From 75d8d22bde7f625458b38d91018b12e5cfd548ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Thu, 15 Feb 2024 12:18:15 -0500 Subject: [PATCH] fix --- data/data/fields.csv | 6 +- protoBuilds/04711e/04711e.ot2.apiv2.py.json | 1559 +++++++++++++++++ protoBuilds/04711e/README.json | 30 + protoBuilds/04711e/metadata.json | 20 + protocols/04711e/04711e.ot2.apiv2.py | 82 + protocols/04711e/README.md | 55 + protocols/04711e/fields.json | 29 + .../labware/opentrons_24_tuberack_2000ul.json | 322 ++++ .../labware/pcrplate_96_wellplate_200ul.json | 1127 ++++++++++++ 9 files changed, 3227 insertions(+), 3 deletions(-) create mode 100644 protoBuilds/04711e/04711e.ot2.apiv2.py.json create mode 100644 protoBuilds/04711e/README.json create mode 100644 protoBuilds/04711e/metadata.json create mode 100644 protocols/04711e/04711e.ot2.apiv2.py create mode 100644 protocols/04711e/README.md create mode 100644 protocols/04711e/fields.json create mode 100644 protocols/04711e/labware/opentrons_24_tuberack_2000ul.json create mode 100644 protocols/04711e/labware/pcrplate_96_wellplate_200ul.json diff --git a/data/data/fields.csv b/data/data/fields.csv index 5d0061a5b..39ef167da 100644 --- a/data/data/fields.csv +++ b/data/data/fields.csv @@ -728,7 +728,7 @@ lysis,1 lysis_vol,1 m10_mount,2 m1k,1 -m20_mount,81 +m20_mount,82 m300_mount,112 m300_type,2 m_mount,1 @@ -913,7 +913,7 @@ num_rounds,1 num_row,1 num_rows_a,1 num_rows_b,1 -num_samp,74 +num_samp,75 num_samp_p1,1 num_samp_p2,1 num_samp_plate1,1 @@ -1006,7 +1006,7 @@ p2num,1 p300_gen,1 p300_mixing_height,1 p300_mnt,3 -p300_mount,158 +p300_mount,159 p300_mount_1,1 p300_multi_mount,7 p300_rate,1 diff --git a/protoBuilds/04711e/04711e.ot2.apiv2.py.json b/protoBuilds/04711e/04711e.ot2.apiv2.py.json new file mode 100644 index 000000000..0bbd8f420 --- /dev/null +++ b/protoBuilds/04711e/04711e.ot2.apiv2.py.json @@ -0,0 +1,1559 @@ +{ + "content": "# flake8: noqa\n\nimport math\n\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_samp,\n p300_mount, m20_mount] = get_values( # noqa: F821\n \"num_samp\", \"p300_mount\", \"m20_mount\")\n\n # num_samp = 16\n # p300_mount = 'left'\n # m20_mount = 'right'\n\n # labware\n tuberack = ctx.load_labware('opentrons_24_tuberack_2000ul', 4)\n\n source_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 1)\n middle_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 2)\n final_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 3)\n\n tip300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [6]]\n tip20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in [10, 11]]\n\n # pipettes\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tip300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount,\n tip_racks=tip20)\n\n # mapping\n mmx = tuberack['A1']\n primer = tuberack['A2']\n final_mmx = tuberack['A3']\n num_col = math.ceil(num_samp/8)\n\n # protocol\n ctx.comment('\\n---------------MAKING MASTERMIX----------------\\n\\n')\n mmx_vol = 9.1\n primer_vol = 5.57\n\n p300.pick_up_tip()\n p300.transfer(mmx_vol*num_samp*1.15, mmx, final_mmx, new_tip='never')\n p300.drop_tip()\n\n total_vol = num_samp*(primer_vol+mmx_vol)\n p300.pick_up_tip()\n p300.transfer(primer_vol*num_samp*1.15, primer, final_mmx, new_tip='never')\n p300.mix(20, total_vol if total_vol < 300 else 300, final_mmx)\n p300.drop_tip()\n\n vol_per_col_well = (mmx_vol+primer_vol)*12*1.1\n p300.pick_up_tip()\n for well in middle_plate.columns()[0]:\n p300.aspirate(vol_per_col_well, final_mmx)\n p300.dispense(vol_per_col_well, well)\n p300.drop_tip()\n\n ctx.comment('\\n---------------DISTRIBUTING MASTERMIX----------------\\n\\n')\n m20.pick_up_tip()\n for col in final_plate.rows()[0][:num_col]:\n m20.aspirate(14.7, middle_plate.rows()[0][0])\n m20.dispense(14.7, col)\n m20.drop_tip()\n\n ctx.comment('\\n---------------DISTRIBUTING SAMPLE----------------\\n\\n')\n for s, d in zip(source_plate.rows()[0][:num_col], final_plate.rows()[0]):\n m20.pick_up_tip()\n m20.aspirate(4, s)\n m20.dispense(4, d)\n m20.mix(5, 15, d)\n m20.drop_tip()\n", + "custom_labware_defs": [ + { + "brand": { + "brand": "pcr plate", + "brandId": [ + "1234" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 14.5 + }, + "groups": [ + { + "metadata": { + "wellBottomShape": "v" + }, + "wells": [ + "A1", + "B1", + "C1", + "D1", + "E1", + "F1", + "G1", + "H1", + "A2", + "B2", + "C2", + "D2", + "E2", + "F2", + "G2", + "H2", + "A3", + "B3", + "C3", + "D3", + "E3", + "F3", + "G3", + "H3", + "A4", + "B4", + "C4", + "D4", + "E4", + "F4", + "G4", + "H4", + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5", + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6", + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7", + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8", + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9", + "A10", + "B10", + "C10", + "D10", + "E10", + "F10", + "G10", + "H10", + "A11", + "B11", + "C11", + "D11", + "E11", + "F11", + "G11", + "H11", + "A12", + "B12", + "C12", + "D12", + "E12", + "F12", + "G12", + "H12" + ] + } + ], + "metadata": { + "displayCategory": "wellPlate", + "displayName": "Pcr Plate 96 Well Plate 200 \u00b5L", + "displayVolumeUnits": "\u00b5L", + "tags": [] + }, + "namespace": "custom_beta", + "ordering": [ + [ + "A1", + "B1", + "C1", + "D1", + "E1", + "F1", + "G1", + "H1" + ], + [ + "A2", + "B2", + "C2", + "D2", + "E2", + "F2", + "G2", + "H2" + ], + [ + "A3", + "B3", + "C3", + "D3", + "E3", + "F3", + "G3", + "H3" + ], + [ + "A4", + "B4", + "C4", + "D4", + "E4", + "F4", + "G4", + "H4" + ], + [ + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5" + ], + [ + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6" + ], + [ + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7" + ], + [ + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8" + ], + [ + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9" + ], + [ + "A10", + "B10", + "C10", + "D10", + "E10", + "F10", + "G10", + "H10" + ], + [ + "A11", + "B11", + "C11", + "D11", + "E11", + "F11", + "G11", + "H11" + ], + [ + "A12", + "B12", + "C12", + "D12", + "E12", + "F12", + "G12", + "H12" + ] + ], + "parameters": { + "format": "irregular", + "isMagneticModuleCompatible": false, + "isTiprack": false, + "loadName": "pcrplate_96_wellplate_200ul", + "quirks": [] + }, + "schemaVersion": 2, + "version": 1, + "wells": { + "A1": { + "depth": 12, + "diameter": 8, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 14.38, + "y": 74.24, + "z": 2.5 + }, + "A10": { + "depth": 12, + "diameter": 8, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 95.38, + "y": 74.24, + "z": 2.5 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+ "label": "Left", + "value": "left" + } + ], + "type": "dropDown" + } + ], + "instruments": [ + { + "mount": "left", + "name": "p300_single_gen2" + }, + { + "mount": "right", + "name": "p20_multi_gen2" + } + ], + "labware": [ + { + "name": "Pcr Plate 96 Well Plate 200 \u00b5L on 1", + "share": false, + "slot": "1", + "type": "pcrplate_96_wellplate_200ul" + }, + { + "name": "Pcr Plate 96 Well Plate 200 \u00b5L on 2", + "share": false, + "slot": "2", + "type": "pcrplate_96_wellplate_200ul" + }, + { + "name": "Pcr Plate 96 Well Plate 200 \u00b5L on 3", + "share": false, + "slot": "3", + "type": "pcrplate_96_wellplate_200ul" + }, + { + "name": "Opentrons 24 Tube Rack with starstedt 2 mL on 4", + "share": false, + "slot": "4", + "type": "opentrons_24_tuberack_2000ul" + }, + { + "name": "Opentrons 96 Tip Rack 300 \u00b5L on 6", + "share": false, + "slot": "6", + "type": "opentrons_96_tiprack_300ul" + }, + { + "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 10", + "share": false, + "slot": "10", + "type": "opentrons_96_filtertiprack_20ul" + }, + { + "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 11", + "share": false, + "slot": "11", + "type": "opentrons_96_filtertiprack_20ul" + }, + { + "name": "Opentrons Fixed Trash on 12", + "share": false, + "slot": "12", + "type": "opentrons_1_trash_1100ml_fixed" + } + ], + "metadata": { + "apiLevel": "2.13", + "author": "Rami Farawi ", + "protocolName": "PCR Prep", + "source": "Custom Protocol Request" + }, + "modules": [] +} \ No newline at end of file diff --git a/protoBuilds/04711e/README.json b/protoBuilds/04711e/README.json new file mode 100644 index 000000000..044e06919 --- /dev/null +++ b/protoBuilds/04711e/README.json @@ -0,0 +1,30 @@ +{ + "author": "Opentrons", + "categories": { + "PCR": [ + "PCR Prep" + ] + }, + "deck-setup": "", + "description": "This protocol creates mastermix according to the number of samples, then distributes the resultant mastermix to a final pcr plate along with sample. For detailed protocol steps, please see below.", + "internal": "04711e", + "labware": "\nPcr Plate 96 Well Plate 200 \u00b5L\nOpentrons 24 Tube Rack with starstedt 2 mL\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", + "markdown": { + "author": "[Opentrons](https://opentrons.com/)\n\n\n", + "categories": "* PCR\n\t* PCR Prep\n\n\n", + "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/04711e/Screen+Shot+2024-02-15+at+12.10.56+PM.png)\n\n\n", + "description": "This protocol creates mastermix according to the number of samples, then distributes the resultant mastermix to a final pcr plate along with sample. For detailed protocol steps, please see below.\n\n\n", + "internal": "04711e\n", + "labware": "* Pcr Plate 96 Well Plate 200 \u00b5L\n* Opentrons 24 Tube Rack with starstedt 2 mL\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* Opentrons 96 Filter Tip Rack 20 \u00b5L\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", + "pipettes": "* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n\n\n", + "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit \"Run\".\n\n\n", + "protocol-steps": "1. Mastermix is made in empty tube in tuberack according to the number of samples.\n2. Mastermix is distributed to the first column of the middle plate on slot 2 (single channel pipette).\n3. Mastermix is distributed to final plate (multi-channel pipette).\n4. Sample is added to final plate.\n\n\n", + "title": "PCR Prep" + }, + "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", + "pipettes": "\nOpentrons P20 8 Channel Electronic Pipette (GEN2)\nOpentrons P300 Single Channel Electronic Pipette (GEN2)\n", + "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit \"Run\".\n", + "protocol-steps": "\nMastermix is made in empty tube in tuberack according to the number of samples.\nMastermix is distributed to the first column of the middle plate on slot 2 (single channel pipette).\nMastermix is distributed to final plate (multi-channel pipette).\nSample is added to final plate.\n", + "title": "PCR Prep" +} \ No newline at end of file diff --git a/protoBuilds/04711e/metadata.json b/protoBuilds/04711e/metadata.json new file mode 100644 index 000000000..3de7c26be --- /dev/null +++ b/protoBuilds/04711e/metadata.json @@ -0,0 +1,20 @@ +{ + "files": { + "OT 1 protocol": [], + "OT 2 protocol": [ + "04711e.ot2.apiv2.py" + ], + "description": [ + "README.md" + ] + }, + "flags": { + "embedded-app": false, + "feature": false, + "hide-from-search": false, + "skip-tests": false + }, + "path": "protocols/04711e", + "slug": "04711e", + "status": "ok" +} \ No newline at end of file diff --git a/protocols/04711e/04711e.ot2.apiv2.py b/protocols/04711e/04711e.ot2.apiv2.py new file mode 100644 index 000000000..4ff15eab4 --- /dev/null +++ b/protocols/04711e/04711e.ot2.apiv2.py @@ -0,0 +1,82 @@ +# flake8: noqa + +import math + +metadata = { + 'protocolName': 'PCR Prep', + 'author': 'Rami Farawi ', + 'source': 'Custom Protocol Request', + 'apiLevel': '2.13' +} + + +def run(ctx): + + [num_samp, + p300_mount, m20_mount] = get_values( # noqa: F821 + "num_samp", "p300_mount", "m20_mount") + + # num_samp = 16 + # p300_mount = 'left' + # m20_mount = 'right' + + # labware + tuberack = ctx.load_labware('opentrons_24_tuberack_2000ul', 4) + + source_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 1) + middle_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 2) + final_plate = ctx.load_labware('pcrplate_96_wellplate_200ul', 3) + + tip300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) + for slot in [6]] + tip20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot) + for slot in [10, 11]] + + # pipettes + p300 = ctx.load_instrument('p300_single_gen2', p300_mount, + tip_racks=tip300) + m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, + tip_racks=tip20) + + # mapping + mmx = tuberack['A1'] + primer = tuberack['A2'] + final_mmx = tuberack['A3'] + num_col = math.ceil(num_samp/8) + + # protocol + ctx.comment('\n---------------MAKING MASTERMIX----------------\n\n') + mmx_vol = 9.1 + primer_vol = 5.57 + + p300.pick_up_tip() + p300.transfer(mmx_vol*num_samp*1.15, mmx, final_mmx, new_tip='never') + p300.drop_tip() + + total_vol = num_samp*(primer_vol+mmx_vol) + p300.pick_up_tip() + p300.transfer(primer_vol*num_samp*1.15, primer, final_mmx, new_tip='never') + p300.mix(20, total_vol if total_vol < 300 else 300, final_mmx) + p300.drop_tip() + + vol_per_col_well = (mmx_vol+primer_vol)*12*1.1 + p300.pick_up_tip() + for well in middle_plate.columns()[0]: + p300.aspirate(vol_per_col_well, final_mmx) + p300.dispense(vol_per_col_well, well) + p300.drop_tip() + + ctx.comment('\n---------------DISTRIBUTING MASTERMIX----------------\n\n') + m20.pick_up_tip() + for col in final_plate.rows()[0][:num_col]: + m20.aspirate(14.7, middle_plate.rows()[0][0]) + m20.dispense(14.7, col) + m20.drop_tip() + + ctx.comment('\n---------------DISTRIBUTING SAMPLE----------------\n\n') + for s, d in zip(source_plate.rows()[0][:num_col], final_plate.rows()[0]): + m20.pick_up_tip() + m20.aspirate(4, s) + m20.dispense(4, d) + m20.mix(5, 15, d) + m20.drop_tip() diff --git a/protocols/04711e/README.md b/protocols/04711e/README.md new file mode 100644 index 000000000..516372d86 --- /dev/null +++ b/protocols/04711e/README.md @@ -0,0 +1,55 @@ +# PCR Prep + + +### Author +[Opentrons](https://opentrons.com/) + + +## Categories +* PCR + * PCR Prep + + +## Description +This protocol creates mastermix according to the number of samples, then distributes the resultant mastermix to a final pcr plate along with sample. For detailed protocol steps, please see below. + + +### Labware +* Pcr Plate 96 Well Plate 200 µL +* Opentrons 24 Tube Rack with starstedt 2 mL +* [Opentrons 96 Tip Rack 300 µL](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips) +* Opentrons 96 Filter Tip Rack 20 µL + + +### Pipettes +* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) +* [Opentrons P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/) + + +### Deck Setup +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/04711e/Screen+Shot+2024-02-15+at+12.10.56+PM.png) + + +### Protocol Steps +1. Mastermix is made in empty tube in tuberack according to the number of samples. +2. Mastermix is distributed to the first column of the middle plate on slot 2 (single channel pipette). +3. Mastermix is distributed to final plate (multi-channel pipette). +4. Sample is added to final plate. + + +### Process +1. Input your protocol parameters above. +2. Download your protocol and unzip if needed. +3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed. +4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab. +5. Set up your deck according to the deck map. +6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2). +7. Hit "Run". + + +### Additional 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/). + + +###### Internal +04711e diff --git a/protocols/04711e/fields.json b/protocols/04711e/fields.json new file mode 100644 index 000000000..512d5a6ab --- /dev/null +++ b/protocols/04711e/fields.json @@ -0,0 +1,29 @@ + + + +[ + { + "type": "int", + "label": "Number of Samples", + "name": "num_samp", + "default": 96 + }, + { + "type": "dropDown", + "label": "P300 Single-Channel Mount", + "name": "p300_mount", + "options": [ + {"label": "Left", "value": "left"}, + {"label": "Right", "value": "right"} + ] + }, + { + "type": "dropDown", + "label": "P20 Multi-Channel Mount", + "name": "m20_mount", + "options": [ + {"label": "Right", "value": "right"}, + {"label": "Left", "value": "left"} + ] + } +] diff --git a/protocols/04711e/labware/opentrons_24_tuberack_2000ul.json b/protocols/04711e/labware/opentrons_24_tuberack_2000ul.json new file mode 100644 index 000000000..dab43f2f5 --- /dev/null +++ b/protocols/04711e/labware/opentrons_24_tuberack_2000ul.json @@ -0,0 +1,322 @@ +{ + "ordering": [ + [ + "A1", + "B1", + "C1", + "D1" + ], + [ + "A2", + "B2", + "C2", + "D2" + ], + [ + "A3", + "B3", + "C3", + "D3" + ], + [ + "A4", + "B4", + "C4", + "D4" + ], + [ + "A5", + "B5", + "C5", + "D5" + ], + [ + "A6", + "B6", + "C6", + "D6" + ] + ], + "brand": { + "brand": "Opentrons", + "brandId": [] + }, + "metadata": { + "displayName": "Opentrons 24 Tube Rack with starstedt 2 mL", + "displayCategory": "tubeRack", + "displayVolumeUnits": "µL", + "tags": [] + }, + "dimensions": { + "xDimension": 127.75, + "yDimension": 85.5, + "zDimension": 84 + }, + "wells": { + "A1": { + "depth": 44, + "totalLiquidVolume": 2000, + "shape": "circular", + "diameter": 10.8, + "x": 18.21, + "y": 75.43, + "z": 40 + }, + "B1": { + "depth": 44, + "totalLiquidVolume": 2000, + "shape": 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