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“ramifarawi” committed Nov 13, 2023
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14 changes: 9 additions & 5 deletions protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"content": "import math\n\nmetadata = {\n 'protocolName': 'Mass Spec Sample Prep',\n 'author': 'Nick <[email protected]',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [num_samples, p20_type, p300_type, p20_mount, p300_mount, plate_def,\n module_type] = get_values( # noqa: F821\n 'num_samples', 'p20_type', 'p300_type', 'p20_mount', 'p300_mount',\n 'plate_def', 'module_type')\n\n waste = ctx.load_labware('nest_1_reservoir_195ml', '1',\n 'waste container (load empty)').wells()[0].top()\n tips20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['6']]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['9']]\n magdeck = ctx.load_module('magnetic module gen2', '4')\n mag_plate = magdeck.load_labware(plate_def)\n reagent_plate = ctx.load_labware(plate_def, '5', 'reagent plate')\n etoh_plate = ctx.load_labware(plate_def, '2', 'ethanol plate')\n acetonitrile_plate = ctx.load_labware(\n plate_def, '3', 'acetonitrile plate')\n if module_type == 'thermocycler':\n temp_module = ctx.load_module('thermocycler')\n heat_func = temp_module.set_block_temperature\n else:\n tips20.insert(-1, ctx.load_labware('opentrons_96_tiprack_20ul', '8'))\n tips300.insert(\n -1, ctx.load_labware('opentrons_96_tiprack_300ul', '11'))\n temp_module = ctx.load_module('temperature module gen2', '7')\n heat_func = temp_module.set_temperature\n\n sample_plate = temp_module.load_labware(plate_def, 'sample plate')\n num_cols = math.ceil(num_samples/8)\n samples_s = sample_plate.wells()[:num_samples]\n samples_m = sample_plate.rows()[0][:num_cols]\n mag_samples_s = mag_plate.wells()[:num_samples]\n mag_samples_m = mag_plate.rows()[0][:num_cols]\n\n p20 = ctx.load_instrument(p20_type, p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument(p300_type, p300_mount,\n tip_racks=tips300)\n\n if p20.channels == 1:\n dtt = reagent_plate.columns()[0]\n caa = reagent_plate.columns()[1]\n mag_bead_stock = reagent_plate.columns()[2]\n acetonitrile = acetonitrile_plate.wells()[:num_samples]\n else:\n dtt = reagent_plate.rows()[0][0]\n caa = reagent_plate.rows()[0][1]\n mag_bead_stock = reagent_plate.rows()[0][2]\n acetonitrile = acetonitrile_plate.rows()[0][:num_cols]\n\n if p300.channels == 1:\n etoh = etoh_plate.wells()[:num_samples]\n abc = reagent_plate.columns()[3:5]\n trypsin = reagent_plate.columns()[5]\n else:\n etoh = etoh_plate.rows()[0][:num_cols]\n abc = reagent_plate.rows()[0][3:5]\n trypsin = reagent_plate.rows()[0][5]\n\n heat_func(60)\n\n tip_log = {}\n if p20.channels == 1:\n tip_list20 = [tip for rack in tips20 for tip in rack.wells()]\n else:\n tip_list20 = [tip for rack in tips20 for tip in rack.rows()[0]]\n if p300.channels == 1:\n tip_list300 = [tip for rack in tips300 for tip in rack.wells()]\n else:\n tip_list300 = [tip for rack in tips300 for tip in rack.rows()[0]]\n\n tip_log['tips'] = {\n p20: tip_list20,\n p300: tip_list300}\n tip_log['max'] = {\n p20: len(tip_log['tips'][p20]),\n p300: len(tip_log['tips'][p300])}\n tip_log['count'] = {p20: 0, p300: 0}\n\n def _pick_up(pip, loc=None):\n if tip_log['count'][pip] == tip_log['max'][pip] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log['count'][pip] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log['tips'][pip][tip_log['count'][pip]])\n tip_log['count'][pip] += 1\n\n \"\"\" Reduction and Alkylation \"\"\"\n samples = samples_s if p20.channels == 1 else samples_m\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, dtt, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n ctx.delay(minutes=30, msg='Incubating 30 minutes at 60C for reduction.')\n\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, caa, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n heat_func(25)\n ctx.delay(minutes=30, msg='Incubating 30 minutes at RT (25C) for \\\nalkylation.')\n\n \"\"\" Protein Binding \"\"\"\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, mag_bead_stock, s, mix_after=(2, 5),\n new_tip='never')\n p20.drop_tip()\n\n for i, (s, a) in enumerate(zip(samples, acetonitrile)):\n _pick_up(p20)\n p20.transfer(15, a, s, mix_after=(2, 20),\n new_tip='never')\n p20.drop_tip(tips20[0].wells()[i])\n\n ctx.pause('Please move plate from thermocycler to magnetic module. Resume \\\nwhen the plate has been moved.')\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes.')\n\n mag_samples = mag_samples_s if p20.channels == 1 else mag_samples_m\n for i, m in enumerate(mag_samples):\n _pick_up(p20, tips20[0].wells()[i])\n p20.transfer(43, m.bottom(1), waste, new_tip='never')\n p20.drop_tip()\n\n \"\"\" Ethanol Wash \"\"\"\n mag_samples = mag_samples_s if p300.channels == 1 else mag_samples_m\n for wash in range(2):\n magdeck.disengage()\n for i, (m, e) in enumerate(zip(mag_samples, etoh)):\n _pick_up(p300)\n p300.transfer(200, e, m, mix_after=(10, 50), new_tip='never')\n p300.drop_tip(tips300[0].wells()[i])\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes.')\n\n for i, m in enumerate(mag_samples):\n _pick_up(p300)\n p300.transfer(230, m.bottom(1), waste, new_tip='never')\n p300.drop_tip(tips300[0].wells()[i])\n\n ctx.pause('Please replace the ethanol plate (slot 6) with a fresh \\\nplate of ethanol before resuming.')\n\n \"\"\" Acetonitrile Wash \"\"\"\n magdeck.disengage()\n for i, (m, a) in enumerate(zip(mag_samples, acetonitrile)):\n _pick_up(p300, tips300[0].wells()[i])\n p300.transfer(171.5, a, m, mix_after=(10, 50), new_tip='never')\n p300.drop_tip(tips300[0].wells()[i])\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes.')\n\n for i, m in enumerate(mag_samples):\n _pick_up(p300, tips300[0].wells()[i])\n p300.transfer(230, m.bottom(1), waste, new_tip='never')\n p300.drop_tip()\n\n \"\"\" On-Bead Digestion \"\"\"\n if p300.channels == 1:\n samples = samples_s\n for i, s in enumerate(samples):\n _pick_up(p300)\n p300.transfer(35, abc[i//48][(i % 48) % 8], s, new_tip='never')\n p300.drop_tip()\n else:\n samples = samples_m\n for i, s in enumerate(samples):\n _pick_up(p300)\n p300.transfer(35, abc[i//6], s, new_tip='never')\n p300.drop_tip()\n\n if p20.channels == 1:\n samples = samples_s\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, trypsin[i % 8], s, mix_after=(2, 5),\n new_tip='never')\n p20.drop_tip()\n else:\n samples = samples_m\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, trypsin, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n heat_func(37)\n ctx.comment('Protocol complete. Please shake the plate from the magnetic \\\nmodule to resuspend the beads, and replace on the thermocycler now set at \\\n37C.')\n",
"content": "import math\n\nmetadata = {\n 'protocolName': 'Mass Spec Sample Prep',\n 'author': 'Nick <[email protected]',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [num_samples, p20_type, p300_type, p20_mount, p300_mount, plate_def,\n module_type] = get_values( # noqa: F821\n 'num_samples', 'p20_type', 'p300_type', 'p20_mount', 'p300_mount',\n 'plate_def', 'module_type')\n\n waste = ctx.load_labware('nest_1_reservoir_195ml', '1',\n 'waste container (load empty)').wells()[0].top()\n tips20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['6']]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['9']]\n magdeck = ctx.load_module('magnetic module gen2', '4')\n mag_plate = magdeck.load_labware(plate_def)\n reagent_plate = ctx.load_labware(plate_def, '5', 'reagent plate')\n etoh_plate = ctx.load_labware(plate_def, '2', 'ethanol plate')\n acetonitrile_plate = ctx.load_labware(\n plate_def, '3', 'acetonitrile plate')\n if module_type == 'thermocycler':\n temp_module = ctx.load_module('thermocycler')\n heat_func = temp_module.set_block_temperature\n else:\n tips20.insert(-1, ctx.load_labware('opentrons_96_tiprack_20ul', '8'))\n tips300.insert(\n -1, ctx.load_labware('opentrons_96_tiprack_300ul', '11'))\n temp_module = ctx.load_module('temperature module gen2', '7')\n heat_func = temp_module.set_temperature\n\n sample_plate = temp_module.load_labware(plate_def, 'sample plate')\n num_cols = math.ceil(num_samples/8)\n samples_s = sample_plate.wells()[:num_samples]\n samples_m = sample_plate.rows()[0][:num_cols]\n mag_samples_s = mag_plate.wells()[:num_samples]\n mag_samples_m = mag_plate.rows()[0][:num_cols]\n\n p20 = ctx.load_instrument(p20_type, p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument(p300_type, p300_mount,\n tip_racks=tips300)\n\n if p20.channels == 1:\n dtt = reagent_plate.columns()[0]\n caa = reagent_plate.columns()[1]\n mag_bead_stock = reagent_plate.columns()[2]\n acetonitrile = acetonitrile_plate.wells()[:num_samples]\n else:\n dtt = reagent_plate.rows()[0][0]\n caa = reagent_plate.rows()[0][1]\n mag_bead_stock = reagent_plate.rows()[0][2]\n acetonitrile = acetonitrile_plate.rows()[0][:num_cols]\n\n if p300.channels == 1:\n etoh = etoh_plate.wells()[:num_samples]\n abc = reagent_plate.columns()[3:5]\n trypsin = reagent_plate.columns()[5]\n else:\n etoh = etoh_plate.rows()[0][:num_cols]\n abc = reagent_plate.rows()[0][3:5]\n trypsin = reagent_plate.rows()[0][5]\n\n heat_func(60)\n\n tip_log = {}\n if p20.channels == 1:\n tip_list20 = [tip for rack in tips20 for tip in rack.wells()]\n else:\n tip_list20 = [tip for rack in tips20 for tip in rack.rows()[0]]\n if p300.channels == 1:\n tip_list300 = [tip for rack in tips300 for tip in rack.wells()]\n else:\n tip_list300 = [tip for rack in tips300 for tip in rack.rows()[0]]\n\n tip_log['tips'] = {\n p20: tip_list20,\n p300: tip_list300}\n tip_log['max'] = {\n p20: len(tip_log['tips'][p20]),\n p300: len(tip_log['tips'][p300])}\n tip_log['count'] = {p20: 0, p300: 0}\n\n def _pick_up(pip, loc=None):\n if tip_log['count'][pip] == tip_log['max'][pip] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log['count'][pip] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log['tips'][pip][tip_log['count'][pip]])\n tip_log['count'][pip] += 1\n\n \"\"\" Reduction and Alkylation \"\"\"\n samples = samples_s if p20.channels == 1 else samples_m\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, dtt, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n ctx.delay(minutes=30, msg='Incubating 30 minutes at 60C for reduction.')\n\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, caa, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n ctx.pause('Put plate back in temperature module.')\n heat_func(25)\n ctx.delay(minutes=30, msg='Incubating 30 minutes at RT (25C) for \\\nalkylation.')\n\n \"\"\" Protein Binding \"\"\"\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, mag_bead_stock, s, mix_after=(2, 5),\n new_tip='never')\n p20.drop_tip()\n\n for i, (s, a) in enumerate(zip(samples, acetonitrile)):\n _pick_up(p20)\n p20.transfer(15, a, s, mix_after=(2, 20),\n new_tip='never')\n p20.return_tip()\n\n ctx.pause('Please move plate from thermocycler to magnetic module. Resume \\\nwhen the plate has been moved.')\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes.')\n\n mag_samples = mag_samples_s if p20.channels == 1 else mag_samples_m\n for i, m in enumerate(mag_samples):\n _pick_up(p20, tips20[0].wells()[i])\n p20.transfer(43, m.bottom(1), waste, new_tip='never')\n p20.drop_tip()\n\n \"\"\" Ethanol Wash \"\"\"\n mag_samples = mag_samples_s if p300.channels == 1 else mag_samples_m\n for wash in range(2):\n magdeck.disengage()\n for i, (m, e) in enumerate(zip(mag_samples, etoh)):\n _pick_up(p300)\n p300.transfer(200, e, m, mix_after=(10, 50), new_tip='never')\n p300.return_tip()\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes.')\n\n for i, m in enumerate(mag_samples):\n _pick_up(p300)\n p300.transfer(230, m.bottom(1), waste, new_tip='never')\n p300.return_tip()\n\n ctx.pause('Please replace the ethanol plate (slot 6) with a fresh \\\nplate of ethanol before resuming.')\n\n \"\"\" Acetonitrile Wash \"\"\"\n magdeck.disengage()\n for i, (m, a) in enumerate(zip(mag_samples, acetonitrile)):\n _pick_up(p300, tips300[0].wells()[i])\n p300.transfer(171.5, a, m, mix_after=(10, 50), new_tip='never')\n p300.return_tip()\n\n magdeck.engage()\n ctx.delay(minutes=5, msg='Incubating on magnet for 5 minutes')\n\n for i, m in enumerate(mag_samples):\n _pick_up(p300, tips300[0].wells()[i])\n p300.transfer(230, m.bottom(1), waste, new_tip='never')\n p300.drop_tip()\n\n \"\"\" On-Bead Digestion \"\"\"\n if p300.channels == 1:\n samples = samples_s\n for i, s in enumerate(samples):\n _pick_up(p300)\n p300.transfer(35, abc[i//48][(i % 48) % 8], s, new_tip='never')\n p300.drop_tip()\n else:\n samples = samples_m\n for i, s in enumerate(samples):\n _pick_up(p300)\n p300.transfer(35, abc[i//6], s, new_tip='never')\n p300.drop_tip()\n\n if p20.channels == 1:\n samples = samples_s\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, trypsin[i % 8], s, mix_after=(2, 5),\n new_tip='never')\n p20.drop_tip()\n else:\n samples = samples_m\n for i, s in enumerate(samples):\n _pick_up(p20)\n p20.transfer(5, trypsin, s, mix_after=(2, 5), new_tip='never')\n p20.drop_tip()\n\n heat_func(37)\n ctx.pause('Put plate back in temperature module')\n ctx.comment('Protocol complete. Please shake the plate from the magnetic \\\nmodule to resuspend the beads, and replace on the thermocycler now set at \\\n37C.')\n",
"custom_labware_defs": [],
"fields": [
{
Expand All @@ -13,11 +13,11 @@
"name": "p20_type",
"options": [
{
"label": "multi",
"label": "multi (GEN2)",
"value": "p20_multi_gen2"
},
{
"label": "single",
"label": "single (GEN2)",
"value": "p20_single_gen2"
}
],
Expand All @@ -28,11 +28,15 @@
"name": "p300_type",
"options": [
{
"label": "multi",
"label": "multi (GEN2)",
"value": "p300_multi_gen2"
},
{
"label": "single",
"label": "multi (GEN1)",
"value": "p300_multi"
},
{
"label": "single (GEN2)",
"value": "p300_single_gen2"
}
],
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5 changes: 2 additions & 3 deletions protocols/2bba96/2bba96.ot2.apiv2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,11 @@
from types import MethodType
import math
import csv
from opentrons.protocols.api_support.types import APIVersion

metadata = {
'title': 'Custom Dilution From CSV',
'author': 'Steve Plonk',
'apiLevel': '2.13'
'apiLevel': '2.10'
}


Expand Down Expand Up @@ -71,7 +70,7 @@ def pause_attention(message):
class WellH(Well):
def __init__(self, well, min_height=5, comp_coeff=1.15,
current_volume=0):
super().__init__(well.parent, well._core, APIVersion(2, 13))
super().__init__(well._impl)
self.well = well
self.min_height = min_height
self.comp_coeff = comp_coeff
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2 changes: 1 addition & 1 deletion protocols/5c7384/mass_spec_sample_prep.ot2.apiv2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ def _pick_up(pip, loc=None):
p20.transfer(5, caa, s, mix_after=(2, 5), new_tip='never')
p20.drop_tip()

ctx.pause('Put plate back in temperature module')
ctx.pause('Put plate back in temperature module.')
heat_func(25)
ctx.delay(minutes=30, msg='Incubating 30 minutes at RT (25C) for \
alkylation.')
Expand Down

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