From b1181e6b82ba47adeb4c0270332b65ad40ed86d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Fri, 16 Feb 2024 15:30:00 -0500 Subject: [PATCH] fix --- data/data/fields.csv | 9 +- protoBuilds/0f0850/0f0850.ot2.apiv2.py.json | 1585 +++++++++++++++++ protoBuilds/0f0850/README.json | 36 + protoBuilds/0f0850/metadata.json | 20 + protocols/0f0850/0f0850.ot2.apiv2.py | 147 ++ protocols/0f0850/README.md | 63 + protocols/0f0850/fields.json | 51 + .../labware/genesee_96_wellplate_200ul.json | 1127 ++++++++++++ .../labware/tuberack_24_wellplate_1500ul.json | 323 ++++ 9 files changed, 3359 insertions(+), 2 deletions(-) create mode 100644 protoBuilds/0f0850/0f0850.ot2.apiv2.py.json create mode 100644 protoBuilds/0f0850/README.json create mode 100644 protoBuilds/0f0850/metadata.json create mode 100644 protocols/0f0850/0f0850.ot2.apiv2.py create mode 100644 protocols/0f0850/README.md create mode 100644 protocols/0f0850/fields.json create mode 100644 protocols/0f0850/labware/genesee_96_wellplate_200ul.json create mode 100644 protocols/0f0850/labware/tuberack_24_wellplate_1500ul.json diff --git a/data/data/fields.csv b/data/data/fields.csv index 39ef167da..aafb0d04f 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,82 +m20_mount,83 m300_mount,112 m300_type,2 m_mount,1 @@ -914,6 +914,8 @@ num_row,1 num_rows_a,1 num_rows_b,1 num_samp,75 +num_samp_lysis,1 +num_samp_mmx,1 num_samp_p1,1 num_samp_p2,1 num_samp_plate1,1 @@ -1006,7 +1008,7 @@ p2num,1 p300_gen,1 p300_mixing_height,1 p300_mnt,3 -p300_mount,159 +p300_mount,160 p300_mount_1,1 p300_multi_mount,7 p300_rate,1 @@ -1663,6 +1665,7 @@ vol_h_lysate,1 vol_ic,1 vol_initial,1 vol_lys_buffer,1 +vol_lysis_mix,1 vol_media_tubes,1 vol_meoh,1 vol_mix,2 @@ -1670,10 +1673,12 @@ vol_mm,3 vol_mobile_phase,1 vol_mq,1 vol_neutralization_buffer,1 +vol_pcr_mix,1 vol_peptide1,1 vol_peptide2,1 vol_peptide3,1 vol_pma_ca,1 +vol_primer,1 vol_reagent,1 vol_refill,1 vol_removal,1 diff --git a/protoBuilds/0f0850/0f0850.ot2.apiv2.py.json b/protoBuilds/0f0850/0f0850.ot2.apiv2.py.json new file mode 100644 index 000000000..9d157713e --- /dev/null +++ b/protoBuilds/0f0850/0f0850.ot2.apiv2.py.json @@ -0,0 +1,1585 @@ +{ + "content": "# flake8: noqa\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'Mastermix Creation and Distribution',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_samp_mmx, num_samp_lysis, vol_primer, vol_pcr_mix,\n vol_lysis_mix, m20_mount, p300_mount] = get_values( # noqa: F821\n \"num_samp_mmx\", \"num_samp_lysis\", \"vol_primer\", \"vol_pcr_mix\",\n \"vol_lysis_mix\", \"m20_mount\", \"p300_mount\")\n\n # num_samp_mmx = 96\n # num_samp_lysis = 48\n # vol_primer = 0.5\n # vol_pcr_mix = 10\n # vol_lysis_mix = 20\n # m20_mount = 'left'\n # p20_mount = 'right'\n\n # labware\n temp_mod = ctx.load_module('temperature module gen2', 4)\n reagent_block = temp_mod.load_labware('tuberack_24_wellplate_1500ul')\n lysis_plate = ctx.load_labware('opentrons_96_aluminumblock_biorad_wellplate_200ul', 5)\n mmx_plate = ctx.load_labware('genesee_96_wellplate_200ul', 6)\n\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in [10, 11]]\n\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in [9]]\n\n # pipettes\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount, tip_racks=tips300)\n\n\n num_chan = 1\n tips_ordered = [\n tip\n for row in tips20[0].rows()[\n len(tips20[0].rows())-num_chan::-1*num_chan]\n for tip in row]\n\n tip_count = 0\n\n def pick_up_one():\n\n mounted_on = {\"left\": types.Mount.LEFT, \"right\": types.Mount.RIGHT}\n\n pick_up_current = 0.1 # 150 mA for single tip\n ctx._hw_manager.hardware._attached_instruments[\n mounted_on[m20.mount]].update_config_item(\n 'pick_up_current', pick_up_current)\n nonlocal tip_count\n m20.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # mapping\n temp_mod.set_temperature(4)\n taq_mid_red = reagent_block.rows()[0][0]\n forward_primer = reagent_block.rows()[0][1]\n reverse_primer = reagent_block.rows()[0][2]\n h20 = reagent_block.rows()[0][3]\n\n worm_lysis_buffer_A = reagent_block.rows()[1][0]\n worm_lysis_buffer_B = reagent_block.rows()[1][2]\n\n taq_mid_red_vol = 5*num_samp_mmx\n forward_primer_vol = vol_primer*num_samp_mmx\n reverse_primer_vol = vol_primer*num_samp_mmx\n h20_vol_mmx = 3*num_samp_mmx\n h20_vol_lysis = 7*num_samp_lysis\n worm_lysis_buffer_A_vol = 3*num_samp_lysis\n worm_lysis_buffer_B_vol = num_samp_lysis\n\n # protocol\n ctx.comment('\\n---------------Making Mastermix, Buffer Mix----------------\\n\\n')\n\n mmx_reagents = [taq_mid_red, forward_primer, reverse_primer, h20]\n mmx_vols = [taq_mid_red_vol, forward_primer_vol, reverse_primer_vol, h20_vol_mmx]\n dest_tube_mmx = reagent_block['A6']\n\n for i, (mmx_reagent, vol) in enumerate(zip(mmx_reagents, mmx_vols)):\n\n if vol > 20:\n p300.pick_up_tip()\n pip = p300\n else:\n pick_up_one()\n pip = m20\n pip.transfer(vol*1.15, mmx_reagent, dest_tube_mmx, new_tip='never')\n\n if i == len(mmx_reagents)-1:\n if not p300.has_tip:\n p300.pick_up_tip()\n p300.mix(15, 200, dest_tube_mmx)\n\n\n if p300.has_tip:\n p300.drop_tip()\n if m20.has_tip:\n m20.drop_tip()\n\n # lysis_buffer\n lysis_reagents = [worm_lysis_buffer_A, worm_lysis_buffer_B, h20]\n lysis_vols = [taq_mid_red_vol, forward_primer_vol, reverse_primer_vol, h20_vol_lysis]\n dest_tube_lysis = reagent_block['B6']\n\n for i, (lysis_reagent, vol) in enumerate(zip(lysis_reagents, lysis_vols)):\n\n if vol > 20:\n p300.pick_up_tip()\n pip = p300\n else:\n pick_up_one()\n pip = m20\n pip.transfer(vol*1.15, lysis_reagent, dest_tube_lysis, new_tip='never')\n\n if i == len(lysis_reagents)-1:\n if not p300.has_tip:\n p300.pick_up_tip()\n p300.mix(15, 200, dest_tube_lysis)\n\n if p300.has_tip:\n p300.drop_tip()\n if m20.has_tip:\n m20.drop_tip()\n\n pick_up_one()\n for well in mmx_plate.wells()[:num_samp_mmx]:\n m20.aspirate(vol_pcr_mix, dest_tube_mmx)\n m20.dispense(vol_pcr_mix, well)\n m20.drop_tip()\n\n lysis_wells = [well for col in lysis_plate.columns()[::2] for well in col][:num_samp_lysis]\n pick_up_one()\n for well in lysis_wells:\n m20.aspirate(vol_lysis_mix, dest_tube_lysis)\n m20.dispense(vol_lysis_mix, well)\n m20.drop_tip()\n", + "custom_labware_defs": [ + { + "brand": { + "brand": "tuberack", + "brandId": [ + "123" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 43.7 + }, + "groups": [ + { + "metadata": { + "wellBottomShape": "v" + }, + "wells": [ + "A1", + "B1", + "C1", + "D1", + "A2", + "B2", + "C2", + "D2", + "A3", + "B3", + "C3", + "D3", + "A4", + "B4", + "C4", + "D4", + "A5", + "B5", + "C5", + "D5", + "A6", + "B6", + "C6", + "D6" + ] + } + ], + "metadata": { + "displayCategory": "wellPlate", + "displayName": "Tuberack 24 Well Plate 1500 \u00b5L", + "displayVolumeUnits": "\u00b5L", + "tags": [] + }, + "namespace": "custom_beta", + "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" + ] + ], + "parameters": { + "format": "irregular", + "isMagneticModuleCompatible": false, + "isTiprack": false, + "loadName": "tuberack_24_wellplate_1500ul", + "quirks": [] + }, + "schemaVersion": 2, + "version": 1, + "wells": { + "A1": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 20.75, + "y": 68.6, + "z": 5.8 + }, + "A2": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 38, + "y": 68.6, + "z": 5.8 + }, + "A3": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 55.25, + "y": 68.6, + "z": 5.8 + }, + "A4": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 72.5, + "y": 68.6, + "z": 5.8 + }, + "A5": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 89.75, + "y": 68.6, + "z": 5.8 + }, + "A6": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 107, + "y": 68.6, + "z": 5.8 + }, + "B1": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 20.75, + "y": 51.35, + "z": 5.8 + }, + "B2": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 38, + "y": 51.35, + "z": 5.8 + }, + "B3": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 55.25, + "y": 51.35, + "z": 5.8 + }, + "B4": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 72.5, + "y": 51.35, + "z": 5.8 + }, + "B5": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 89.75, + "y": 51.35, + "z": 5.8 + }, + "B6": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 107, + "y": 51.35, + "z": 5.8 + }, + "C1": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 20.75, + "y": 34.1, + "z": 5.8 + }, + "C2": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 38, + "y": 34.1, + "z": 5.8 + }, + "C3": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 55.25, + "y": 34.1, + "z": 5.8 + }, + "C4": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 72.5, + "y": 34.1, + "z": 5.8 + }, + "C5": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 89.75, + "y": 34.1, + "z": 5.8 + }, + "C6": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 107, + "y": 34.1, + "z": 5.8 + }, + "D1": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 20.75, + "y": 16.85, + "z": 5.8 + }, + "D2": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 38, + "y": 16.85, + "z": 5.8 + }, + "D3": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 55.25, + "y": 16.85, + "z": 5.8 + }, + "D4": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 72.5, + "y": 16.85, + "z": 5.8 + }, + "D5": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 89.75, + "y": 16.85, + "z": 5.8 + }, + "D6": { + "depth": 37.9, + "diameter": 10.2, + "shape": "circular", + "totalLiquidVolume": 1500, + "x": 107, + "y": 16.85, + "z": 5.8 + } + } + }, + { + "brand": { + "brand": "Genesee", + "brandId": [ + "Olympus #24-301" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 28.3 + }, + "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": "Genesee 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": "genesee_96_wellplate_200ul", + "quirks": [] + }, + "schemaVersion": 2, + "version": 1, + "wells": { + "A1": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 14.38, + "y": 74.24, + "z": 5.6 + }, + "A10": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 95.38, + "y": 74.24, + "z": 5.6 + }, + "A11": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 104.38, + "y": 74.24, + "z": 5.6 + }, + "A12": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 113.38, + "y": 74.24, + "z": 5.6 + }, + "A2": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 23.38, + "y": 74.24, + "z": 5.6 + }, + "A3": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 32.38, + "y": 74.24, + "z": 5.6 + }, + "A4": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 41.38, + "y": 74.24, + "z": 5.6 + }, + "A5": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 50.38, + "y": 74.24, + "z": 5.6 + }, + "A6": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 59.38, + "y": 74.24, + "z": 5.6 + }, + "A7": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 68.38, + "y": 74.24, + 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"depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 77.38, + "y": 11.24, + "z": 5.6 + }, + "H9": { + "depth": 22.7, + "diameter": 5.46, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 86.38, + "y": 11.24, + "z": 5.6 + } + } + } + ], + "fields": [ + { + "default": 96, + "label": "Number of Mastermix Samples (1-96)", + "name": "num_samp_mmx", + "type": "int" + }, + { + "default": 48, + "label": "Number of Lysis Mastermix Samples (1-48)", + "name": "num_samp_lysis", + "type": "int" + }, + { + "default": 0.5, + "label": "Volume of Forward/Reverse Primer", + "name": "vol_primer", + "type": "float" + }, + { + "default": 15, + "label": "Volume of PCR mix in each well (1-20ul)", + "name": "vol_pcr_mix", + "type": "int" + }, + { + "default": 15, + "label": "Volume of Lysis mix in each well (1-20ul)", + "name": "vol_lysis_mix", + "type": "int" + }, + { + "label": "P20 Multi-Channel Mount", + "name": "m20_mount", + "options": [ + { + "label": "Left", + "value": "left" + }, + { + "label": "Right", + "value": "right" + } + ], + "type": "dropDown" + }, + { + "label": "P300 Single-Channel Mount", + "name": "p300_mount", + "options": [ + { + "label": "Right", + "value": "right" + }, + { + "label": "Left", + "value": "left" + } + ], + "type": "dropDown" + } + ], + "instruments": [ + { + "mount": "left", + "name": "p20_multi_gen2" + }, + { + "mount": "right", + "name": "p300_single_gen2" + } + ], + "labware": [ + { + "name": "Tuberack 24 Well Plate 1500 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tuberack_24_wellplate_1500ul" + }, + { + "name": "Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on 5", + "share": false, + "slot": "5", + "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" + }, + { + "name": "Genesee 96 Well Plate 200 \u00b5L on 6", + "share": false, + "slot": "6", + "type": "genesee_96_wellplate_200ul" + }, + { + "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", + "share": false, + "slot": "9", + "type": "opentrons_96_filtertiprack_200ul" + }, + { + "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": "Mastermix Creation and Distribution", + "source": "Custom Protocol Request" + }, + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Tuberack 24 Well Plate 1500 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] +} \ No newline at end of file diff --git a/protoBuilds/0f0850/README.json b/protoBuilds/0f0850/README.json new file mode 100644 index 000000000..a24e4d4ac --- /dev/null +++ b/protoBuilds/0f0850/README.json @@ -0,0 +1,36 @@ +{ + "author": "Opentrons", + "categories": { + "Sample Prep": [ + "Plate Filling" + ] + }, + "deck-setup": "", + "description": "This protocol preps a 96 plate with PCR mastermix, as well as a 48 palte with Lysis mastermix. The mastermixes are created on deck beefore distribution. For more details, please see below.", + "internal": "0f0850", + "labware": "\nTuberack 24 Well Plate 1500 \u00b5L\nGenesee 96 Well Plate 200 \u00b5L #Olympus #24-301\nOpentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", + "markdown": { + "author": "[Opentrons](https://opentrons.com/)\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/0f0850/deck.png)\n\n\n", + "description": "This protocol preps a 96 plate with PCR mastermix, as well as a 48 palte with Lysis mastermix. The mastermixes are created on deck beefore distribution. For more details, please see below.\n\n\n", + "internal": "0f0850\n", + "labware": "* Tuberack 24 Well Plate 1500 \u00b5L\n* Genesee 96 Well Plate 200 \u00b5L #Olympus #24-301\n* [Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set)\n* Opentrons 96 Filter Tip Rack 200 \u00b5L\n* Opentrons 96 Filter Tip Rack 20 \u00b5L\n\n\n", + "modules": "* [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/)\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 P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\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. Make pcr mastermix in empty tube on tube rack.\n2. Make lysis mastermix in empty tube on tube rack.\n3. Distribute pcr mastermix and lysis mastermix to 96 and 48 plate respectively. \n\n\n", + "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0f0850/reagents.png)\n\n\n", + "title": "Mastermix Creation and Distribution" + }, + "modules": [ + "Opentrons Temperature Module (GEN2)" + ], + "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", + "pipettes": "\nOpentrons P300 Single Channel Electronic Pipette (GEN2)\nOpentrons P20 8 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": "\nMake pcr mastermix in empty tube on tube rack.\nMake lysis mastermix in empty tube on tube rack.\nDistribute pcr mastermix and lysis mastermix to 96 and 48 plate respectively. \n", + "reagent-setup": "", + "title": "Mastermix Creation and Distribution" +} \ No newline at end of file diff --git a/protoBuilds/0f0850/metadata.json b/protoBuilds/0f0850/metadata.json new file mode 100644 index 000000000..0241cc984 --- /dev/null +++ b/protoBuilds/0f0850/metadata.json @@ -0,0 +1,20 @@ +{ + "files": { + "OT 1 protocol": [], + "OT 2 protocol": [ + "0f0850.ot2.apiv2.py" + ], + "description": [ + "README.md" + ] + }, + "flags": { + "embedded-app": false, + "feature": false, + "hide-from-search": false, + "skip-tests": false + }, + "path": "protocols/0f0850", + "slug": "0f0850", + "status": "ok" +} \ No newline at end of file diff --git a/protocols/0f0850/0f0850.ot2.apiv2.py b/protocols/0f0850/0f0850.ot2.apiv2.py new file mode 100644 index 000000000..32c9a26e6 --- /dev/null +++ b/protocols/0f0850/0f0850.ot2.apiv2.py @@ -0,0 +1,147 @@ +# flake8: noqa +from opentrons import types + +metadata = { + 'protocolName': 'Mastermix Creation and Distribution', + 'author': 'Rami Farawi ', + 'source': 'Custom Protocol Request', + 'apiLevel': '2.13' +} + + +def run(ctx): + + [num_samp_mmx, num_samp_lysis, vol_primer, vol_pcr_mix, + vol_lysis_mix, m20_mount, p300_mount] = get_values( # noqa: F821 + "num_samp_mmx", "num_samp_lysis", "vol_primer", "vol_pcr_mix", + "vol_lysis_mix", "m20_mount", "p300_mount") + + # num_samp_mmx = 96 + # num_samp_lysis = 48 + # vol_primer = 0.5 + # vol_pcr_mix = 10 + # vol_lysis_mix = 20 + # m20_mount = 'left' + # p20_mount = 'right' + + # labware + temp_mod = ctx.load_module('temperature module gen2', 4) + reagent_block = temp_mod.load_labware('tuberack_24_wellplate_1500ul') + lysis_plate = ctx.load_labware('opentrons_96_aluminumblock_biorad_wellplate_200ul', 5) + mmx_plate = ctx.load_labware('genesee_96_wellplate_200ul', 6) + + tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot) + for slot in [10, 11]] + + tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot) + for slot in [9]] + + # pipettes + m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20) + p300 = ctx.load_instrument('p300_single_gen2', p300_mount, tip_racks=tips300) + + + num_chan = 1 + tips_ordered = [ + tip + for row in tips20[0].rows()[ + len(tips20[0].rows())-num_chan::-1*num_chan] + for tip in row] + + tip_count = 0 + + def pick_up_one(): + + mounted_on = {"left": types.Mount.LEFT, "right": types.Mount.RIGHT} + + pick_up_current = 0.1 # 150 mA for single tip + ctx._hw_manager.hardware._attached_instruments[ + mounted_on[m20.mount]].update_config_item( + 'pick_up_current', pick_up_current) + nonlocal tip_count + m20.pick_up_tip(tips_ordered[tip_count]) + tip_count += 1 + + # mapping + temp_mod.set_temperature(4) + taq_mid_red = reagent_block.rows()[0][0] + forward_primer = reagent_block.rows()[0][1] + reverse_primer = reagent_block.rows()[0][2] + h20 = reagent_block.rows()[0][3] + + worm_lysis_buffer_A = reagent_block.rows()[1][0] + worm_lysis_buffer_B = reagent_block.rows()[1][2] + + taq_mid_red_vol = 5*num_samp_mmx + forward_primer_vol = vol_primer*num_samp_mmx + reverse_primer_vol = vol_primer*num_samp_mmx + h20_vol_mmx = 3*num_samp_mmx + h20_vol_lysis = 7*num_samp_lysis + worm_lysis_buffer_A_vol = 3*num_samp_lysis + worm_lysis_buffer_B_vol = num_samp_lysis + + # protocol + ctx.comment('\n---------------Making Mastermix, Buffer Mix----------------\n\n') + + mmx_reagents = [taq_mid_red, forward_primer, reverse_primer, h20] + mmx_vols = [taq_mid_red_vol, forward_primer_vol, reverse_primer_vol, h20_vol_mmx] + dest_tube_mmx = reagent_block['A6'] + + for i, (mmx_reagent, vol) in enumerate(zip(mmx_reagents, mmx_vols)): + + if vol > 20: + p300.pick_up_tip() + pip = p300 + else: + pick_up_one() + pip = m20 + pip.transfer(vol*1.15, mmx_reagent, dest_tube_mmx, new_tip='never') + + if i == len(mmx_reagents)-1: + if not p300.has_tip: + p300.pick_up_tip() + p300.mix(15, 200, dest_tube_mmx) + + + if p300.has_tip: + p300.drop_tip() + if m20.has_tip: + m20.drop_tip() + + # lysis_buffer + lysis_reagents = [worm_lysis_buffer_A, worm_lysis_buffer_B, h20] + lysis_vols = [taq_mid_red_vol, forward_primer_vol, reverse_primer_vol, h20_vol_lysis] + dest_tube_lysis = reagent_block['B6'] + + for i, (lysis_reagent, vol) in enumerate(zip(lysis_reagents, lysis_vols)): + + if vol > 20: + p300.pick_up_tip() + pip = p300 + else: + pick_up_one() + pip = m20 + pip.transfer(vol*1.15, lysis_reagent, dest_tube_lysis, new_tip='never') + + if i == len(lysis_reagents)-1: + if not p300.has_tip: + p300.pick_up_tip() + p300.mix(15, 200, dest_tube_lysis) + + if p300.has_tip: + p300.drop_tip() + if m20.has_tip: + m20.drop_tip() + + pick_up_one() + for well in mmx_plate.wells()[:num_samp_mmx]: + m20.aspirate(vol_pcr_mix, dest_tube_mmx) + m20.dispense(vol_pcr_mix, well) + m20.drop_tip() + + lysis_wells = [well for col in lysis_plate.columns()[::2] for well in col][:num_samp_lysis] + pick_up_one() + for well in lysis_wells: + m20.aspirate(vol_lysis_mix, dest_tube_lysis) + m20.dispense(vol_lysis_mix, well) + m20.drop_tip() diff --git a/protocols/0f0850/README.md b/protocols/0f0850/README.md new file mode 100644 index 000000000..947969dac --- /dev/null +++ b/protocols/0f0850/README.md @@ -0,0 +1,63 @@ +# Mastermix Creation and Distribution + + +### Author +[Opentrons](https://opentrons.com/) + + +## Categories +* Sample Prep + * Plate Filling + + +## Description +This protocol preps a 96 plate with PCR mastermix, as well as a 48 palte with Lysis mastermix. The mastermixes are created on deck beefore distribution. For more details, please see below. + + +### Modules +* [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/) + + +### Labware +* Tuberack 24 Well Plate 1500 µL +* Genesee 96 Well Plate 200 µL #Olympus #24-301 +* [Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 µL](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set) +* Opentrons 96 Filter Tip Rack 200 µL +* Opentrons 96 Filter Tip Rack 20 µL + + +### Pipettes +* [Opentrons P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/) +* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) + + +### Deck Setup +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0f0850/deck.png) + + +### Reagent Setup +![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0f0850/reagents.png) + + +### Protocol Steps +1. Make pcr mastermix in empty tube on tube rack. +2. Make lysis mastermix in empty tube on tube rack. +3. Distribute pcr mastermix and lysis mastermix to 96 and 48 plate respectively. + + +### 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 +0f0850 diff --git a/protocols/0f0850/fields.json b/protocols/0f0850/fields.json new file mode 100644 index 000000000..6e17c101b --- /dev/null +++ b/protocols/0f0850/fields.json @@ -0,0 +1,51 @@ +[ + { + "type": "int", + "label": "Number of Mastermix Samples (1-96)", + "name": "num_samp_mmx", + "default": 96 + }, + { + "type": "int", + "label": "Number of Lysis Mastermix Samples (1-48)", + "name": "num_samp_lysis", + "default": 48 + }, + { + "type": "float", + "label": "Volume of Forward/Reverse Primer", + "name": "vol_primer", + "default": 0.5 + }, + { + "type": "int", + "label": "Volume of PCR mix in each well (1-20ul)", + "name": "vol_pcr_mix", + "default": 15 + }, + + { + "type": "int", + "label": "Volume of Lysis mix in each well (1-20ul)", + "name": "vol_lysis_mix", + "default": 15 + }, + { + "type": "dropDown", + "label": "P20 Multi-Channel Mount", + "name": "m20_mount", + "options": [ + {"label": "Left", "value": "left"}, + {"label": "Right", "value": "right"} + ] + }, + { + "type": "dropDown", + "label": "P300 Single-Channel Mount", + "name": "p300_mount", + "options": [ + {"label": "Right", "value": "right"}, + {"label": "Left", "value": "left"} + ] + } +] diff --git a/protocols/0f0850/labware/genesee_96_wellplate_200ul.json b/protocols/0f0850/labware/genesee_96_wellplate_200ul.json new file mode 100644 index 000000000..3cfcb0444 --- /dev/null +++ b/protocols/0f0850/labware/genesee_96_wellplate_200ul.json @@ -0,0 +1,1127 @@ +{ + "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" + ] + ], + "brand": { + "brand": "Genesee", + "brandId": [ + "Olympus #24-301" + ] + }, + "metadata": { + "displayName": "Genesee 96 Well Plate 200 µL", + "displayCategory": "wellPlate", + "displayVolumeUnits": "µL", + "tags": [] + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 28.3 + }, + "wells": { + "A1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 74.24, + "z": 5.6 + }, + "B1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 65.24, + "z": 5.6 + }, + "C1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 56.24, + "z": 5.6 + }, + "D1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 47.24, + "z": 5.6 + }, + "E1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 38.24, + "z": 5.6 + }, + "F1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 29.24, + "z": 5.6 + }, + "G1": { + "depth": 22.7, + "totalLiquidVolume": 200, + "shape": "circular", + "diameter": 5.46, + "x": 14.38, + "y": 20.24, + "z": 5.6 + }, + "H1": { + "depth": 22.7, + "totalLiquidVolume": 200, + 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