From 0a55deff85c6d230aeb7b2c92aac79971ca0b505 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Thu, 1 Feb 2024 11:34:36 -0500 Subject: [PATCH 1/3] fix --- .../00c517multi1-pt2.ot2.apiv2.py | 137 ++ protocols/00c517multi1-pt2/fields.json | 17 + ...Print 96 Tube Rack with Nippon 0.2 mL.json | 1 + .../Agilent 96 Well Plate 500 \302\265L.json" | 1 + .../labware/agilent_96_c18omix_200ul.json | 1126 +++++++++++++++ .../labware/agilent_96_wellplate_1200ul.json | 1127 +++++++++++++++ .../labware/agilent_96_wellplate_1400ul.json | 1223 +++++++++++++++++ .../protifistrap_96_wellplate_400ul.json | 1127 +++++++++++++++ .../00c517multi1/00c517multi1.ot2.apiv2.py | 111 ++ protocols/00c517multi1/fields.json | 35 + ...Print 96 Tube Rack with Nippon 0.2 mL.json | 1 + .../Agilent 96 Well Plate 500 \302\265L.json" | 1 + .../labware/agilent_96_c18omix_200ul.json | 1126 +++++++++++++++ .../labware/agilent_96_wellplate_1200ul.json | 1127 +++++++++++++++ .../labware/agilent_96_wellplate_1400ul.json | 1223 +++++++++++++++++ .../protifistrap_96_wellplate_400ul.json | 1127 +++++++++++++++ 16 files changed, 9510 insertions(+) create mode 100644 protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py create mode 100644 protocols/00c517multi1-pt2/fields.json create mode 100644 protocols/00c517multi1-pt2/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json create mode 100644 "protocols/00c517multi1-pt2/labware/Agilent 96 Well Plate 500 \302\265L.json" create mode 100644 protocols/00c517multi1-pt2/labware/agilent_96_c18omix_200ul.json create mode 100644 protocols/00c517multi1-pt2/labware/agilent_96_wellplate_1200ul.json create mode 100644 protocols/00c517multi1-pt2/labware/agilent_96_wellplate_1400ul.json create mode 100644 protocols/00c517multi1-pt2/labware/protifistrap_96_wellplate_400ul.json create mode 100644 protocols/00c517multi1/00c517multi1.ot2.apiv2.py create mode 100644 protocols/00c517multi1/fields.json create mode 100644 protocols/00c517multi1/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json create mode 100644 "protocols/00c517multi1/labware/Agilent 96 Well Plate 500 \302\265L.json" create mode 100644 protocols/00c517multi1/labware/agilent_96_c18omix_200ul.json create mode 100644 protocols/00c517multi1/labware/agilent_96_wellplate_1200ul.json create mode 100644 protocols/00c517multi1/labware/agilent_96_wellplate_1400ul.json create mode 100644 protocols/00c517multi1/labware/protifistrap_96_wellplate_400ul.json diff --git a/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py b/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py new file mode 100644 index 000000000..a66aacc21 --- /dev/null +++ b/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py @@ -0,0 +1,137 @@ +import math + +metadata = { + 'protocolName': 'VIB UGENT - Multi-channel Workflow Part 2', + 'author': 'Rami Farawi ', + 'source': 'Custom Protocol Request', + 'apiLevel': '2.15' +} + + +def run(ctx): + + [num_samp, m300_mount] = get_values( # noqa: F821 + "num_samp", "m300_mount") + + # m300_mount = 'left' + # num_samp = 96 + + # labware + c_18_tiprack = ctx.load_labware('agilent_96_c18omix_200ul', 1) + agilent_1200 = ctx.load_labware('agilent_96_wellplate_1200ul', 2) + + waste_res = ctx.load_labware('nest_1_reservoir_195ml', 5) + wash_buff_res = ctx.load_labware('nest_12_reservoir_15ml', 10) # up to number of columns of sample # noqa: E501 + reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4) + agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot) + for slot in [7, 8, 9]] + + tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) + for slot in [6, 11]] + + # pipettes + m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, + tip_racks=tips300) + + # mapping + # trypsin = reagent_plate.rows()[0][0] + acn = reagent_plate.rows()[0][0] + equil_buffer = reagent_plate.rows()[0][1:3] + eb = reagent_plate.rows()[0][3:5] + waste = waste_res['A1'] + wash_buff_plate = agilent_500[0] + elution_buff_plates = agilent_500[1:3] + + num_col = math.ceil(num_samp/8) + sample_cols = agilent_1200.rows()[0][:num_col] + + tip_ctr = 0 + + def pick_up_c18(): + nonlocal tip_ctr + m300.pick_up_tip(c_18_tiprack.rows()[0][tip_ctr]) + tip_ctr += 1 + + ctx.pause(''' + + Place the following labware on deck: + Opentrons tip rack with C18 OMIX tips on slot 1, + Agilent plate (round wells, 1200 µl) containing dried peptides on slot 2, + a 12 column reservoir containing 12 ml 2%ACN 0.1% TFA (column 1), + 20 ml equilibration buffer (column 2, 3), and 10mL elution buffer + in columns 4, 5 + a 12 column reservoir containing 8mL wash buffer in each column up to + the number of sample columns + and 20 ml elution buffer (column 8) in slot 4, + a one well reservoir on slot 5 (for waste), + a 300 µl tiprack on slot 6 + and 3 96-well plates (Agilent 500 µl) in slots 7, 8 & 9. + + + ''') + + # protocol + ctx.comment('\n---------------43 - ADD ACN----------------\n\n') + for col in sample_cols: + m300.pick_up_tip() + m300.aspirate(100, acn) + m300.dispense(100, col) + m300.mix(5, 80, col) + m300.drop_tip() + + ctx.pause(''' + Add sample to lunatic chip manually to measure peptide concentration + ''') + + ctx.comment('\n---------------46 - ADDING WASH BUFFER----------------\n\n') + m300.pick_up_tip() + for wash_well, col in zip(wash_buff_res.rows()[0], + wash_buff_plate.rows()[0][:num_col]): + m300.transfer(400, wash_well, col, new_tip='never') + m300.drop_tip() + + ctx.comment('\n-------------46 - ADDING ELUTION BUFFER--------------\n\n') + m300.pick_up_tip() + for eb_well, plate in zip(eb, elution_buff_plates): + for col in plate.rows()[0][:num_col]: + m300.aspirate(100, eb_well) + m300.dispense(100, col) + m300.drop_tip() + + ctx.comment('\n-------------46 - WASH STEPS--------------\n\n') + for i, (wash_buff_res_col, + wash_buff_col, + eb1_col, + eb2_col, + sample_col) in enumerate( + zip(wash_buff_res.rows()[0], + wash_buff_plate.rows()[0], + elution_buff_plates[0].rows()[0][:num_col], + elution_buff_plates[0].rows()[0][:num_col], + sample_cols, + )): + pick_up_c18() + for _ in range(3): + m300.aspirate(100, equil_buffer[0 if i < 6 else 1], rate=0.2) # ONE COLUMN PER 6 SAMPLES + m300.dispense(100, waste.top()) + + for _ in range(5): + m300.aspirate(100, wash_buff_res_col) + m300.dispense(100, waste.top(), rate=0.2) + + m300.mix(20, 100, sample_col, rate=0.2) + m300.aspirate(100, sample_col) + m300.dispense(100, waste.top()) + + for _ in range(3): + m300.aspirate(100, wash_buff_col) + m300.dispense(100, waste.top()) + + m300.mix(10, 100, eb1_col, rate=0.2) + m300.mix(10, 100, eb2_col, rate=0.2) + m300.aspirate(100, eb2_col) + m300.dispense(100, eb1_col) + + m300.drop_tip() + + ctx.comment('\n\n\n') diff --git a/protocols/00c517multi1-pt2/fields.json b/protocols/00c517multi1-pt2/fields.json new file mode 100644 index 000000000..eff209069 --- /dev/null +++ b/protocols/00c517multi1-pt2/fields.json @@ -0,0 +1,17 @@ +[ + { + "type": "int", + "label": "Number of samples (8-96)", + "name": "num_samp", + "default": 96 + }, + { + "type": "dropDown", + "label": "P300 Multi-Channel Mount", + "name": "m300_mount", + "options": [ + {"label": "Left", "value": "left"}, + {"label": "Right", "value": "right"} + ] + } +] diff --git a/protocols/00c517multi1-pt2/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json b/protocols/00c517multi1-pt2/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json new file mode 100644 index 000000000..700f0be37 --- /dev/null +++ b/protocols/00c517multi1-pt2/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json @@ -0,0 +1 @@ +{"brand":{"brand":"3DPrint","brandId":["U0014"]},"cornerOffsetFromSlot":{"x":0,"y":0,"z":0},"dimensions":{"xDimension":128,"yDimension":85.78,"zDimension":31.68},"groups":[{"brand":{"brand":"Nippon","brandId":["FG-028"]},"metadata":{"displayCategory":"tubeRack","wellBottomShape":"u"},"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":"tubeRack","displayName":"3DPrint 96 Tube Rack with Nippon 0.2 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+ "parameters": { + "format": "irregular", + "quirks": [], + "isTiprack": false, + "isMagneticModuleCompatible": false, + "loadName": "protifistrap_96_wellplate_400ul" + }, + "namespace": "custom_beta", + "version": 1, + "schemaVersion": 2, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } +} \ No newline at end of file diff --git a/protocols/00c517multi1/00c517multi1.ot2.apiv2.py b/protocols/00c517multi1/00c517multi1.ot2.apiv2.py new file mode 100644 index 000000000..5f33dd3a0 --- /dev/null +++ b/protocols/00c517multi1/00c517multi1.ot2.apiv2.py @@ -0,0 +1,111 @@ +import math + +metadata = { + 'protocolName': 'VIB UGENT - Multi-channel Workflow Part 1', + 'author': 'Rami Farawi ', + 'source': 'Custom Protocol Request', + 'apiLevel': '2.15' +} + + +def run(ctx): + + [num_samp, test_mode, m300_mount, m20_mount] = get_values( # noqa: F821 + "num_samp", "test_mode", "m300_mount", "m20_mount") + + # m300_mount = 'left' + # m20_mount = 'right' + # num_samp = 96 + + # labware + strip_tube_plate = ctx.load_labware('3dprint_96_tuberack_200ul', 1) + agilent_1400 = ctx.load_labware('agilent_96_wellplate_1400ul', 2) + s_trap_plate = ctx.load_labware('protifistrap_96_wellplate_400ul', 3) + reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4) + # agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot) + # for slot in [7, 8, 9, 11]] + try: + hs_mod = ctx.load_module('heaterShakerModuleV1', 10) + hs_plate = hs_mod.load_labware('agilent_96_wellplate_1400ul') + hs_mod.close_labware_latch() + except ValueError: + hs_plate = ctx.load_labware('agilent_96_wellplate_1400ul', 10) + hs_plate = hs_plate + tips20 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) + for slot in [5]] + tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) + for slot in [6]] + + # pipettes + m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, + tip_racks=tips300) + m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20) + + # mapping + trypsin = reagent_plate.rows()[0][0] + + num_col = math.ceil(num_samp/8) + sample_cols = agilent_1400.rows()[0][:num_col] + + # protocol + ctx.pause(''' + Place the following labware on the deck: 3D-print tuberack containing + a PCR strip with TCEP/CAA on slot 1, + sample plate (Agilent with square wells, 1400 µl) containing 50 µl sample + on slot 2, S-trap plate on slot 3, 12-well reservoir on slot 4, + 20 µl tip rack on slot 5 and 300 µl tiprack on slot 6. + Make sure the heater-shaker is on slot 10. + ''') + ctx.comment('\n---------------27 - ADD TCEP+CAA----------------\n\n') + tcep = strip_tube_plate.wells()[0] + for col in sample_cols: + m20.pick_up_tip() + m20.aspirate(7, tcep) + m20.dispense(7, col) + m20.mix(3, 20, col) + m20.drop_tip() + + # step 30 + if not test_mode: + hs_mod.set_and_wait_for_temperature(95) + else: + ctx.comment('skipping temperature to 95 for test mode') + hs_mod.open_labware_latch() + ctx.pause(''' + Wrap plate with tin foil and transfer plate to heater-shaker + at 95°C. Incubate for 10 min on heater-shaker. + TCEP/CAA can be removed from slot 1 + ''') + hs_mod.close_labware_latch() + hs_mod.set_and_wait_for_shake_speed(750) + if not test_mode: + ctx.delay(minutes=10) + else: + ctx.comment('skipping 10 minute delay for test mode') + hs_mod.deactivate_heater() + hs_mod.deactivate_shaker() + + ctx.pause(''' + Put plate containing reduced and alkylated samples on ice for 1 min. + After cool-down process manually until protease digest. + Put S-Trap plate containing sample on slot 3. + ''') + + ctx.comment('\n---------------40 - ADD TRYPSIN----------------\n\n') + m300.pick_up_tip() + for col in s_trap_plate.rows()[0][:num_col]: + m300.aspirate(125, trypsin) + m300.dispense(125, col) + m300.drop_tip() + + ctx.pause(''' + Check that all protease solution is at the bottom of the S-trap columns. + If not, tap the S-trap plate until all solution is + covering the S-trap material. + Incubate S-trap plate with cover + (do not seal tightly!) in incubator at 37°C overnight. + Do not shake! + Store leftover trypsin solution at -20°C. After digestion, perform elution + with the TECAN Resolvex A200 or centrifuge. + Dry eluted peptides (in 96-well plate) with a vaccuum concentrator. + ''') diff --git a/protocols/00c517multi1/fields.json b/protocols/00c517multi1/fields.json new file mode 100644 index 000000000..b008512bc --- /dev/null +++ b/protocols/00c517multi1/fields.json @@ -0,0 +1,35 @@ +[ + { + "type": "int", + "label": "Number of samples (8-96)", + "name": "num_samp", + "default": 96 + }, + { + "type": "dropDown", + "label": "Test Mode or Real Mode (skip incubation times)?", + "name": "test_mode", + "options": [ + {"label": "Real Mode", "value": false}, + {"label": "Test Mode (skip incubation times)", "value": true} + ] + }, + { + "type": "dropDown", + "label": "P300 Multi-Channel Mount", + "name": "m300_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/00c517multi1/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json b/protocols/00c517multi1/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json new file mode 100644 index 000000000..700f0be37 --- /dev/null +++ b/protocols/00c517multi1/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json @@ -0,0 +1 @@ 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114.25, + "y": 74.2, + "z": 27.7 + }, + "B12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 65.35, + "z": 27.7 + }, + "C12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 56.5, + "z": 27.7 + }, + "D12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 47.65, + "z": 27.7 + }, + "E12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 38.8, + "z": 27.7 + }, + "F12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 29.95, + "z": 27.7 + }, + "G12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 21.1, + "z": 27.7 + }, + "H12": { + "depth": 17.2, + "totalLiquidVolume": 400, + "shape": "circular", + "diameter": 6, + "x": 114.25, + "y": 12.25, + "z": 27.7 + } + }, + "groups": [ + { + "metadata": { + "wellBottomShape": "flat" + }, + "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" + ] + } + ], + "parameters": { + "format": "irregular", + "quirks": [], + "isTiprack": false, + "isMagneticModuleCompatible": false, + "loadName": "protifistrap_96_wellplate_400ul" + }, + "namespace": "custom_beta", + "version": 1, + "schemaVersion": 2, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } +} \ No newline at end of file From 9b622d85f0843bf2f0dc786bec16b0851d1145ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Thu, 1 Feb 2024 11:51:29 -0500 Subject: [PATCH 2/3] fix --- data/data/fields.csv | 8 +- .../00c517multi1-pt2.ot2.apiv2.py.json | 6973 ++++++++++++++++ protoBuilds/00c517multi1-pt2/README.json | 32 + protoBuilds/00c517multi1-pt2/metadata.json | 20 + .../00c517multi1.ot2.apiv2.py.json | 6989 +++++++++++++++++ protoBuilds/00c517multi1/README.json | 32 + protoBuilds/00c517multi1/metadata.json | 20 + .../00c517multi1-pt2.ot2.apiv2.py | 2 +- protocols/00c517multi1-pt2/README.md | 60 + .../00c517multi1/00c517multi1.ot2.apiv2.py | 35 +- protocols/00c517multi1/README.md | 61 + 11 files changed, 14216 insertions(+), 16 deletions(-) create mode 100644 protoBuilds/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py.json create mode 100644 protoBuilds/00c517multi1-pt2/README.json create mode 100644 protoBuilds/00c517multi1-pt2/metadata.json create mode 100644 protoBuilds/00c517multi1/00c517multi1.ot2.apiv2.py.json create mode 100644 protoBuilds/00c517multi1/README.json create mode 100644 protoBuilds/00c517multi1/metadata.json create mode 100644 protocols/00c517multi1-pt2/README.md create mode 100644 protocols/00c517multi1/README.md diff --git a/data/data/fields.csv b/data/data/fields.csv index 8e2ee317a..40bd4f8c1 100644 --- a/data/data/fields.csv +++ b/data/data/fields.csv @@ -725,8 +725,8 @@ lysis,1 lysis_vol,1 m10_mount,2 m1k,1 -m20_mount,80 -m300_mount,110 +m20_mount,81 +m300_mount,112 m300_type,2 m_mount,1 mag_bead_mix_resuspend_reps,1 @@ -910,7 +910,7 @@ num_rounds,1 num_row,1 num_rows_a,1 num_rows_b,1 -num_samp,71 +num_samp,73 num_samp_p1,1 num_samp_p2,1 num_samp_plate1,1 @@ -1471,7 +1471,7 @@ temperature2,1 tempgen,1 template_vol,1 test_method,1 -test_mode,1 +test_mode,2 test_mode_beads,1 test_plates,1 tfa_540,1 diff --git a/protoBuilds/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py.json b/protoBuilds/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py.json new file mode 100644 index 000000000..ab8fbd759 --- /dev/null +++ b/protoBuilds/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py.json @@ -0,0 +1,6973 @@ +{ + "content": "import math\n\nmetadata = {\n 'protocolName': 'VIB UGENT - Multi-channel Workflow Part 2',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.15'\n}\n\n\ndef run(ctx):\n\n [num_samp, m300_mount] = get_values( # noqa: F821\n \"num_samp\", \"m300_mount\")\n\n # m300_mount = 'left'\n # num_samp = 96\n\n # labware\n c_18_tiprack = ctx.load_labware('agilent_96_c18omix_200ul', 1)\n agilent_1200 = ctx.load_labware('agilent_96_wellplate_1200ul', 2)\n\n waste_res = ctx.load_labware('nest_1_reservoir_195ml', 5)\n wash_buff_res = ctx.load_labware('nest_12_reservoir_15ml', 10) # up to number of columns of sample # noqa: E501\n reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4)\n agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot)\n for slot in [7, 8, 9]]\n\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [6, 11]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tips300)\n\n # mapping\n # trypsin = reagent_plate.rows()[0][0]\n acn = reagent_plate.rows()[0][0]\n equil_buffer = reagent_plate.rows()[0][1:3]\n eb = reagent_plate.rows()[0][3:5]\n waste = waste_res['A1']\n wash_buff_plate = agilent_500[0]\n elution_buff_plates = agilent_500[1:3]\n\n num_col = math.ceil(num_samp/8)\n sample_cols = agilent_1200.rows()[0][:num_col]\n\n tip_ctr = 0\n\n def pick_up_c18():\n nonlocal tip_ctr\n m300.pick_up_tip(c_18_tiprack.rows()[0][tip_ctr])\n tip_ctr += 1\n\n ctx.pause('''\n\n Place the following labware on deck:\n Opentrons tip rack with C18 OMIX tips on slot 1,\n Agilent plate (round wells, 1200 \u00b5l) containing dried peptides on slot 2,\n a 12 column reservoir containing 12 ml 2%ACN 0.1% TFA (column 1),\n 20 ml equilibration buffer (column 2, 3), and 10mL elution buffer\n in columns 4, 5\n a 12 column reservoir containing 8mL wash buffer in each column up to\n the number of sample columns\n and 20 ml elution buffer (column 8) in slot 4,\n a one well reservoir on slot 5 (for waste),\n a 300 \u00b5l tiprack on slot 6\n and 3 96-well plates (Agilent 500 \u00b5l) in slots 7, 8 & 9.\n\n\n ''')\n\n # protocol\n ctx.comment('\\n---------------43 - ADD ACN----------------\\n\\n')\n for col in sample_cols:\n m300.pick_up_tip()\n m300.aspirate(100, acn)\n m300.dispense(100, col)\n m300.mix(5, 80, col)\n m300.drop_tip()\n\n ctx.pause('''\n Add sample to lunatic chip manually to measure peptide concentration\n ''')\n\n ctx.comment('\\n---------------46 - ADDING WASH BUFFER----------------\\n\\n')\n m300.pick_up_tip()\n for wash_well, col in zip(wash_buff_res.rows()[0],\n wash_buff_plate.rows()[0][:num_col]):\n m300.transfer(400, wash_well, col, new_tip='never')\n m300.drop_tip()\n\n ctx.comment('\\n-------------46 - ADDING ELUTION BUFFER--------------\\n\\n')\n m300.pick_up_tip()\n for eb_well, plate in zip(eb, elution_buff_plates):\n for col in plate.rows()[0][:num_col]:\n m300.aspirate(100, eb_well)\n m300.dispense(100, col)\n m300.drop_tip()\n\n ctx.comment('\\n-------------46 - WASH STEPS--------------\\n\\n')\n for i, (wash_buff_res_col,\n wash_buff_col,\n eb1_col,\n eb2_col,\n sample_col) in enumerate(\n zip(wash_buff_res.rows()[0],\n wash_buff_plate.rows()[0],\n elution_buff_plates[0].rows()[0][:num_col],\n elution_buff_plates[0].rows()[0][:num_col],\n sample_cols,\n )):\n pick_up_c18()\n for _ in range(3):\n m300.aspirate(100, equil_buffer[0 if i < 6 else 1], rate=0.2)\n m300.dispense(100, waste.top())\n\n for _ in range(5):\n m300.aspirate(100, wash_buff_res_col)\n m300.dispense(100, waste.top(), rate=0.2)\n\n m300.mix(20, 100, sample_col, rate=0.2)\n m300.aspirate(100, sample_col)\n m300.dispense(100, waste.top())\n\n for _ in range(3):\n m300.aspirate(100, wash_buff_col)\n m300.dispense(100, waste.top())\n\n m300.mix(10, 100, eb1_col, rate=0.2)\n m300.mix(10, 100, eb2_col, rate=0.2)\n m300.aspirate(100, eb2_col)\n m300.dispense(100, eb1_col)\n\n m300.drop_tip()\n\n ctx.comment('\\n\\n\\n')\n", + "custom_labware_defs": [ + { + "brand": { + "brand": "Agilent", + "brandId": [ + "C18_OMIX_200uL" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 63.8 + }, + "groups": [ + { + "metadata": {}, + "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": "tipRack", + "displayName": "Agilent 96 C18 OMIX 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": true, + "loadName": "agilent_96_c18omix_200ul", + "quirks": [], + "tipLength": 50.4 + }, + "schemaVersion": 2, + "version": 1, + "wells": { + "A1": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 14.38, + "y": 74.24, + "z": 13.4 + }, + "A10": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 95.38, + "y": 74.24, + "z": 13.4 + }, + "A11": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 104.38, + "y": 74.24, + "z": 13.4 + }, + "A12": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 113.38, + "y": 74.24, + "z": 13.4 + }, + "A2": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 23.38, + "y": 74.24, + "z": 13.4 + }, + "A3": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 32.38, + "y": 74.24, + "z": 13.4 + }, + "A4": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 41.38, + "y": 74.24, + "z": 13.4 + }, + "A5": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 50.38, + "y": 74.24, + "z": 13.4 + }, + "A6": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 59.38, + "y": 74.24, + "z": 13.4 + }, + "A7": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 68.38, + "y": 74.24, + "z": 13.4 + }, + "A8": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 77.38, + "y": 74.24, + "z": 13.4 + }, + "A9": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 86.38, + "y": 74.24, + "z": 13.4 + }, + "B1": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 14.38, + "y": 65.24, + "z": 13.4 + }, + "B10": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 95.38, + "y": 65.24, + "z": 13.4 + }, + "B11": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 104.38, + "y": 65.24, + "z": 13.4 + }, + "B12": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 113.38, + "y": 65.24, + "z": 13.4 + }, + "B2": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 23.38, + "y": 65.24, + "z": 13.4 + }, + "B3": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 32.38, + "y": 65.24, + "z": 13.4 + }, + "B4": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 41.38, + "y": 65.24, + "z": 13.4 + }, + "B5": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 50.38, + "y": 65.24, + "z": 13.4 + }, + "B6": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 59.38, + "y": 65.24, + "z": 13.4 + }, + "B7": { + "depth": 50.4, + "diameter": 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"y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H11": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 104.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H12": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 113.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H2": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 23.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H3": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 32.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H4": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 41.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H5": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 50.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H6": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 59.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H7": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 68.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H8": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 77.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H9": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 86.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + } + } + } + ], + "fields": [ + { + "default": 96, + "label": "Number of samples (8-96)", + "name": "num_samp", + "type": "int" + }, + { + "label": "P300 Multi-Channel Mount", + "name": "m300_mount", + "options": [ + { + "label": "Left", + "value": "left" + }, + { + "label": "Right", + "value": "right" + } + ], + "type": "dropDown" + } + ], + "instruments": [ + { + "mount": "left", + "name": "p300_multi_gen2" + } + ], + "labware": [ + { + "name": "Agilent 96 C18 OMIX 200 \u00b5l on 1", + "share": false, + "slot": "1", + "type": "agilent_96_c18omix_200ul" + }, + { + "name": "Agilent 96 Well Plate 1200 \u00b5L on 2", + "share": false, + "slot": "2", + "type": "agilent_96_wellplate_1200ul" + }, + { + "name": "NEST 12 Well Reservoir 15 mL on 4", + "share": false, + "slot": "4", + "type": "nest_12_reservoir_15ml" + }, + { + "name": "NEST 1 Well Reservoir 195 mL on 5", + "share": false, + "slot": "5", + "type": "nest_1_reservoir_195ml" + }, + { + "name": "Opentrons 96 Tip Rack 300 \u00b5L on 6", + "share": false, + "slot": "6", + "type": "opentrons_96_tiprack_300ul" + }, + { + "name": "Agilent 96 Well Plate 500 \u00b5L on 7", + "share": false, + "slot": "7", + "type": "agilent_96_wellplate_500ul" + }, + { + "name": "Agilent 96 Well Plate 500 \u00b5L on 8", + "share": false, + "slot": "8", + "type": "agilent_96_wellplate_500ul" + }, + { + "name": "Agilent 96 Well Plate 500 \u00b5L on 9", + "share": false, + "slot": "9", + "type": "agilent_96_wellplate_500ul" + }, + { + "name": "NEST 12 Well Reservoir 15 mL on 10", + "share": false, + "slot": "10", + "type": "nest_12_reservoir_15ml" + }, + { + "name": "Opentrons 96 Tip Rack 300 \u00b5L on 11", + "share": false, + "slot": "11", + "type": "opentrons_96_tiprack_300ul" + }, + { + "name": "Opentrons Fixed Trash on 12", + "share": false, + "slot": "12", + "type": "opentrons_1_trash_1100ml_fixed" + } + ], + "metadata": { + "apiLevel": "2.15", + "author": "Rami Farawi ", + "protocolName": "VIB UGENT - Multi-channel Workflow Part 2", + "source": "Custom Protocol Request" + }, + "modules": [] +} \ No newline at end of file diff --git a/protoBuilds/00c517multi1-pt2/README.json b/protoBuilds/00c517multi1-pt2/README.json new file mode 100644 index 000000000..badde870d --- /dev/null +++ b/protoBuilds/00c517multi1-pt2/README.json @@ -0,0 +1,32 @@ +{ + "author": "Opentrons", + "categories": { + "Broad Category": [ + "Specific Category" + ] + }, + "deck-setup": "", + "description": "This protocol does stuff!", + "internal": "00c517multi1-pt2", + "labware": "\nAgilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\nAgilent 96 Well Plate 1200 \u00b5L #round well\nProtifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\nAgilent 96 Well Plate 500 \u00b5L #5042-1385\nAgilent 96 Well Plate 1400 \u00b5L #204355-100\nNEST 12 Well Reservoir 15 mL #360102\nNEST 1 Well Reservoir 195 mL #360103\nOpentrons 96 Tip Rack 300 \u00b5L\n", + "markdown": { + "author": "[Opentrons](https://opentrons.com/)\n\n\n", + "categories": "* Broad Category\n\t* Specific Category\n\n\n", + "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/deck.png)\n\n\n", + "description": "This protocol does stuff!\n\n\n", + "internal": "00c517multi1-pt2\n", + "labware": "* Agilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\n* Agilent 96 Well Plate 1200 \u00b5L #round well\n* Protifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\n* Agilent 96 Well Plate 500 \u00b5L #5042-1385\n* Agilent 96 Well Plate 1400 \u00b5L #204355-100\n* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102)\n* [NEST 1 Well Reservoir 195 mL #360103](http://www.cell-nest.com/page94?_l=en&product_id=102)\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-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", + "pipettes": "* [Opentrons P300 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. Step 1...\n\n\n", + "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/reagents.png)\n\n\n", + "title": "VIB UGENT - Multi-channel Workflow Part 2" + }, + "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", + "pipettes": "\nOpentrons P300 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": "\nStep 1...\n", + "reagent-setup": "", + "title": "VIB UGENT - Multi-channel Workflow Part 2" +} \ No newline at end of file diff --git a/protoBuilds/00c517multi1-pt2/metadata.json b/protoBuilds/00c517multi1-pt2/metadata.json new file mode 100644 index 000000000..73f7cd60b --- /dev/null +++ b/protoBuilds/00c517multi1-pt2/metadata.json @@ -0,0 +1,20 @@ +{ + "files": { + "OT 1 protocol": [], + "OT 2 protocol": [ + "00c517multi1-pt2.ot2.apiv2.py" + ], + "description": [ + "README.md" + ] + }, + "flags": { + "embedded-app": false, + "feature": false, + "hide-from-search": false, + "skip-tests": false + }, + "path": "protocols/00c517multi1-pt2", + "slug": "00c517multi1-pt2", + "status": "ok" +} \ No newline at end of file diff --git a/protoBuilds/00c517multi1/00c517multi1.ot2.apiv2.py.json b/protoBuilds/00c517multi1/00c517multi1.ot2.apiv2.py.json new file mode 100644 index 000000000..98ae506d4 --- /dev/null +++ b/protoBuilds/00c517multi1/00c517multi1.ot2.apiv2.py.json @@ -0,0 +1,6989 @@ +{ + "content": "import math\n\nmetadata = {\n 'protocolName': 'VIB UGENT - Multi-channel Workflow Part 1',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [num_samp, test_mode, m300_mount, m20_mount] = get_values( # noqa: F821\n \"num_samp\", \"test_mode\", \"m300_mount\", \"m20_mount\")\n\n # m300_mount = 'left'\n # m20_mount = 'right'\n # num_samp = 96\n\n # labware\n strip_tube_plate = ctx.load_labware('3dprint_96_tuberack_200ul', 1)\n agilent_1400 = ctx.load_labware('agilent_96_wellplate_1400ul', 2)\n s_trap_plate = ctx.load_labware('protifistrap_96_wellplate_400ul', 3)\n reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4)\n # agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot)\n # for slot in [7, 8, 9, 11]]\n if not ctx.is_simulating:\n hs_mod = ctx.load_module('heaterShakerModuleV1', 10)\n hs_plate = hs_mod.load_labware('agilent_96_wellplate_1400ul')\n hs_mod.close_labware_latch()\n else:\n hs_plate = ctx.load_labware('agilent_96_wellplate_1400ul', 10)\n hs_plate = hs_plate\n tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in [5]]\n tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in [6]]\n\n # pipettes\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tips300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n\n # mapping\n trypsin = reagent_plate.rows()[0][0]\n\n num_col = math.ceil(num_samp/8)\n sample_cols = agilent_1400.rows()[0][:num_col]\n\n # protocol\n ctx.pause('''\n Place the following labware on the deck: 3D-print tuberack containing\n a PCR strip with TCEP/CAA on slot 1,\n sample plate (Agilent with square wells, 1400 \u00b5l) containing 50 \u00b5l sample\n on slot 2, S-trap plate on slot 3, 12-well reservoir on slot 4,\n 20 \u00b5l tip rack on slot 5 and 300 \u00b5l tiprack on slot 6.\n Make sure the heater-shaker is on slot 10.\n ''')\n ctx.comment('\\n---------------27 - ADD TCEP+CAA----------------\\n\\n')\n tcep = strip_tube_plate.wells()[0]\n for col in sample_cols:\n m20.pick_up_tip()\n m20.aspirate(7, tcep)\n m20.dispense(7, col)\n m20.mix(3, 20, col)\n m20.drop_tip()\n # step 30\n\n if not test_mode:\n if not ctx.is_simulating:\n hs_mod.set_and_wait_for_temperature(95)\n else:\n ctx.comment('skipping temperature to 95 for test mode')\n\n if not ctx.is_simulating:\n hs_mod.open_labware_latch()\n\n ctx.pause('''\n Wrap plate with tin foil and transfer plate to heater-shaker\n at 95\u00b0C. Incubate for 10 min on heater-shaker.\n TCEP/CAA can be removed from slot 1\n ''')\n\n try:\n\n hs_mod.close_labware_latch()\n hs_mod.set_and_wait_for_shake_speed(750)\n except UnboundLocalError:\n pass\n\n if not test_mode:\n ctx.delay(minutes=10)\n else:\n ctx.comment('skipping 10 minute delay for test mode')\n try:\n hs_mod.deactivate_heater()\n hs_mod.deactivate_shaker()\n except UnboundLocalError:\n pass\n\n ctx.pause('''\n Put plate containing reduced and alkylated samples on ice for 1 min.\n After cool-down process manually until protease digest.\n Put S-Trap plate containing sample on slot 3.\n ''')\n\n ctx.comment('\\n---------------40 - ADD TRYPSIN----------------\\n\\n')\n m300.pick_up_tip()\n for col in s_trap_plate.rows()[0][:num_col]:\n m300.aspirate(125, trypsin)\n m300.dispense(125, col)\n m300.drop_tip()\n\n ctx.pause('''\n Check that all protease solution is at the bottom of the S-trap columns.\n If not, tap the S-trap plate until all solution is\n covering the S-trap material.\n Incubate S-trap plate with cover\n (do not seal tightly!) in incubator at 37\u00b0C overnight.\n Do not shake!\n Store leftover trypsin solution at -20\u00b0C. After digestion, perform elution\n with the TECAN Resolvex A200 or centrifuge.\n Dry eluted peptides (in 96-well plate) with a vaccuum concentrator.\n ''')\n", + "custom_labware_defs": [ + { + "brand": { + "brand": "Agilent", + "brandId": [ + "C18_OMIX_200uL" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 63.8 + }, + "groups": [ + { + "metadata": {}, + "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": "tipRack", + "displayName": "Agilent 96 C18 OMIX 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": true, + "loadName": "agilent_96_c18omix_200ul", + "quirks": [], + "tipLength": 50.4 + }, + "schemaVersion": 2, + "version": 1, + "wells": { + "A1": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 14.38, + "y": 74.24, + "z": 13.4 + }, + "A10": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 95.38, + "y": 74.24, + "z": 13.4 + }, + "A11": { + "depth": 50.4, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 200, + "x": 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"yDimension": 8.1, + "z": 4.82 + }, + "F8": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 77.5, + "xDimension": 8.1, + "y": 30.15, + "yDimension": 8.1, + "z": 4.82 + }, + "F9": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 86.5, + "xDimension": 8.1, + "y": 30.15, + "yDimension": 8.1, + "z": 4.82 + }, + "G1": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 14.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G10": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 95.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G11": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 104.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G12": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 113.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G2": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 23.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G3": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 32.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G4": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 41.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G5": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 50.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G6": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 59.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G7": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 68.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G8": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 77.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "G9": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 86.5, + "xDimension": 8.1, + "y": 21.25, + "yDimension": 8.1, + "z": 4.82 + }, + "H1": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 14.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H10": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 95.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H11": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 104.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H12": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 113.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H2": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 23.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H3": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 32.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H4": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 41.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H5": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 50.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H6": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 59.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H7": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 68.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H8": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 77.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + }, + "H9": { + "depth": 25.78, + "shape": "rectangular", + "totalLiquidVolume": 1400, + "x": 86.5, + "xDimension": 8.1, + "y": 12.35, + "yDimension": 8.1, + "z": 4.82 + } + } + } + ], + "fields": [ + { + "default": 96, + "label": "Number of samples (8-96)", + "name": "num_samp", + "type": "int" + }, + { + "label": "Test Mode or Real Mode (skip incubation times)?", + "name": "test_mode", + "options": [ + { + "label": "Real Mode", + "value": false + }, + { + "label": "Test Mode (skip incubation times)", + "value": true + } + ], + "type": "dropDown" + }, + { + "label": "P300 Multi-Channel Mount", + "name": "m300_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" + } + ], + "type": "dropDown" + } + ], + "instruments": [ + { + "mount": "left", + "name": "p300_multi_gen2" + }, + { + "mount": "right", + "name": "p20_multi_gen2" + } + ], + "labware": [ + { + "name": "3DPrint 96 Tube Rack with Nippon 0.2 mL on 1", + "share": false, + "slot": "1", + "type": "3dprint_96_tuberack_200ul" + }, + { + "name": "Agilent 96 Well Plate 1400 \u00b5L on 2", + "share": false, + "slot": "2", + "type": "agilent_96_wellplate_1400ul" + }, + { + "name": "Protifi_S-trap 96 Well Plate 400 \u00b5L on 3", + "share": false, + "slot": "3", + "type": "protifistrap_96_wellplate_400ul" + }, + { + "name": "NEST 12 Well Reservoir 15 mL on 4", + "share": false, + "slot": "4", + "type": "nest_12_reservoir_15ml" + }, + { + "name": "Opentrons 96 Tip Rack 20 \u00b5L on 5", + "share": false, + "slot": "5", + "type": "opentrons_96_tiprack_20ul" + }, + { + "name": "Opentrons 96 Tip Rack 300 \u00b5L on 6", + "share": false, + "slot": "6", + "type": "opentrons_96_tiprack_300ul" + }, + { + "name": "Agilent 96 Well Plate 1400 \u00b5L on 10", + "share": false, + "slot": "10", + "type": "agilent_96_wellplate_1400ul" + }, + { + "name": "Opentrons Fixed Trash on 12", + "share": false, + "slot": "12", + "type": "opentrons_1_trash_1100ml_fixed" + } + ], + "metadata": { + "apiLevel": "2.13", + "author": "Rami Farawi ", + "protocolName": "VIB UGENT - Multi-channel Workflow Part 1", + "source": "Custom Protocol Request" + }, + "modules": [] +} \ No newline at end of file diff --git a/protoBuilds/00c517multi1/README.json b/protoBuilds/00c517multi1/README.json new file mode 100644 index 000000000..b7b824cf5 --- /dev/null +++ b/protoBuilds/00c517multi1/README.json @@ -0,0 +1,32 @@ +{ + "author": "Opentrons", + "categories": { + "Broad Category": [ + "Specific Category" + ] + }, + "deck-setup": "", + "description": "This protocol does stuff!", + "internal": "00c517multi1", + "labware": "\nAgilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\nAgilent 96 Well Plate 1200 \u00b5L #round well\nProtifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\nAgilent 96 Well Plate 500 \u00b5L #5042-1385\nAgilent 96 Well Plate 1400 \u00b5L #204355-100\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\n", + "markdown": { + "author": "[Opentrons](https://opentrons.com/)\n\n\n", + "categories": "* Broad Category\n\t* Specific Category\n\n\n", + "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/deck.png)\n\n\n", + "description": "This protocol does stuff!\n\n\n", + "internal": "00c517multi1\n", + "labware": "* Agilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\n* Agilent 96 Well Plate 1200 \u00b5L #round well\n* Protifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\n* Agilent 96 Well Plate 500 \u00b5L #5042-1385\n* Agilent 96 Well Plate 1400 \u00b5L #204355-100\n* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102)\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-300ul-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", + "pipettes": "* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P300 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. Step 1...\n\n\n", + "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/reagents.png)\n\n\n", + "title": "VIB UGENT - Multi-channel Workflow Part 1" + }, + "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 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": "\nStep 1...\n", + "reagent-setup": "", + "title": "VIB UGENT - Multi-channel Workflow Part 1" +} \ No newline at end of file diff --git a/protoBuilds/00c517multi1/metadata.json b/protoBuilds/00c517multi1/metadata.json new file mode 100644 index 000000000..c88c3f04b --- /dev/null +++ b/protoBuilds/00c517multi1/metadata.json @@ -0,0 +1,20 @@ +{ + "files": { + "OT 1 protocol": [], + "OT 2 protocol": [ + "00c517multi1.ot2.apiv2.py" + ], + "description": [ + "README.md" + ] + }, + "flags": { + "embedded-app": false, + "feature": false, + "hide-from-search": false, + "skip-tests": false + }, + "path": "protocols/00c517multi1", + "slug": "00c517multi1", + "status": "ok" +} \ No newline at end of file diff --git a/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py b/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py index a66aacc21..b5a5f6fe2 100644 --- a/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py +++ b/protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py @@ -112,7 +112,7 @@ def pick_up_c18(): )): pick_up_c18() for _ in range(3): - m300.aspirate(100, equil_buffer[0 if i < 6 else 1], rate=0.2) # ONE COLUMN PER 6 SAMPLES + m300.aspirate(100, equil_buffer[0 if i < 6 else 1], rate=0.2) m300.dispense(100, waste.top()) for _ in range(5): diff --git a/protocols/00c517multi1-pt2/README.md b/protocols/00c517multi1-pt2/README.md new file mode 100644 index 000000000..463ac25aa --- /dev/null +++ b/protocols/00c517multi1-pt2/README.md @@ -0,0 +1,60 @@ +# VIB UGENT - Multi-channel Workflow Part 2 + + +### Author +[Opentrons](https://opentrons.com/) + + +## Categories +* Broad Category + * Specific Category + + +## Description +This protocol does stuff! + + +### Labware +* Agilent 96 C18 OMIX 200 µl #C18_OMIX_200uL +* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014 +* Agilent 96 Well Plate 1200 µL #round well +* Protifi_S-trap 96 Well Plate 400 µL #S-trap +* Agilent 96 Well Plate 500 µL #5042-1385 +* Agilent 96 Well Plate 1400 µL #204355-100 +* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102) +* [NEST 1 Well Reservoir 195 mL #360103](http://www.cell-nest.com/page94?_l=en&product_id=102) +* [Opentrons 96 Tip Rack 300 µL](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips) + + +### Pipettes +* [Opentrons P300 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/00c517multi1-pt2/deck.png) + + +### Reagent Setup +![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/reagents.png) + + +### Protocol Steps +1. Step 1... + + +### 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 +00c517multi1-pt2 diff --git a/protocols/00c517multi1/00c517multi1.ot2.apiv2.py b/protocols/00c517multi1/00c517multi1.ot2.apiv2.py index 5f33dd3a0..4173977d4 100644 --- a/protocols/00c517multi1/00c517multi1.ot2.apiv2.py +++ b/protocols/00c517multi1/00c517multi1.ot2.apiv2.py @@ -4,7 +4,7 @@ 'protocolName': 'VIB UGENT - Multi-channel Workflow Part 1', 'author': 'Rami Farawi ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.15' + 'apiLevel': '2.13' } @@ -24,14 +24,14 @@ def run(ctx): reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4) # agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot) # for slot in [7, 8, 9, 11]] - try: + if not ctx.is_simulating: hs_mod = ctx.load_module('heaterShakerModuleV1', 10) hs_plate = hs_mod.load_labware('agilent_96_wellplate_1400ul') hs_mod.close_labware_latch() - except ValueError: + else: hs_plate = ctx.load_labware('agilent_96_wellplate_1400ul', 10) hs_plate = hs_plate - tips20 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) + tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot) for slot in [5]] tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot) for slot in [6]] @@ -64,26 +64,39 @@ def run(ctx): m20.dispense(7, col) m20.mix(3, 20, col) m20.drop_tip() - # step 30 + if not test_mode: - hs_mod.set_and_wait_for_temperature(95) + if not ctx.is_simulating: + hs_mod.set_and_wait_for_temperature(95) else: ctx.comment('skipping temperature to 95 for test mode') - hs_mod.open_labware_latch() + + if not ctx.is_simulating: + hs_mod.open_labware_latch() + ctx.pause(''' Wrap plate with tin foil and transfer plate to heater-shaker at 95°C. Incubate for 10 min on heater-shaker. TCEP/CAA can be removed from slot 1 ''') - hs_mod.close_labware_latch() - hs_mod.set_and_wait_for_shake_speed(750) + + try: + + hs_mod.close_labware_latch() + hs_mod.set_and_wait_for_shake_speed(750) + except UnboundLocalError: + pass + if not test_mode: ctx.delay(minutes=10) else: ctx.comment('skipping 10 minute delay for test mode') - hs_mod.deactivate_heater() - hs_mod.deactivate_shaker() + try: + hs_mod.deactivate_heater() + hs_mod.deactivate_shaker() + except UnboundLocalError: + pass ctx.pause(''' Put plate containing reduced and alkylated samples on ice for 1 min. diff --git a/protocols/00c517multi1/README.md b/protocols/00c517multi1/README.md new file mode 100644 index 000000000..60195a308 --- /dev/null +++ b/protocols/00c517multi1/README.md @@ -0,0 +1,61 @@ +# VIB UGENT - Multi-channel Workflow Part 1 + + +### Author +[Opentrons](https://opentrons.com/) + + +## Categories +* Broad Category + * Specific Category + + +## Description +This protocol does stuff! + + +### Labware +* Agilent 96 C18 OMIX 200 µl #C18_OMIX_200uL +* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014 +* Agilent 96 Well Plate 1200 µL #round well +* Protifi_S-trap 96 Well Plate 400 µL #S-trap +* Agilent 96 Well Plate 500 µL #5042-1385 +* Agilent 96 Well Plate 1400 µL #204355-100 +* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102) +* [Opentrons 96 Tip Rack 20 µL](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips) +* [Opentrons 96 Tip Rack 300 µL](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips) + + +### Pipettes +* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) +* [Opentrons P300 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/00c517multi1/deck.png) + + +### Reagent Setup +![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/reagents.png) + + +### Protocol Steps +1. Step 1... + + +### 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 +00c517multi1 From 7479fd6455bf4dd8a72bc4a4fe7c4b8afa604efd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Thu, 1 Feb 2024 12:19:09 -0500 Subject: [PATCH 3/3] fix --- protoBuilds/00c517multi1-pt2/README.json | 16 ++++++---------- protoBuilds/00c517multi1/README.json | 16 ++++++---------- protocols/00c517multi1-pt2/README.md | 14 ++++---------- protocols/00c517multi1/README.md | 14 ++++---------- 4 files changed, 20 insertions(+), 40 deletions(-) diff --git a/protoBuilds/00c517multi1-pt2/README.json b/protoBuilds/00c517multi1-pt2/README.json index badde870d..b8054aaa1 100644 --- a/protoBuilds/00c517multi1-pt2/README.json +++ b/protoBuilds/00c517multi1-pt2/README.json @@ -1,32 +1,28 @@ { "author": "Opentrons", "categories": { - "Broad Category": [ - "Specific Category" + "Sample Prep": [ + "Plate Filling" ] }, "deck-setup": "", - "description": "This protocol does stuff!", + "description": "This protocol performs steps 41.2-end of this SOP. One reservoir well of wash buffer should be used for each column of samples. One equilibration buffer reservoir well is used per 6 columns of sample. One elution buffer reservoir well is used per elution buffer plate.", "internal": "00c517multi1-pt2", "labware": "\nAgilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\nAgilent 96 Well Plate 1200 \u00b5L #round well\nProtifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\nAgilent 96 Well Plate 500 \u00b5L #5042-1385\nAgilent 96 Well Plate 1400 \u00b5L #204355-100\nNEST 12 Well Reservoir 15 mL #360102\nNEST 1 Well Reservoir 195 mL #360103\nOpentrons 96 Tip Rack 300 \u00b5L\n", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n\n", - "categories": "* Broad Category\n\t* Specific Category\n\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/deck.png)\n\n\n", - "description": "This protocol does stuff!\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/00c517-multi/pt2.png)\n\n\n\n\n", + "description": "[This protocol performs steps 41.2-end of this SOP](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/VIB-UGENT_Customized_protocol_S-trap_steps_Multi.xlsx). One reservoir well of wash buffer should be used for each column of samples. One equilibration buffer reservoir well is used per 6 columns of sample. One elution buffer reservoir well is used per elution buffer plate.\n\n\n", "internal": "00c517multi1-pt2\n", "labware": "* Agilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\n* Agilent 96 Well Plate 1200 \u00b5L #round well\n* Protifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\n* Agilent 96 Well Plate 500 \u00b5L #5042-1385\n* Agilent 96 Well Plate 1400 \u00b5L #204355-100\n* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102)\n* [NEST 1 Well Reservoir 195 mL #360103](http://www.cell-nest.com/page94?_l=en&product_id=102)\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-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", "pipettes": "* [Opentrons P300 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. Step 1...\n\n\n", - "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/reagents.png)\n\n\n", "title": "VIB UGENT - Multi-channel Workflow Part 2" }, "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 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": "\nStep 1...\n", - "reagent-setup": "", "title": "VIB UGENT - Multi-channel Workflow Part 2" } \ No newline at end of file diff --git a/protoBuilds/00c517multi1/README.json b/protoBuilds/00c517multi1/README.json index b7b824cf5..6228aab0f 100644 --- a/protoBuilds/00c517multi1/README.json +++ b/protoBuilds/00c517multi1/README.json @@ -1,32 +1,28 @@ { "author": "Opentrons", "categories": { - "Broad Category": [ - "Specific Category" + "Sample Prep": [ + "Plate Filling" ] }, "deck-setup": "", - "description": "This protocol does stuff!", + "description": "This protocol performs steps 23-41.1 of this SOP", "internal": "00c517multi1", "labware": "\nAgilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\nAgilent 96 Well Plate 1200 \u00b5L #round well\nProtifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\nAgilent 96 Well Plate 500 \u00b5L #5042-1385\nAgilent 96 Well Plate 1400 \u00b5L #204355-100\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\n", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n\n", - "categories": "* Broad Category\n\t* Specific Category\n\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/deck.png)\n\n\n", - "description": "This protocol does stuff!\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/00c517-multi/pt1.png)\n\n\n\n\n", + "description": "[This protocol performs steps 23-41.1 of this SOP](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/VIB-UGENT_Customized_protocol_S-trap_steps_Multi.xlsx)\n\n\n", "internal": "00c517multi1\n", "labware": "* Agilent 96 C18 OMIX 200 \u00b5l #C18_OMIX_200uL\n* 3DPrint 96 Tube Rack with Nippon 0.2 mL #U0014\n* Agilent 96 Well Plate 1200 \u00b5L #round well\n* Protifi_S-trap 96 Well Plate 400 \u00b5L #S-trap\n* Agilent 96 Well Plate 500 \u00b5L #5042-1385\n* Agilent 96 Well Plate 1400 \u00b5L #204355-100\n* [NEST 12 Well Reservoir 15 mL #360102](http://www.cell-nest.com/page94?_l=en&product_id=102)\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-300ul-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", "pipettes": "* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P300 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. Step 1...\n\n\n", - "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/reagents.png)\n\n\n", "title": "VIB UGENT - Multi-channel Workflow Part 1" }, "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 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": "\nStep 1...\n", - "reagent-setup": "", "title": "VIB UGENT - Multi-channel Workflow Part 1" } \ No newline at end of file diff --git a/protocols/00c517multi1-pt2/README.md b/protocols/00c517multi1-pt2/README.md index 463ac25aa..8ef4e6d8f 100644 --- a/protocols/00c517multi1-pt2/README.md +++ b/protocols/00c517multi1-pt2/README.md @@ -6,12 +6,12 @@ ## Categories -* Broad Category - * Specific Category +* Sample Prep + * Plate Filling ## Description -This protocol does stuff! +[This protocol performs steps 41.2-end of this SOP](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/VIB-UGENT_Customized_protocol_S-trap_steps_Multi.xlsx). One reservoir well of wash buffer should be used for each column of samples. One equilibration buffer reservoir well is used per 6 columns of sample. One elution buffer reservoir well is used per elution buffer plate. ### Labware @@ -31,15 +31,9 @@ This protocol does stuff! ### Deck Setup -![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/deck.png) +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/pt2.png) -### Reagent Setup -![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1-pt2/reagents.png) - - -### Protocol Steps -1. Step 1... ### Process diff --git a/protocols/00c517multi1/README.md b/protocols/00c517multi1/README.md index 60195a308..357ef5239 100644 --- a/protocols/00c517multi1/README.md +++ b/protocols/00c517multi1/README.md @@ -6,12 +6,12 @@ ## Categories -* Broad Category - * Specific Category +* Sample Prep + * Plate Filling ## Description -This protocol does stuff! +[This protocol performs steps 23-41.1 of this SOP](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/VIB-UGENT_Customized_protocol_S-trap_steps_Multi.xlsx) ### Labware @@ -32,15 +32,9 @@ This protocol does stuff! ### Deck Setup -![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/deck.png) +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517-multi/pt1.png) -### Reagent Setup -![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/00c517multi1/reagents.png) - - -### Protocol Steps -1. Step 1... ### Process