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Merge pull request #5051 from Opentrons/0f7910-add-csv
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fix(protocols/0f7910): add transfer volume to csv
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@ramifarawi
ramifarawi authored Mar 6, 2024
2 parents 1fba176 + 2060173 commit b4f7b24
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Showing 6 changed files with 18 additions and 23 deletions.
2 changes: 1 addition & 1 deletion data/data/fields.csv
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Expand Up @@ -1554,7 +1554,7 @@ transfer2,1
transfer_csv,21
transfer_scheme,2
transfer_to_storage,1
transfer_vol,10
transfer_vol,9
transfer_volume,3
transfercsv,2
transfervol,1
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10 changes: 2 additions & 8 deletions protoBuilds/0f7910/0f7910.ot2.apiv2.py.json
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@@ -1,9 +1,9 @@
{
"content": "from opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'Plate Filling with CSV Import',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [csv_samp,\n source_format,\n dest_format,\n transfer_vol,\n starting_tip,\n p300_mount,\n p20_mount] = get_values( # noqa: F821\n \"csv_samp\",\n \"source_format\",\n \"dest_format\",\n \"transfer_vol\",\n \"starting_tip\",\n \"p300_mount\",\n \"p20_mount\")\n\n # mapping\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n unique_list = []\n for row in csv_lines:\n source_plate_slot = int(row[1])\n if source_plate_slot not in unique_list:\n unique_list.append(source_plate_slot)\n\n starting_tip -= starting_tip\n\n # labware\n source_plates = [ctx.load_labware(\n 'corning_96_wellplate_360ul_flat'\n if source_format == \"96\"\n else \"corning_384_wellplate_112ul_flat\", slot)\n for slot in unique_list]\n source_plates = source_plates\n\n dest_plate = ctx.load_labware(\n 'corning_96_wellplate_360ul_flat'\n if dest_format == \"96\"\n else \"corning_384_wellplate_112ul_flat\", 2\n if dest_format == \"384\"\n else 1)\n\n if transfer_vol > 20:\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [10]]\n else:\n tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in [11]]\n\n # pipettes\n if transfer_vol > 20:\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n else:\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tips20)\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks.\")\n pip.reset_tipracks()\n pick_up(pip)\n\n # protocol\n pip = p20 if transfer_vol <= 20 else p300\n pip.flow_rate.aspirate = 1\n pip.flow_rate.dispense = 2\n if transfer_vol > 20:\n pip.starting_tip = tips300[0].wells()[starting_tip]\n else:\n pip.starting_tip = tips20[0].wells()[starting_tip]\n for row in csv_lines:\n source_plate_slot = int(row[1])\n source_well_name = row[2]\n dest_well_name = row[4]\n\n source = ctx.loaded_labwares[source_plate_slot].wells_by_name()[source_well_name] # noqa: E501\n dest = dest_plate.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.transfer(transfer_vol, source.bottom(z=0.2), dest, new_tip='never',\n blow_out=True, blowout_location='destination well')\n pip.drop_tip()\n ctx.comment('\\n\\n')\n",
"content": "from opentrons import protocol_api\n\n\nmetadata = {\n 'protocolName': 'Plate Filling with CSV Import',\n 'author': 'Rami Farawi <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [csv_samp,\n source_format,\n dest_format,\n starting_tip,\n p300_mount,\n p20_mount] = get_values( # noqa: F821\n \"csv_samp\",\n \"source_format\",\n \"dest_format\",\n \"starting_tip\",\n \"p300_mount\",\n \"p20_mount\")\n\n # mapping\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n unique_list = []\n for row in csv_lines:\n source_plate_slot = int(row[1])\n if source_plate_slot not in unique_list:\n unique_list.append(source_plate_slot)\n\n starting_tip -= starting_tip\n\n # labware\n source_plates = [ctx.load_labware(\n 'corning_96_wellplate_360ul_flat'\n if source_format == \"96\"\n else \"corning_384_wellplate_112ul_flat\", slot)\n for slot in unique_list]\n source_plates = source_plates\n\n dest_plate = ctx.load_labware(\n 'corning_96_wellplate_360ul_flat'\n if dest_format == \"96\"\n else \"corning_384_wellplate_112ul_flat\", 2\n if dest_format == \"384\"\n else 1)\n transfer_vol = float(csv_lines[0][5])\n\n if transfer_vol > 20:\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [10]]\n else:\n tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in [11]]\n\n # pipettes\n if transfer_vol > 20:\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n else:\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tips20)\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks.\")\n pip.reset_tipracks()\n pick_up(pip)\n\n # protocol\n\n pip = p20 if transfer_vol <= 20 else p300\n pip.flow_rate.aspirate = 1\n pip.flow_rate.dispense = 2\n\n if transfer_vol > 20:\n pip.starting_tip = tips300[0].wells()[starting_tip]\n else:\n pip.starting_tip = tips20[0].wells()[starting_tip]\n\n for row in csv_lines:\n source_plate_slot = int(row[1])\n source_well_name = row[2]\n dest_well_name = row[4]\n\n source = ctx.loaded_labwares[source_plate_slot].wells_by_name()[source_well_name] # noqa: E501\n dest = dest_plate.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.mix(1, transfer_vol, source.bottom(z=0.2))\n pip.aspirate(transfer_vol, source.bottom(z=0.2))\n pip.dispense(transfer_vol, dest)\n pip.move_to(dest.top(z=-3))\n ctx.delay(seconds=1)\n pip.blow_out()\n pip.drop_tip()\n ctx.comment('\\n\\n')\n",
"custom_labware_defs": [],
"fields": [
{
"default": "Source plate Barcode,Source plate location,Source well,Destination plate Barcode,Destination well\nDDDD,3,C1,ABCD,A1\nEEEE,3,A1,BBBD,B1",
"default": "Source plate Barcode,Source plate location,Source well,Destination plate Barcode,Destination well\nDDDD,3,C1,ABCD,A1,12.4\nEEEE,3,A1,BBBD,B1,12.4",
"label": ".CSV File",
"name": "csv_samp",
"type": "textFile"
Expand Down Expand Up @@ -38,12 +38,6 @@
],
"type": "dropDown"
},
{
"default": 12,
"label": "Transfer Volume",
"name": "transfer_vol",
"type": "int"
},
{
"default": 1,
"label": "Starting Tip in Tip Rack (1-96, by column)",
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4 changes: 2 additions & 2 deletions protoBuilds/0f7910/README.json
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Expand Up @@ -6,14 +6,14 @@
]
},
"deck-setup": "",
"description": "Select the format for the source and destination plates. See diagram below. If a 384 plate is selected for destination plate, it should always be in slot 2. If a 96 plate is selected for destination, it should always be in slot 1. Source plates always start from slot 3 to 9, and tip racks are always the same. You can select which tip the protocol will start on in the fields below. If the global transfer volume is over 20ul, then the P300 will be used. If the transfer volume is 20 or less, the P20 will be used. A value of \"8\" for the starting position of the tip would mean to start H1 of the tip rack, and a value of 10 would mean to start at B2 of the tip rack, since it iterates down by column. The csv should be formatted as such in the header:\nSource plate barcode, Source plate slot (3-9), Source well (A1, B1, etc.), Destination plate barcode, Destination well",
"description": "Select the format for the source and destination plates. See diagram below. If a 384 plate is selected for destination plate, it should always be in slot 2. If a 96 plate is selected for destination, it should always be in slot 1. Source plates always start from slot 3 to 9, and tip racks are always the same. You can select which tip the protocol will start on in the fields below. If the global transfer volume is over 20ul, then the P300 will be used. If the transfer volume is 20 or less, the P20 will be used. A value of \"8\" for the starting position of the tip would mean to start H1 of the tip rack, and a value of 10 would mean to start at B2 of the tip rack, since it iterates down by column. The csv should be formatted as such in the header:\nSource plate barcode, Source plate slot (3-9), Source well, Dest plate barcode, Dest well, Transfer Vol (ul)",
"internal": "0f7910",
"labware": "\nCorning 384 Well Plate 112 \u00b5L Flat\nCorning 96 Well Plate 360 \u00b5L\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\n",
"markdown": {
"author": "[Opentrons](https://opentrons.com/)\n\n\n\n\n",
"categories": "* Sample Prep\n\t* Plate Filling\n\n\n",
"deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0f7910/Screen+Shot+2022-12-20+at+10.41.56+AM.png)\n\n\n",
"description": "Select the format for the source and destination plates. See diagram below. If a 384 plate is selected for destination plate, it should always be in slot 2. If a 96 plate is selected for destination, it should always be in slot 1. Source plates always start from slot 3 to 9, and tip racks are always the same. You can select which tip the protocol will start on in the fields below. If the global transfer volume is over 20ul, then the P300 will be used. If the transfer volume is 20 or less, the P20 will be used. A value of \"8\" for the starting position of the tip would mean to start H1 of the tip rack, and a value of 10 would mean to start at B2 of the tip rack, since it iterates down by column. The csv should be formatted as such in the header:\n\n```\nSource plate barcode, Source plate slot (3-9), Source well (A1, B1, etc.), Destination plate barcode, Destination well\n```\n\n\n",
"description": "Select the format for the source and destination plates. See diagram below. If a 384 plate is selected for destination plate, it should always be in slot 2. If a 96 plate is selected for destination, it should always be in slot 1. Source plates always start from slot 3 to 9, and tip racks are always the same. You can select which tip the protocol will start on in the fields below. If the global transfer volume is over 20ul, then the P300 will be used. If the transfer volume is 20 or less, the P20 will be used. A value of \"8\" for the starting position of the tip would mean to start H1 of the tip rack, and a value of 10 would mean to start at B2 of the tip rack, since it iterates down by column. The csv should be formatted as such in the header:\n\n```\nSource plate barcode, Source plate slot (3-9), Source well, Dest plate barcode, Dest well, Transfer Vol (ul)\n```\n\n\n",
"internal": "0f7910\n",
"labware": "* Corning 384 Well Plate 112 \u00b5L Flat\n* Corning 96 Well Plate 360 \u00b5L\n* [Opentrons 96 Tip Rack 20 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n\n\n",
"notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n\n",
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15 changes: 11 additions & 4 deletions protocols/0f7910/0f7910.ot2.apiv2.py
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@@ -1,5 +1,6 @@
from opentrons import protocol_api


metadata = {
'protocolName': 'Plate Filling with CSV Import',
'author': 'Rami Farawi <[email protected]>',
Expand All @@ -13,14 +14,12 @@ def run(ctx):
[csv_samp,
source_format,
dest_format,
transfer_vol,
starting_tip,
p300_mount,
p20_mount] = get_values( # noqa: F821
"csv_samp",
"source_format",
"dest_format",
"transfer_vol",
"starting_tip",
"p300_mount",
"p20_mount")
Expand Down Expand Up @@ -52,6 +51,7 @@ def run(ctx):
else "corning_384_wellplate_112ul_flat", 2
if dest_format == "384"
else 1)
transfer_vol = float(csv_lines[0][5])

if transfer_vol > 20:
tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)
Expand All @@ -78,13 +78,16 @@ def pick_up(pip):
pick_up(pip)

# protocol

pip = p20 if transfer_vol <= 20 else p300
pip.flow_rate.aspirate = 1
pip.flow_rate.dispense = 2

if transfer_vol > 20:
pip.starting_tip = tips300[0].wells()[starting_tip]
else:
pip.starting_tip = tips20[0].wells()[starting_tip]

for row in csv_lines:
source_plate_slot = int(row[1])
source_well_name = row[2]
Expand All @@ -94,7 +97,11 @@ def pick_up(pip):
dest = dest_plate.wells_by_name()[dest_well_name]

pick_up(pip)
pip.transfer(transfer_vol, source.bottom(z=0.2), dest, new_tip='never',
blow_out=True, blowout_location='destination well')
pip.mix(1, transfer_vol, source.bottom(z=0.2))
pip.aspirate(transfer_vol, source.bottom(z=0.2))
pip.dispense(transfer_vol, dest)
pip.move_to(dest.top(z=-3))
ctx.delay(seconds=1)
pip.blow_out()
pip.drop_tip()
ctx.comment('\n\n')
2 changes: 1 addition & 1 deletion protocols/0f7910/README.md
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Expand Up @@ -16,7 +16,7 @@
Select the format for the source and destination plates. See diagram below. If a 384 plate is selected for destination plate, it should always be in slot 2. If a 96 plate is selected for destination, it should always be in slot 1. Source plates always start from slot 3 to 9, and tip racks are always the same. You can select which tip the protocol will start on in the fields below. If the global transfer volume is over 20ul, then the P300 will be used. If the transfer volume is 20 or less, the P20 will be used. A value of "8" for the starting position of the tip would mean to start H1 of the tip rack, and a value of 10 would mean to start at B2 of the tip rack, since it iterates down by column. The csv should be formatted as such in the header:

```
Source plate barcode, Source plate slot (3-9), Source well (A1, B1, etc.), Destination plate barcode, Destination well
Source plate barcode, Source plate slot (3-9), Source well, Dest plate barcode, Dest well, Transfer Vol (ul)
```


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8 changes: 1 addition & 7 deletions protocols/0f7910/fields.json
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Expand Up @@ -3,7 +3,7 @@
"type": "textFile",
"label": ".CSV File",
"name": "csv_samp",
"default": "Source plate Barcode,Source plate location,Source well,Destination plate Barcode,Destination well\nDDDD,3,C1,ABCD,A1\nEEEE,3,A1,BBBD,B1"
"default": "Source plate Barcode,Source plate location,Source well,Destination plate Barcode,Destination well\nDDDD,3,C1,ABCD,A1,12.4\nEEEE,3,A1,BBBD,B1,12.4"
},
{
"type": "dropDown",
Expand All @@ -23,12 +23,6 @@
{"label": "384", "value": "384"}
]
},
{
"type": "float",
"label": "Transfer Volume (ul)",
"name": "transfer_vol",
"default": 12.0
},
{
"type": "int",
"label": "Starting Tip in Tip Rack (1-96, by column)",
Expand Down

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