-
Notifications
You must be signed in to change notification settings - Fork 52
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
“ramifarawi”
committed
Nov 7, 2023
1 parent
ae16d27
commit 3cea57b
Showing
9 changed files
with
301 additions
and
100 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| { | ||
| "content": "import math\n\nmetadata = {\n 'protocolName': 'Normalization Using .csv File',\n 'author': 'Parrish Payne <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [input_csv, init_vol_buff, labware_pcr_plate, labware_temp_deck,\n p20_mount, p300_mount] = get_values( # noqa: F821\n \"input_csv\", \"init_vol_buff\", \"labware_pcr_plate\", \"labware_temp_deck\",\n \"p20_mount\", \"p300_mount\")\n\n # labware\n tiprack20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot,\n '20ul tiprack')\n for slot in ['1', '8']]\n tiprack300 = [\n ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', slot, '200ul tiprack')\n for slot in ['2', '9']]\n tempdeck = ctx.load_module('temperature module gen2', '3')\n dna_plate = tempdeck.load_labware(labware_temp_deck) # noqa: E501\n tube_rack = ctx.load_labware(\n 'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', '5')\n dest_plate = ctx.load_labware(labware_pcr_plate, '6', 'end-point-plate') # noqa: E501\n\n # pipettes\n p20 = ctx.load_instrument(\n 'p20_single_gen2', p20_mount, tip_racks=tiprack20)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tiprack300)\n\n # Helper Functions\n # liquid height tracking\n v_naught_buff = init_vol_buff*1000\n\n radius_sds = tube_rack.wells_by_name()['A3'].diameter/2\n\n h_naught_buff = 0.85*v_naught_buff/(math.pi*radius_sds**2)\n\n h_buff = h_naught_buff\n\n def adjust_height(volume_from_loop):\n nonlocal h_buff\n\n radius = radius_sds\n\n dh = (volume_from_loop/(math.pi*radius**2))*1.33\n\n h_buff -= dh\n\n if h_buff < 12:\n h_buff = 1\n\n def slow_withdraw(pip, well, delay_seconds=2.0):\n pip.default_speed /= 16\n if delay_seconds > 0:\n ctx.delay(seconds=delay_seconds)\n pip.move_to(well.top())\n pip.default_speed *= 16\n\n # mapping\n\n buffer = tube_rack.wells_by_name()['A3']\n\n # parse\n all_rows = [[val.strip() for val in line.split(',')]\n for line in input_csv.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # Adding buffer to the wells\n for row in all_rows:\n well = row[0]\n dest_well = dest_plate.wells_by_name()[well]\n volume = float(row[7])\n\n if volume > 20:\n if not p300.has_tip:\n p300.pick_up_tip()\n p300.aspirate(volume, buffer.bottom(h_buff))\n p300.dispense(volume, dest_well)\n\n else:\n if not p20.has_tip:\n p20.pick_up_tip()\n p20.aspirate(volume, buffer.bottom(h_buff))\n p20.dispense(volume, dest_well)\n\n adjust_height(volume)\n\n if p20.has_tip:\n p20.drop_tip()\n if p300.has_tip:\n p300.drop_tip()\n\n # Adding sample to the wells\n for row in all_rows:\n\n well = row[0]\n source_well = dna_plate.wells_by_name()[well]\n dest_well = dest_plate.wells_by_name()[well]\n\n volume = float(row[6])\n mix_reps = 2\n\n if volume > 20:\n p300.pick_up_tip()\n p300.aspirate(volume, source_well)\n p300.dispense(volume, dest_well)\n p300.mix(mix_reps, 20)\n p300.blow_out()\n p300.drop_tip()\n\n else:\n p20.pick_up_tip()\n p20.aspirate(volume, source_well)\n p20.dispense(volume, dest_well)\n p20.mix(mix_reps, 10)\n p20.blow_out()\n p20.drop_tip()\n", | ||
| "content": "# flake8: noqa\nfrom opentrons import protocol_api\nimport math\n\nmetadata = {\n 'protocolName': 'Normalization Using .csv File',\n 'author': 'Parrish Payne <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\ndef run(ctx):\n\n [input_csv, init_vol_buff, labware_pcr_plate,\n labware_dna_plate, temp_mod, temperature,\n p20_mount, p300_mount] = get_values( # noqa: F821\n \"input_csv\", \"init_vol_buff\", \"labware_pcr_plate\",\n \"labware_dna_plate\", \"temp_mod\", \"temperature\",\n \"p20_mount\", \"p300_mount\")\n\n if not 4 <= temperature <= 95:\n raise Exception(\n \"Temperature module range is between 4 and 95\u00baC\")\n\n # modules\n temp_mod = None\n if temp_mod:\n temp_mod = ctx.load_module(\"temperature module gen2\", '3')\n\n # labware\n tiprack20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot,\n '20ul tiprack')\n for slot in ['1', '8']]\n tiprack300 = [\n ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', slot, '200ul tiprack')\n for slot in ['2', '9']]\n\n dna_plate = None\n if temp_mod == True and labware_dna_plate == \"eppendorftwin.tec_96_wellplate_150ul\":\n dna_plate = temp_mod.load_labware(\"eppendorftwin.tec96_96_aluminumblock_150ul\", 'sample plate')\n\n elif temp_mod == True and labware_dna_plate == \"starlab_96_wellplate_200ul\":\n dna_plate = temp_mod.load_labware(\"starlab_96_aluminumblock_200ul\", 'sample plate')\n\n else:\n dna_plate = ctx.load_labware(labware_dna_plate, '3', 'sample plate')\n\n tube_rack = ctx.load_labware(\n 'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', '5')\n dest_plate = ctx.load_labware(labware_pcr_plate, '6', 'end-point-plate') # noqa: E501\n\n # pipettes\n p20 = ctx.load_instrument(\n 'p20_single_gen2', p20_mount, tip_racks=tiprack20)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tiprack300)\n\n # Helper Functions\n # liquid height tracking\n v_naught_buff = init_vol_buff*1000\n\n radius_sds = tube_rack.wells_by_name()['A3'].diameter/2\n\n h_naught_buff = 0.85*v_naught_buff/(math.pi*radius_sds**2)\n\n h_buff = h_naught_buff\n\n def adjust_height(volume_from_loop):\n nonlocal h_buff\n\n radius = radius_sds\n\n dh = (volume_from_loop/(math.pi*radius**2))*1.33\n\n h_buff -= dh\n\n if h_buff < 12:\n h_buff = 1\n\n def slow_withdraw(pip, well, delay_seconds=2.0):\n pip.default_speed /= 16\n if delay_seconds > 0:\n ctx.delay(seconds=delay_seconds)\n pip.move_to(well.top())\n pip.default_speed *= 16\n\n # Set temperature module temperature\n if temp_mod:\n ctx.comment(\"\\n\\nSetting temperature module to {} \u00baC\\n\".\n format(temperature))\n temp_mod.set_temperature(temperature)\n\n # mapping\n buffer = tube_rack.wells_by_name()['A3']\n\n # parse\n all_rows = [[val.strip() for val in line.split(',')]\n for line in input_csv.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # Adding buffer to the wells\n for row in all_rows:\n well = row[0]\n dest_well = dest_plate.wells_by_name()[well]\n volume = float(row[7])\n\n if volume > 0:\n if volume > 20:\n if not p300.has_tip:\n p300.pick_up_tip()\n p300.aspirate(volume, buffer.bottom(h_buff))\n p300.dispense(volume, dest_well)\n\n else:\n if not p20.has_tip:\n p20.pick_up_tip()\n p20.aspirate(volume, buffer.bottom(h_buff))\n p20.dispense(volume, dest_well)\n\n adjust_height(volume)\n\n if p20.has_tip:\n p20.drop_tip()\n if p300.has_tip:\n p300.drop_tip()\n\n # Adding sample to the wells\n for row in all_rows:\n\n well = row[0]\n source_well = dna_plate.wells_by_name()[well]\n dest_well = dest_plate.wells_by_name()[well]\n\n volume = float(row[6])\n mix_reps = 2\n tip_height = 0.5\n\n if volume > 0:\n if volume > 20:\n p300.pick_up_tip()\n p300.aspirate(volume, source_well.bottom(tip_height))\n p300.dispense(volume, dest_well)\n p300.mix(mix_reps, 20)\n p300.blow_out()\n p300.drop_tip()\n\n else:\n p20.pick_up_tip()\n p20.aspirate(volume, source_well.bottom(tip_height))\n p20.dispense(volume, dest_well)\n p20.mix(mix_reps, 10)\n p20.blow_out()\n p20.drop_tip()\n", | ||
| "custom_labware_defs": [ | ||
| { | ||
| "brand": { | ||
|
|
@@ -4546,7 +4546,7 @@ | |
| }, | ||
| { | ||
| "label": "Labware on the Temperature Module", | ||
| "name": "labware_temp_deck", | ||
| "name": "labware_dna_plate", | ||
| "options": [ | ||
| { | ||
| "label": "eppendorftwin.tec96_96_aluminumblock_150ul", | ||
|
|
@@ -4559,6 +4559,27 @@ | |
| ], | ||
| "type": "dropDown" | ||
| }, | ||
| { | ||
| "label": "Use temperature module on slot 3?", | ||
| "name": "temp_mod", | ||
| "options": [ | ||
| { | ||
| "label": "Use temperature module", | ||
| "value": true | ||
| }, | ||
| { | ||
| "label": "Do not use temperature module", | ||
| "value": false | ||
| } | ||
| ], | ||
| "type": "dropDown" | ||
| }, | ||
| { | ||
| "default": 4, | ||
| "label": "Temperature module temperature (4-95C)", | ||
| "name": "temperature", | ||
| "type": "int" | ||
| }, | ||
| { | ||
| "label": "P20 single-channel Mount", | ||
| "name": "p20_mount", | ||
|
|
@@ -4614,7 +4635,7 @@ | |
| "type": "opentrons_96_filtertiprack_200ul" | ||
| }, | ||
| { | ||
| "name": "Eppendorf Twin.Tec 96 96 Aluminum Block 150 \u00b5L on Temperature Module GEN2 on 3", | ||
| "name": "sample plate on 3", | ||
| "share": false, | ||
| "slot": "3", | ||
| "type": "eppendorftwin.tec96_96_aluminumblock_150ul" | ||
|
|
@@ -4656,12 +4677,5 @@ | |
| "protocolName": "Normalization Using .csv File", | ||
| "source": "Custom Protocol Request" | ||
| }, | ||
| "modules": [ | ||
| { | ||
| "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Eppendorf Twin.Tec 96 96 Aluminum Block 150 \u00b5L on Temperature Module GEN2 on 3", | ||
| "share": false, | ||
| "slot": "3", | ||
| "type": "tempdeck" | ||
| } | ||
| ] | ||
| "modules": [] | ||
| } | ||
Oops, something went wrong.