range(5)])]\n\n for source, lc, tfervol in zip(\n [value for value in source_dict.values()],\n ['aqueous', 'viscous', 'volatile', 'aqueous'],\n [10, 1000, 1500, 100]):\n\n source.liq_class = lc\n source.liq_vol = 1.1*(tfervol*8*num_cols)\n\n for source, transfervolume, plate in zip(\n [source_dict[reagent] for reagent in [\n 'Proteinase K Solution',\n 'Wash Buffer',\n '80 Percent EtOH',\n '80 Percent EtOH',\n 'Elution Solution']],\n [10, 1000, 1000, 500, 100],\n processingplates):\n\n pip = p20m if transfervolume <= 20 else p300m\n\n # python dict to store and dispatch extended aspirate\n pip_aspirate = {'viscous': extended1(pip.aspirate),\n 'volatile': extended2(pip.aspirate),\n 'aqueous': pip.aspirate}\n\n # python dict to store and dispatch extended dispense\n pip_dispense = {'viscous': extended3(pip.dispense),\n 'volatile': extended4(pip.dispense),\n 'aqueous': extended5(pip.dispense)}\n\n vol_airgap = 20 if source.liq_class == 'volatile' else 0\n\n reps = math.ceil(\n transfervolume / (\n pip.tip_racks[0].wells()[0].max_volume - vol_airgap))\n\n v = transfervolume / reps\n\n pip.pick_up_tip()\n\n for column in plate.columns()[:num_cols]:\n\n dest = column[0].top(\n ) if v > 50 else column[0].bottom(1)\n\n for rep in range(reps):\n\n source.liq_vol -= v*pip.channels\n\n tipheight = liq_height(\n source) - 3 if liq_height(source) - 3 > 1 else 1\n\n pip_aspirate[source.liq_class](v, source.bottom(tipheight))\n\n pip_dispense[source.liq_class](v+vol_airgap, dest)\n\n pip.drop_tip()\n\n ctx.comment(\"Finished set up of five processing plates\")\n",
"content": "import math\n\nmetadata = {\n 'protocolName': 'KingFisher Flex Plate Set Up',\n 'author': 'Steve Plonk <[email protected]>',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n # get parameter values from json\n [num_cols, labware_processing_plate, labware_reservoir_12well,\n labware_reservoir_1well,\n m300_mount, m20_mount] = get_values( # noqa: F821\n \"num_cols\", \"labware_processing_plate\", \"labware_reservoir_12well\",\n \"labware_reservoir_1well\", \"m300_mount\", \"m20_mount\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=5)\n if not 1 <= num_cols <= 12:\n raise Exception('Invalid number of columns (must be 1-12).')\n\n # tips, p300 and p20 multi\n tips300 = [ctx.load_labware(\n \"opentrons_96_filtertiprack_200ul\", str(slot)) for slot in [11]]\n p300m = ctx.load_instrument(\n \"p300_multi_gen2\", m300_mount, tip_racks=tips300)\n\n tips20 = [ctx.load_labware(\n \"opentrons_96_filtertiprack_20ul\", str(slot)) for slot in [10]]\n p20m = ctx.load_instrument(\n \"p20_multi_gen2\", m20_mount, tip_racks=tips20)\n\n # yield list chunks of size n\n def create_chunks(list_name, n):\n for i in range(0, len(list_name), n):\n yield list_name[i:i+n]\n\n # return liquid height in a well\n def liq_height(well, effective_diameter=None):\n if well.diameter:\n if effective_diameter:\n radius = effective_diameter / 2\n else:\n radius = well.diameter / 2\n csa = math.pi*(radius**2)\n else:\n csa = well.length*well.width\n return well.liq_vol / csa\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\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 # to extend aspirate\n def extended1(func):\n \"\"\"\n Extend aspirate method.\n\n For viscous liquids.\n Half default flow rate.\n Delay after aspiration.\n Slow departure of tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs, rate=0.5)\n ctx.delay(seconds=1)\n slow_tip_withdrawal(func.__self__, [*args][1].labware.object)\n return wrapper\n\n # to extend aspirate\n def extended2(func):\n \"\"\"\n Extend aspirate method.\n\n For volatile liquids.\n Post-aspirate air gap.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.air_gap(20)\n return wrapper\n\n # to extend dispense\n def extended3(func):\n \"\"\"\n Extend dispense method.\n\n For viscous liquids.\n Half default flow rate.\n Delay after dispense.\n Blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs, rate=0.5)\n ctx.delay(seconds=1)\n # func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n # to extend dispense\n def extended4(func):\n \"\"\"\n Extend dispense method.\n\n For volatile liquids.\n Delayed blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.move_to([*args][1].labware.object.top())\n ctx.delay(seconds=0.5)\n # func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n # to extend dispense\n def extended5(func):\n \"\"\"\n Extend dispense method.\n\n For aqueous liquids.\n Blow out at top of well.\n Touch tip.\n \"\"\"\n def wrapper(*args, **kwargs):\n func(*args, **kwargs)\n func.__self__.blow_out([*args][1].labware.object.top())\n func.__self__.touch_tip()\n return wrapper\n\n washreservoir = ctx.load_labware(\n labware_reservoir_1well, '8', 'Wash Buffer')\n\n etohreservoir = ctx.load_labware(\n labware_reservoir_1well, '9', '80 Percent EtOH')\n\n twelvewellreservoir = ctx.load_labware(\n labware_reservoir_12well, '7', '12-Well Reservoir')\n\n source_dict = {\n 'Proteinase K Solution': twelvewellreservoir.wells_by_name()['A1'],\n 'Wash Buffer': washreservoir.wells()[0],\n '80 Percent EtOH': etohreservoir.wells()[0],\n 'Elution Solution': twelvewellreservoir.wells_by_name()['A12']}\n\n processingplates = [\n ctx.load_labware(\n labware_processing_plate, str(slot+1), name) for name, slot in zip(\n ['Sample Plate',\n 'Wash Plate 1',\n 'Wash Plate 2',\n 'Wash Plate 3',\n 'Elution Plate 4'],\n [*range(5)])]\n\n for source, lc, tfervol in zip(\n [value for value in source_dict.values()],\n ['aqueous', 'viscous', 'volatile', 'aqueous'],\n [10, 1000, 1500, 100]):\n\n source.liq_class = lc\n source.liq_vol = 1.1*(tfervol*8*num_cols)\n\n for source, transfervolume, plate in zip(\n [source_dict[reagent] for reagent in [\n 'Proteinase K Solution',\n 'Wash Buffer',\n '80 Percent EtOH',\n '80 Percent EtOH',\n 'Elution Solution']],\n [10, 1000, 1000, 500, 100],\n processingplates):\n\n pip = p20m if transfervolume <= 20 else p300m\n\n # python dict to store and dispatch extended aspirate\n pip_aspirate = {'viscous': extended1(pip.aspirate),\n 'volatile': extended2(pip.aspirate),\n 'aqueous': pip.aspirate}\n\n # python dict to store and dispatch extended dispense\n pip_dispense = {'viscous': extended3(pip.dispense),\n 'volatile': extended4(pip.dispense),\n 'aqueous': extended5(pip.dispense)}\n\n vol_airgap = 20 if source.liq_class == 'volatile' else 0\n\n reps = math.ceil(\n transfervolume / (\n pip.tip_racks[0].wells()[0].max_volume - vol_airgap))\n\n v = transfervolume / reps\n\n pip.pick_up_tip()\n\n for column in plate.columns()[:num_cols]:\n\n dest = column[0].top(\n ) if v > 50 else column[0].bottom(1)\n\n for rep in range(reps):\n\n source.liq_vol -= v*pip.channels\n\n tipheight = liq_height(\n source) - 3 if liq_height(source) - 3 > 1 else 1\n\n pip_aspirate[source.liq_class](v, source.bottom(tipheight))\n\n pip_dispense[source.liq_class](v+vol_airgap, dest)\n\n pip.drop_tip()\n\n ctx.comment(\"Finished set up of five processing plates\")\n",
"custom_labware_defs": [
{
"brand": {
Expand Down Expand Up @@ -1396,4 +1396,4 @@
"protocolName": "KingFisher Flex Plate Set Up"
},
"modules": []
}
}
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