Mercurial > repos > tduigou > dnabot
changeset 1:c3db8a581ca5 draft
Deleted selected files
| author | tduigou |
|---|---|
| date | Tue, 14 Dec 2021 14:47:32 +0000 |
| parents | ed297a952c06 |
| children | e6f30afcf8f8 |
| files | test-data/dnabot_scripts/output/1_clip_ot2_APIv1.py test-data/dnabot_scripts/output/1_clip_ot2_APIv2.8.py test-data/dnabot_scripts/output/1_clip_ot2_Thermocycler_APIv2.8.py test-data/dnabot_scripts/output/2_purification_ot2_APIv1.py test-data/dnabot_scripts/output/2_purification_ot2_APIv2.8.py test-data/dnabot_scripts/output/3_assembly_ot2_APIv1.py test-data/dnabot_scripts/output/3_assembly_ot2_APIv2.8.py test-data/dnabot_scripts/output/3_assembly_ot2_Thermocycler_APIv2.8.py test-data/dnabot_scripts/output/4_transformation_ot2_APIv1.py test-data/dnabot_scripts/output/4_transformation_ot2_APIv2.8.py test-data/dnabot_scripts/output/4_transformation_ot2_Thermocycler_APIv2.8.py test-data/dnabot_scripts/output/metainformation/dataset_4472_clip_run_info.csv test-data/dnabot_scripts/output/metainformation/dataset_4472_final_assembly_run_info.csv test-data/dnabot_scripts/output/metainformation/dataset_4472_wells.txt |
| diffstat | 14 files changed, 0 insertions(+), 2378 deletions(-) [+] |
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--- a/test-data/dnabot_scripts/output/1_clip_ot2_APIv1.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -from opentrons import labware, instruments, modules, robot - - -clips_dict={"prefixes_wells": ["B8", "B7", "C5", "C12", "C7", "B7", "C4", "C9", "C10", "B7", "C8", "C11", "C5"], "prefixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "suffixes_wells": ["A7", "C1", "C3", "C2", "A8", "C1", "C2", "C3", "A8", "C2", "C3", "C1", "A8"], "suffixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "parts_wells": ["A1", "A10", "A3", "A11", "A6", "A9", "A2", "A5", "A7", "A10", "A8", "A4", "A12"], "parts_plates": ["5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5"], "parts_vols": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], "water_vols": [7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0]} - - -def clip( - prefixes_wells, - prefixes_plates, - suffixes_wells, - suffixes_plates, - parts_wells, - parts_plates, - parts_vols, - water_vols, - tiprack_type="tiprack-10ul"): - """Implements linker ligation reactions using an opentrons OT-2.""" - - # Constants - INITIAL_TIP = 'A1' - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9'] - PIPETTE_TYPE = 'P10_Single' - PIPETTE_MOUNT = 'right' - SOURCE_PLATE_TYPE = '4ti-0960_FrameStar' - DESTINATION_PLATE_TYPE = '4ti-0960_FrameStar' - DESTINATION_PLATE_POSITION = '1' - TUBE_RACK_TYPE = 'tube-rack_E1415-1500' - TUBE_RACK_POSITION = '4' - MASTER_MIX_WELL = 'A1' - WATER_WELL = 'A2' - INITIAL_DESTINATION_WELL = 'A1' - MASTER_MIX_VOLUME = 20 - LINKER_MIX_SETTINGS = (1, 3) - PART_MIX_SETTINGS = (4, 5) - - # Tiprack slots - total_tips = 4 * len(parts_wells) - letter_dict = {'A': 0, 'B': 1, 'C': 2, - 'D': 3, 'E': 4, 'F': 5, 'G': 6, 'H': 7} - tiprack_1_tips = ( - 13 - int(INITIAL_TIP[1:])) * 8 - letter_dict[INITIAL_TIP[0]] - if total_tips > tiprack_1_tips: - tiprack_num = 1 + (total_tips - tiprack_1_tips) // 96 + \ - (1 if (total_tips - tiprack_1_tips) % 96 > 0 else 0) - else: - tiprack_num = 1 - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - - # Define source plates - source_plates = {} - source_plates_keys = list(set((prefixes_plates + suffixes_plates + parts_plates))) - for key in source_plates_keys: - source_plates[key] = labware.load(SOURCE_PLATE_TYPE, key) - - # Define remaining labware - tipracks = [labware.load(tiprack_type, slot) for slot in slots] - if PIPETTE_TYPE != 'P10_Single': - print('Define labware must be changed to use', PIPETTE_TYPE) - exit() - pipette = instruments.P10_Single(mount=PIPETTE_MOUNT, tip_racks=tipracks) - pipette.start_at_tip(tipracks[0].well(INITIAL_TIP)) - destination_plate = labware.load( - DESTINATION_PLATE_TYPE, DESTINATION_PLATE_POSITION) - tube_rack = labware.load(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - master_mix = tube_rack.wells(MASTER_MIX_WELL) - water = tube_rack.wells(WATER_WELL) - destination_wells = destination_plate.wells( - INITIAL_DESTINATION_WELL, length=int(len(parts_wells))) - - # Transfers - pipette.pick_up_tip() - pipette.transfer(MASTER_MIX_VOLUME, master_mix, - destination_wells, new_tip='never') - pipette.drop_tip() - pipette.transfer(water_vols, water, - destination_wells, new_tip='always') - for clip_num in range(len(parts_wells)): - pipette.transfer(1, source_plates[prefixes_plates[clip_num]].wells(prefixes_wells[clip_num]), - destination_wells[clip_num], mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(1, source_plates[suffixes_plates[clip_num]].wells(suffixes_wells[clip_num]), - destination_wells[clip_num], mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(parts_vols[clip_num], source_plates[parts_plates[clip_num]].wells(parts_wells[clip_num]), - destination_wells[clip_num], mix_after=PART_MIX_SETTINGS) - - -clip(**clips_dict) - -# Robot comments -for c in robot.commands(): - print(c) \ No newline at end of file
--- a/test-data/dnabot_scripts/output/1_clip_ot2_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -from opentrons import protocol_api - -# Rename to 'clip_template' and paste into 'template_ot2_scripts' folder in DNA-BOT to use -# Code has been reordered to better group relevant commands and take the constants out of def clip() - -#metadata -metadata = { - 'apiLevel': '2.8', - 'protocolName': 'CLIP_No_Thermocycler', - 'description': 'Implements linker ligation reactions using an opentrons OT-2. This version does not include the Thermocycler module.'} - -# example dictionary produced by DNA-BOT for a single construct containing 5 parts, un-comment and run to test the template -#clips_dict={"prefixes_wells": ["A8", "A7", "C5", "C7", "C10"], "prefixes_plates": ["2", "2", "2", "2", "2"], "suffixes_wells": ["B7", "C1", "C2", "C3", "B8"], "suffixes_plates": ["2", "2", "2", "2", "2"], "parts_wells": ["E2", "F2", "C2", "B2", "D2"], "parts_plates": ["5", "5", "5", "5", "5"], "parts_vols": [1, 1, 1, 1, 1], "water_vols": [7.0, 7.0, 7.0, 7.0, 7.0]} - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - -clips_dict={"prefixes_wells": ["B8", "B7", "C5", "C12", "C7", "B7", "C4", "C9", "C10", "B7", "C8", "C11", "C5"], "prefixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "suffixes_wells": ["A7", "C1", "C3", "C2", "A8", "C1", "C2", "C3", "A8", "C2", "C3", "C1", "A8"], "suffixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "parts_wells": ["A1", "A10", "A3", "A11", "A6", "A9", "A2", "A5", "A7", "A10", "A8", "A4", "A12"], "parts_plates": ["5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5"], "parts_vols": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], "water_vols": [7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0]} -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - - -def run(protocol: protocol_api.ProtocolContext): -# added run function for API 2.8 - - ### Constants - these have been moved out of the def clip() for clarity - - #Tiprack - tiprack_type=__LABWARES['96_tiprack_20ul']['id'] - INITIAL_TIP = 'A1' - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9'] - - # Pipettes - pipette instructions in a single location so redefining pipette type is simpler - PIPETTE_TYPE = __LABWARES['p20_single']['id'] - # API 2 supports gen_1 pipettes like the p10_single - PIPETTE_MOUNT = 'right' - ### Load Pipette - # checks if it's a P10 Single pipette - if PIPETTE_TYPE != 'p20_single_gen2': - print('Define labware must be changed to use', PIPETTE_TYPE) - exit() - - # Source Plates - SOURCE_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - # modified from custom labware as API 2 doesn't support labware.create anymore, so the old add_labware script can't be used - - # Destination Plates - DESTINATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - DESTINATION_PLATE_POSITION = '1' - # INITIAL_DESTINATION_WELL constant removed, as destination_plate.wells() automatically starts from A1 - - # Tube Rack - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - TUBE_RACK_POSITION = '4' - MASTER_MIX_WELL = 'A1' - WATER_WELL = 'A2' - MASTER_MIX_VOLUME = 20 - - # Mix settings - LINKER_MIX_SETTINGS = (1, 3) - PART_MIX_SETTINGS = (4, 5) - - def clip( - prefixes_wells, - prefixes_plates, - suffixes_wells, - suffixes_plates, - parts_wells, - parts_plates, - parts_vols, - water_vols): - - ### Loading Tiprack - # Calculates whether one, two, or three tipracks are needed, which are in slots 3, 6, and 9 respectively - total_tips = 4 * len(parts_wells) - letter_dict = {'A': 0, 'B': 1, 'C': 2, - 'D': 3, 'E': 4, 'F': 5, 'G': 6, 'H': 7} - tiprack_1_tips = ( - 13 - int(INITIAL_TIP[1:])) * 8 - letter_dict[INITIAL_TIP[0]] - if total_tips > tiprack_1_tips: - tiprack_num = 1 + (total_tips - tiprack_1_tips) // 96 + \ - (1 if (total_tips - tiprack_1_tips) % 96 > 0 else 0) - else: - tiprack_num = 1 - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - - # loads the correct number of tipracks - tipracks = [protocol.load_labware(tiprack_type, slot) for slot in slots] - - # Loads pipette according to constants assigned above - pipette = protocol.load_instrument(PIPETTE_TYPE, mount=PIPETTE_MOUNT, tip_racks=tipracks) - - ### Load Destination Plate - # Loads destination plate according to constants assigned above - destination_plate = protocol.load_labware(DESTINATION_PLATE_TYPE, DESTINATION_PLATE_POSITION) - - # Defines where the destination wells are within the destination plate - destination_wells = destination_plate.wells()[0:len(parts_wells)] - - ### Load Tube Rack - # Loads tube rack according to constants assigned above - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - - # Defines positions of master mix and water within the tube rack - master_mix = tube_rack.wells(MASTER_MIX_WELL) - water = tube_rack.wells(WATER_WELL) - - ### Loading Source Plates - # Makes a source plate key for where prefixes, suffixes, and parts are located, according to the dictionary generated by the DNA-BOT - source_plates = {} - source_plates_keys = list(set((prefixes_plates + suffixes_plates + parts_plates))) - - # Loads plates according to the source plate key - for key in source_plates_keys: - source_plates[key]=protocol.load_labware(SOURCE_PLATE_TYPE, key) - - ### Transfers - - # transfer master mix into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - pipette.pick_up_tip() - pipette.transfer(MASTER_MIX_VOLUME, master_mix, destination_wells, blow_out=True, blowout_location='destination well', new_tip='never') - pipette.drop_tip() - - # transfer water into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - pipette.transfer(water_vols, water, destination_wells, blow_out=True, blowout_location='destination well', new_tip='always') - - #transfer prefixes, suffixes, and parts into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - for clip_num in range(len(parts_wells)): - pipette.transfer(1, source_plates[prefixes_plates[clip_num]].wells(prefixes_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(1, source_plates[suffixes_plates[clip_num]].wells(suffixes_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(parts_vols[clip_num], source_plates[parts_plates[clip_num]].wells(parts_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=PART_MIX_SETTINGS) - - # the run function will first define the CLIP function, and then run the CLIP function with the dictionary produced by DNA-BOT - clip(**clips_dict)
--- a/test-data/dnabot_scripts/output/1_clip_ot2_Thermocycler_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,152 +0,0 @@ -from opentrons import protocol_api - -# Rename to 'clip_template' and paste into 'template_ot2_scripts' folder in DNA-BOT to use - -#metadata -metadata = { - 'apiLevel': '2.8', - 'protocolName': 'CLIP_With_Thermocycler', - 'description': 'Implements linker ligation reactions using an opentrons OT-2, including the thermocycler module.'} - - - -# example dictionary produced by DNA-BOT for a single construct containing 5 parts, un-comment and run to test the template -#clips_dict={"prefixes_wells": ["A8", "A7", "C5", "C7", "C10"], "prefixes_plates": ["2", "2", "2", "2", "2"], "suffixes_wells": ["B7", "C1", "C2", "C3", "B8"], "suffixes_plates": ["2", "2", "2", "2", "2"], "parts_wells": ["E2", "F2", "C2", "B2", "D2"], "parts_plates": ["5", "5", "5", "5", "5"], "parts_vols": [1, 1, 1, 1, 1], "water_vols": [7.0, 7.0, 7.0, 7.0, 7.0]} - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - -clips_dict={"prefixes_wells": ["B8", "B7", "C5", "C12", "C7", "B7", "C4", "C9", "C10", "B7", "C8", "C11", "C5"], "prefixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "suffixes_wells": ["A7", "C1", "C3", "C2", "A8", "C1", "C2", "C3", "A8", "C2", "C3", "C1", "A8"], "suffixes_plates": ["2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2"], "parts_wells": ["A1", "A10", "A3", "A11", "A6", "A9", "A2", "A5", "A7", "A10", "A8", "A4", "A12"], "parts_plates": ["5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5"], "parts_vols": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], "water_vols": [7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0, 7.0]} -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - - -def run(protocol: protocol_api.ProtocolContext): -# added run function for API 2.8 - - ### Constants - these have been moved out of the def clip() for clarity - - #Tiprack - tiprack_type=__LABWARES['96_tiprack_20ul']['id'] - INITIAL_TIP = 'A1' - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9'] - - # Pipettes - pipette instructions in a single location so redefining pipette type is simpler - PIPETTE_TYPE = __LABWARES['p20_single']['id'] - PIPETTE_MOUNT = 'right' - ### Load Pipette - # checks if it's a P10 Single pipette - if PIPETTE_TYPE != 'p20_single_gen2': - print('Define labware must be changed to use', PIPETTE_TYPE) - exit() -#Thermocycler Module - tc_mod = protocol.load_module('Thermocycler Module') -# Destination Plates - DESTINATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - # Loads destination plate onto Thermocycler Module - destination_plate = tc_mod.load_labware(DESTINATION_PLATE_TYPE) - - # Source Plates - SOURCE_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - # modified from custom labware as API 2 doesn't support labware.create anymore, so the old add_labware script can't be used - - # Tube Rack - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - # modified from custom labware as API 2 doesn't support labware.create anymore, so the old add_labware script can't be used - TUBE_RACK_POSITION = '4' - MASTER_MIX_WELL = 'A1' - WATER_WELL = 'A2' - MASTER_MIX_VOLUME = 20 - - # Mix settings - LINKER_MIX_SETTINGS = (1, 3) - PART_MIX_SETTINGS = (4, 5) - - def clip( - prefixes_wells, - prefixes_plates, - suffixes_wells, - suffixes_plates, - parts_wells, - parts_plates, - parts_vols, - water_vols): - - ### Loading Tiprack - # Calculates whether one, two, or three tipracks are needed, which are in slots 3, 6, and 9 respectively - total_tips = 4 * len(parts_wells) - letter_dict = {'A': 0, 'B': 1, 'C': 2, - 'D': 3, 'E': 4, 'F': 5, 'G': 6, 'H': 7} - tiprack_1_tips = ( - 13 - int(INITIAL_TIP[1:])) * 8 - letter_dict[INITIAL_TIP[0]] - if total_tips > tiprack_1_tips: - tiprack_num = 1 + (total_tips - tiprack_1_tips) // 96 + \ - (1 if (total_tips - tiprack_1_tips) % 96 > 0 else 0) - else: - tiprack_num = 1 - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - - # loads the correct number of tipracks - tipracks = [protocol.load_labware(tiprack_type, slot) for slot in slots] - # changed to protocol.load_labware for API 2.8 - - # Loads pipette according to constants assigned above - pipette = protocol.load_instrument(PIPETTE_TYPE, mount=PIPETTE_MOUNT, tip_racks=tipracks) - - # Defines where the destination wells are within the destination plate - destination_wells = destination_plate.wells()[0:len(parts_wells)] - - ### Load Tube Rack - # Loads tube rack according to constants assigned above - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - - # Defines positions of master mix and water within the tube rack - master_mix = tube_rack.wells(MASTER_MIX_WELL) - water = tube_rack.wells(WATER_WELL) - - ### Loading Source Plates - # Makes a source plate key for where prefixes, suffixes, and parts are located, according to the dictionary generated by the DNA-BOT - source_plates = {} - source_plates_keys = list(set((prefixes_plates + suffixes_plates + parts_plates))) - - # Loads plates according to the source plate key - for key in source_plates_keys: - source_plates[key]=protocol.load_labware(SOURCE_PLATE_TYPE, key) - - ### Transfers - - # transfer master mix into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - pipette.pick_up_tip() - pipette.transfer(MASTER_MIX_VOLUME, master_mix, destination_wells, blow_out=True, blowout_location='destination well', new_tip='never') - pipette.drop_tip() - - # transfer water into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - pipette.transfer(water_vols, water, destination_wells, blow_out=True, blowout_location='destination well', new_tip='always') - - #transfer prefixes, suffixes, and parts into destination wells - # added blowout into destination wells ('blowout_location' only works for API 2.8 and above) - for clip_num in range(len(parts_wells)): - pipette.transfer(1, source_plates[prefixes_plates[clip_num]].wells(prefixes_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(1, source_plates[suffixes_plates[clip_num]].wells(suffixes_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=LINKER_MIX_SETTINGS) - pipette.transfer(parts_vols[clip_num], source_plates[parts_plates[clip_num]].wells(parts_wells[clip_num]), destination_wells[clip_num], blow_out=True, blowout_location='destination well', new_tip='always', mix_after=PART_MIX_SETTINGS) - - # the run function will first define the CLIP function, and then run the CLIP function with the dictionary produced by DNA-BOT - clip(**clips_dict) - ### PCR Reaction in Thermocycler - - # close lid and set lid temperature, PCR will not start until lid reaches 37C - tc_mod.close_lid() - tc_mod.set_lid_temperature(105) - - # Runs 20 cycles of 37C for 2 minutes and 20C for 1 minute, then holds for 60C for 10 minutes - profile = [ - {'temperature': 37, 'hold_time_minutes': 2}, - {'temperature': 20, 'hold_time_minutes': 1}] - tc_mod.execute_profile(steps=profile, repetitions=20, block_max_volume=30) - tc_mod.set_block_temperature(60, hold_time_minutes=10, block_max_volume=30) - tc_mod.set_block_temperature(4, hold_time_minutes=2, block_max_volume=30) - #Q Does block_max_volume define total volume in block or individual wells? - tc_mod.set_lid_temperature(37) - tc_mod.open_lid()
--- a/test-data/dnabot_scripts/output/2_purification_ot2_APIv1.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,182 +0,0 @@ -from opentrons import labware, instruments, modules, robot - - -sample_number=13 -ethanol_well='A11' - - -def magbead( - sample_number, - ethanol_well, - elution_buffer_well, - sample_volume=30, - bead_ratio=1.8, - elution_buffer_volume=40, - incubation_time=5, - settling_time=2, - drying_time=5, - elution_time=2, - sample_offset=0, - tiprack_type="opentrons_96_tiprack_300ul"): - """Implements magbead purification reactions for BASIC assembly using an opentrons OT-2. - - Selected args: - ethanol_well (str): well in reagent container containing ethanol. - elution_buffer_well (str): well in reagent container containing elution buffer. - sample_offset (int): offset the intial sample column by the specified value. - - """ - - # Constants - PIPETTE_ASPIRATE_RATE = 25 - PIPETTE_DISPENSE_RATE = 150 - TIPS_PER_SAMPLE = 9 - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9', '2', '5'] - MAGDECK_POSITION = '1' - MIX_PLATE_TYPE = '4ti-0960_FrameStar' - MIX_PLATE_POSITION = '4' - REAGENT_CONTAINER_TYPE = '4ti0131_trough-12' - REAGENT_CONTAINER_POSITION = '7' - BEAD_CONTAINER_TYPE = '4ti0136_96_deep-well' - BEAD_CONTAINER_POSITION = '8' - LIQUID_WASTE_WELL = 'A12' - BEADS_WELL = 'A1' - DEAD_TOTAL_VOL = 5 - SLOW_HEAD_SPEEDS = {'x': 600 // 4, 'y': 400 // 4, - 'z': 125 // 10, 'a': 125 // 10} - DEFAULT_HEAD_SPEEDS = {'x': 400, 'y': 400, 'z': 125, 'a': 100} - IMMOBILISE_MIX_REPS = 10 - MAGDECK_HEIGHT = 20 - AIR_VOL_COEFF = 0.1 - ETHANOL_VOL = 150 - WASH_TIME = 0.5 - ETHANOL_DEAD_VOL = 50 - ELUTION_MIX_REPS = 20 - ELUTANT_SEP_TIME = 1 - ELUTION_DEAD_VOL = 2 - - # Errors - if sample_number > 48: - raise ValueError('sample number cannot exceed 48') - - # Tips and pipette - total_tips = sample_number * TIPS_PER_SAMPLE - tiprack_num = total_tips // 96 + (1 if total_tips % 96 > 0 else 0) - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - tipracks = [labware.load(tiprack_type, slot) - for slot in slots] - pipette = instruments.P300_Multi( - mount="left", - tip_racks=tipracks, - aspirate_flow_rate=PIPETTE_ASPIRATE_RATE, - dispense_flow_rate=PIPETTE_DISPENSE_RATE) - - # Define labware - MAGDECK = modules.load('magdeck', MAGDECK_POSITION) - MAGDECK.disengage() - mag_plate = labware.load(MIX_PLATE_TYPE, MAGDECK_POSITION, share=True) - mix_plate = labware.load(MIX_PLATE_TYPE, MIX_PLATE_POSITION) - reagent_container = labware.load( - REAGENT_CONTAINER_TYPE, REAGENT_CONTAINER_POSITION) - bead_container = labware.load(BEAD_CONTAINER_TYPE, BEAD_CONTAINER_POSITION) - col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0) - samples = [col for col in mag_plate.cols( - )[0 + sample_offset:col_num + sample_offset]] - output = [col for col in mag_plate.cols( - )[6 + sample_offset:col_num + 6 + sample_offset]] - mixing = [col for col in mix_plate.cols( - )[0 + sample_offset:col_num + sample_offset]] - - # Define reagents and liquid waste - liquid_waste = reagent_container.wells(LIQUID_WASTE_WELL) - beads = bead_container.wells(BEADS_WELL) - ethanol = reagent_container.wells(ethanol_well) - elution_buffer = reagent_container.wells(elution_buffer_well) - - # Define bead and mix volume - bead_volume = sample_volume * bead_ratio - if bead_volume / 2 > pipette.max_volume: - mix_vol = pipette.max_volume - else: - mix_vol = bead_volume / 2 - total_vol = bead_volume + sample_volume + DEAD_TOTAL_VOL - - # Mix beads and PCR samples and incubate - for target in range(int(len(samples))): - # Aspirate beads - pipette.pick_up_tip() - pipette.aspirate(bead_volume, beads) - robot.head_speed(**SLOW_HEAD_SPEEDS, combined_speed=max(SLOW_HEAD_SPEEDS.values())) - - # Transfer and mix on mix_plate - pipette.aspirate(sample_volume + DEAD_TOTAL_VOL, samples[target]) - pipette.dispense(total_vol, mixing[target]) - pipette.mix(IMMOBILISE_MIX_REPS, mix_vol, mixing[target]) - pipette.blow_out() - - # Dispose of tip - robot.head_speed(**DEFAULT_HEAD_SPEEDS, combined_speed=max(DEFAULT_HEAD_SPEEDS.values())) - pipette.drop_tip() - - # Immobilise sample - pipette.delay(minutes=incubation_time) - - # Transfer sample back to magdeck - for target in range(int(len(samples))): - pipette.transfer(total_vol, mixing[target], samples[target], - blow_out=True) - - # Engagae MagDeck and incubate - MAGDECK.engage(height=MAGDECK_HEIGHT) - pipette.delay(minutes=settling_time) - - # Remove supernatant from magnetic beads - for target in samples: - pipette.transfer(total_vol, target, liquid_waste, blow_out=True) - - # Wash beads twice with 70% ethanol - air_vol = pipette.max_volume * AIR_VOL_COEFF - for cycle in range(2): - for target in samples: - pipette.transfer(ETHANOL_VOL, ethanol, target, air_gap=air_vol) - pipette.delay(minutes=WASH_TIME) - for target in samples: - pipette.transfer(ETHANOL_VOL + ETHANOL_DEAD_VOL, target, liquid_waste, - air_gap=air_vol) - - # Dry at RT - pipette.delay(minutes=drying_time) - - # Disengage MagDeck - MAGDECK.disengage() - - # Mix beads with elution buffer - if elution_buffer_volume / 2 > pipette.max_volume: - mix_vol = pipette.max_volume - else: - mix_vol = elution_buffer_volume / 2 - for target in samples: - pipette.transfer(elution_buffer_volume, elution_buffer, - target, mix_after=(ELUTION_MIX_REPS, mix_vol)) - - # Incubate at RT for "elution_time" minutes - pipette.delay(minutes=elution_time) - - # Engagae MagDeck for 1 minute and remain engaged for DNA elution - MAGDECK.engage(height=MAGDECK_HEIGHT) - pipette.delay(minutes=ELUTANT_SEP_TIME) - - # Transfer clean PCR product to a new well - for target, dest in zip(samples, output): - pipette.transfer(elution_buffer_volume - ELUTION_DEAD_VOL, target, - dest, blow_out=False) - - # Disengage MagDeck - MAGDECK.disengage() - - -magbead(sample_number=sample_number, - ethanol_well=ethanol_well, elution_buffer_well='A1') - -for c in robot.commands(): - print(c)
--- a/test-data/dnabot_scripts/output/2_purification_ot2_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,261 +0,0 @@ -from opentrons import protocol_api - -# Rename to 'purification_template' and paste into 'template_ot2_scripts' folder in DNA-BOT to use - -metadata = { - 'apiLevel': '2.8', - 'protocolName': 'purification_template', - 'description': 'Implements magbead purification reactions for BASIC assembly using an opentrons OT-2'} - - - - -# example values produced by DNA-BOT for a single construct containing 5 parts, un-comment and run to test the template: -#sample_number=8 -#ethanol_well='A3' - -# __LABWARES and __PARAMETERS are expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -# __PARAMETERS={"purif_magdeck_height": {"value": 20.0}, "purif_wash_time": {"value": 0.5}, "purif_bead_ratio": {"value": 1.8}, "purif_incubation_time": {"value": 5.0}, "purif_settling_time": {"value": 2.0}, "purif_drying_time": {"value": 5.0}, "purif_elution_time": {"value": 2.0}, "transfo_incubation_temp": {"value": 4.0}, "transfo_incubation_time": {"value": 20.0}} - -sample_number=13 -ethanol_well='A11' -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -__PARAMETERS={"purif_magdeck_height": {"value": 20}, "purif_wash_time": {"value": 0}, "purif_bead_ratio": {"value": 1}, "purif_incubation_time": {"value": 5}, "purif_settling_time": {"value": 2}, "purif_drying_time": {"value": 5}, "purif_elution_time": {"value": 2}, "transfo_incubation_temp": {"value": 4}, "transfo_incubation_time": {"value": 20}} - - -def run(protocol: protocol_api.ProtocolContext): -# added run function for API verison 2 - - def magbead( - sample_number, - ethanol_well, - elution_buffer_well='A1', - sample_volume=30, - bead_ratio=__PARAMETERS['purif_bead_ratio']['value'], - elution_buffer_volume=40, - incubation_time=__PARAMETERS['purif_incubation_time']['value'], - settling_time=__PARAMETERS['purif_settling_time']['value'], - # if using Gen 2 magentic module, need to change time! see: https://docs.opentrons.com/v2/new_modules.html - # "The GEN2 Magnetic Module uses smaller magnets than the GEN1 version...this means it will take longer for the GEN2 module to attract beads." - # Recommended Magnetic Module GEN2 bead attraction time: - # Total liquid volume <= 50 uL: 5 minutes - # this template was written with the Gen 1 magnetic module, as it is compatible with API version 2 - drying_time=__PARAMETERS['purif_drying_time']['value'], - elution_time=__PARAMETERS['purif_elution_time']['value'], - sample_offset=0, - tiprack_type=__LABWARES['96_tiprack_300ul']['id']): - - """ - - Selected args: - ethanol_well (str): well in reagent container containing ethanol. - elution_buffer_well (str): well in reagent container containing elution buffer. - sample_offset (int): offset the intial sample column by the specified value. - - """ - - - ### Constants - - # Pipettes - PIPETTE_ASPIRATE_RATE = 25 - PIPETTE_DISPENSE_RATE = 150 - TIPS_PER_SAMPLE = 9 - PIPETTE_TYPE = __LABWARES['p300_multi']['id'] - # new constant for easier swapping between pipette types - - # Tiprack - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9', '2', '5'] - - # Magnetic Module - MAGDECK_POSITION = '1' - - # Mix Plate - MIX_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_23']['id'] - # modified from custom labware as API 2 doesn't support labware.create anymore, so the old add_labware script can't be used - # also acts as the type of plate loaded onto the magnetic module - MIX_PLATE_POSITION = '4' - - # Reagents - REAGENT_CONTAINER_TYPE = __LABWARES['12_reservoir_21000ul']['id'] - REAGENT_CONTAINER_POSITION = '7' - - # Beads - BEAD_CONTAINER_TYPE = __LABWARES['96_deepwellplate_2ml']['id'] - BEAD_CONTAINER_POSITION = '8' - - # Settings - LIQUID_WASTE_WELL = 'A5' - BEADS_WELL = 'A1' - DEAD_TOTAL_VOL = 5 - SLOW_HEAD_SPEEDS = {'x': 600 // 4, 'y': 400 // 4, 'z': 125 // 10, 'a': 125 // 10} - DEFAULT_HEAD_SPEEDS = {'x': 400, 'y': 400, 'z': 125, 'a': 100} - IMMOBILISE_MIX_REPS = 10 - MAGDECK_HEIGHT = __PARAMETERS['purif_magdeck_height']['value'] - AIR_VOL_COEFF = 0.1 - ETHANOL_VOL = 150 - WASH_TIME = __PARAMETERS['purif_wash_time']['value'] - ETHANOL_DEAD_VOL = 50 - ELUTION_MIX_REPS = 20 - ELUTANT_SEP_TIME = 1 - ELUTION_DEAD_VOL = 2 - - - ### Errors - if sample_number > 48: - raise ValueError('sample number cannot exceed 48') - - - ### Loading Tiprack - - # Calculates whether one/two/three/four/five tipracks are needed, which are in slots 3, 6, 9, 2, and 5 respectively - total_tips = sample_number * TIPS_PER_SAMPLE - tiprack_num = total_tips // 96 + (1 if total_tips % 96 > 0 else 0) - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - tipracks = [protocol.load_labware(tiprack_type, slot) for slot in slots] - # changed to protocol.load_labware for API version 2 - - - ### Loading Pipettes - - pipette = protocol.load_instrument(PIPETTE_TYPE, mount="left", tip_racks=tipracks) - pipette.aspirate_flow_rate=PIPETTE_ASPIRATE_RATE - pipette.dispense_flow_rate=PIPETTE_DISPENSE_RATE - # for reference: default aspirate/dispense flow rate for p300_multi_gen2 is 94 ul/s - - ### Define Labware - - # Magnetic Module - MAGDECK = protocol.load_module(__LABWARES['mag_deck']['id'], MAGDECK_POSITION) - # 'magdeck' is the gen 1 magnetic module, use 'magnetic module gen2' for the gen 2 magentic module - # if using gen 2 module, need to change settling time! (see comments under Constants) - MAGDECK.disengage() - # disengages the magnets when it is turned on - mag_plate = MAGDECK.load_labware(MIX_PLATE_TYPE) - - # Mix Plate - mix_plate = protocol.load_labware(MIX_PLATE_TYPE, MIX_PLATE_POSITION) - - # Reagents - reagent_container = protocol.load_labware(REAGENT_CONTAINER_TYPE, REAGENT_CONTAINER_POSITION) - - # Beads Container - bead_container = protocol.load_labware(BEAD_CONTAINER_TYPE, BEAD_CONTAINER_POSITION) - - - ### Calculating Columns - - # Total number of columns - col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0) - - # Columns containing samples in location 1 (magentic module) - # generates a list of lists: [[A1, B1, C1...], [A2, B2, C2...]...] - samples = [col for col in mag_plate.columns()[sample_offset : col_num + sample_offset]] - - # Columns to mix beads and samples in location 4 (mix plate) - mixing = [col for col in mix_plate.columns()[sample_offset:col_num + sample_offset]] - - # Columns to dispense output in location 1 (magnetic module) - # purified parts are dispensed 6 rows to the right of their initial location - # this is why the number of samples cannot exceed 48 - - output = [col for col in mag_plate.columns()[6 + sample_offset:col_num + 6 + sample_offset]] - - ### Defining Wells for Reagents, Liquid Waste, and Beads - - liquid_waste = reagent_container.wells(LIQUID_WASTE_WELL) - ethanol = reagent_container.wells(ethanol_well) - elution_buffer = reagent_container.wells(elution_buffer_well) - beads = bead_container[BEADS_WELL] - - ### Define bead and mix volume - bead_volume = sample_volume * bead_ratio - if bead_volume / 2 > pipette.max_volume: - mix_vol = pipette.max_volume - else: - mix_vol = bead_volume / 2 - total_vol = bead_volume + sample_volume + DEAD_TOTAL_VOL - - - ### Steps - - # Mix beads and parts - for target in range(int(len(samples))): - - # Aspirate beads - pipette.pick_up_tip() - pipette.aspirate(bead_volume, beads) - protocol.max_speeds.update(SLOW_HEAD_SPEEDS) - - # Aspirte samples - pipette.aspirate(sample_volume + DEAD_TOTAL_VOL, samples[target][0]) - - # Transfer and mix on mix_plate - pipette.dispense(total_vol, mixing[target][0]) - # similar to above, added [0] because samples[target] returned a list of every well in column 1 rather than just one well - pipette.mix(IMMOBILISE_MIX_REPS, mix_vol, mixing[target][0]) - # similar to above, added [0] because samples[target] returned a list of every well in column 1 rather than just one well - pipette.blow_out() - - # Dispose of tip - protocol.max_speeds.update(DEFAULT_HEAD_SPEEDS) - pipette.drop_tip() - - # Immobilise sample - protocol.delay(minutes=incubation_time) - - # Transfer beads+samples back to magdeck - for target in range(int(len(samples))): - pipette.transfer(total_vol, mixing[target], samples[target], blow_out=True, blowout_location='destination well') - # added blowout_location=destination well because default location of blowout is waste in API version 2 - - # Engagae MagDeck and incubate - MAGDECK.engage(height=MAGDECK_HEIGHT) - protocol.delay(minutes=settling_time) - - # Remove supernatant from magnetic beads - for target in samples: - pipette.transfer(total_vol, target, liquid_waste, blow_out=True) - - # Wash beads twice with 70% ethanol - air_vol = pipette.max_volume * AIR_VOL_COEFF - for cycle in range(2): - for target in samples: - pipette.transfer(ETHANOL_VOL, ethanol, target, air_gap=air_vol) - protocol.delay(minutes=WASH_TIME) - for target in samples: - pipette.transfer(ETHANOL_VOL + ETHANOL_DEAD_VOL, target, liquid_waste, air_gap=air_vol) - - # Dry at room temperature - protocol.delay(minutes=drying_time) - - # Disengage MagDeck - MAGDECK.disengage() - - # Mix beads with elution buffer - if elution_buffer_volume / 2 > pipette.max_volume: - mix_vol = pipette.max_volume - else: - mix_vol = elution_buffer_volume / 2 - for target in samples: - pipette.transfer(elution_buffer_volume, elution_buffer, target, mix_after=(ELUTION_MIX_REPS, mix_vol)) - - # Incubate at room temperature - protocol.delay(minutes=elution_time) - - # Engage MagDeck (remains engaged for DNA elution) - MAGDECK.engage(height=MAGDECK_HEIGHT) - protocol.delay(minutes=ELUTANT_SEP_TIME) - - # Transfer purified parts to a new well - for target, dest in zip(samples, output): - pipette.transfer(elution_buffer_volume - ELUTION_DEAD_VOL, target, - dest, blow_out=False) - - # Disengage MagDeck - MAGDECK.disengage() - - magbead(sample_number=sample_number, ethanol_well=ethanol_well) - # removed elution buffer well='A1', added that to where the function is defined
--- a/test-data/dnabot_scripts/output/3_assembly_ot2_APIv1.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -from opentrons import labware, instruments, modules, robot -import numpy as np - - -final_assembly_dict={"A1": ["A7", "B7", "C7", "D7", "E7"], "B1": ["A7", "F7", "G7", "H7", "A8"], "C1": ["A7", "B8", "C8", "D8", "E8"]} -tiprack_num=1 - - -def final_assembly(final_assembly_dict, tiprack_num, tiprack_type="tiprack-10ul"): - """Implements final assembly reactions using an opentrons OT-2. - - Args: - final_assembly_dict (dict): Dictionary with keys and values corresponding to destination and associated linker-ligated part wells, respectively. - tiprack_num (int): Number of tipracks required during run. - - """ - - # Constants - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9', '2', '5', '8', '11'] - PIPETTE_MOUNT = 'right' - MAG_PLATE_TYPE = '4ti-0960_FrameStar' - MAG_PLATE_POSITION = '1' - TUBE_RACK_TYPE = 'tube-rack_E1415-1500' - TUBE_RACK_POSITION = '7' - DESTINATION_PLATE_TYPE = 'aluminium-block_4ti-0960_FrameStar' - TEMPDECK_SLOT = '4' - TEMP = 20 - TOTAL_VOL = 15 - PART_VOL = 1.5 - MIX_SETTINGS = (1, 3) - - # Errors - sample_number = len(final_assembly_dict.keys()) - if sample_number > 96: - raise ValueError('Final assembly nummber cannot exceed 96.') - - # Tips and pipette - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - tipracks = [labware.load(tiprack_type, slot) - for slot in slots] - pipette = instruments.P10_Single(mount=PIPETTE_MOUNT, tip_racks=tipracks) - - # Define Labware and set temperature - magbead_plate = labware.load(MAG_PLATE_TYPE, MAG_PLATE_POSITION) - tube_rack = labware.load(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - tempdeck = modules.load('tempdeck', TEMPDECK_SLOT) - destination_plate = labware.load( - DESTINATION_PLATE_TYPE, TEMPDECK_SLOT, share=True) - tempdeck.set_temperature(TEMP) - tempdeck.wait_for_temp() - - # Master mix transfers - final_assembly_lens = [] - for values in final_assembly_dict.values(): - final_assembly_lens.append(len(values)) - unique_assemblies_lens = list(set(final_assembly_lens)) - master_mix_well_letters = ['A', 'B', 'C', 'D'] - for x in unique_assemblies_lens: - master_mix_well = master_mix_well_letters[(x - 1) // 6] + str(x - 1) - destination_inds = [i for i, lens in enumerate( - final_assembly_lens) if lens == x] - destination_wells = np.array( - [key for key, value in list(final_assembly_dict.items())]) - destination_wells = list(destination_wells[destination_inds]) - pipette.pick_up_tip() - pipette.transfer(TOTAL_VOL - x * PART_VOL, tube_rack.wells(master_mix_well), - destination_plate.wells(destination_wells), - new_tip='never') - pipette.drop_tip() - - # Part transfers - for key, values in list(final_assembly_dict.items()): - pipette.transfer(PART_VOL, magbead_plate.wells(values), - destination_plate.wells(key), mix_after=MIX_SETTINGS, - new_tip='always') - - tempdeck.deactivate() - - -final_assembly(final_assembly_dict=final_assembly_dict, - tiprack_num=tiprack_num) - -for c in robot.commands(): - print(c)
--- a/test-data/dnabot_scripts/output/3_assembly_ot2_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -from opentrons import protocol_api -import numpy as np -# metadata -metadata = { -'protocolName': 'My Protocol', -'description': 'Simple protocol to get started using OT2', -'apiLevel': '2.8' -} - -# protocol run function. the part after the colon lets your editor know - - -# test dict can be used for simulation -#final_assembly_dict={ "A1": ['A7', 'B7', 'C7', 'F7'], "B1": ['A7', 'B7', 'D7', 'G7'], "C1": ['A7', 'B7', 'E7', 'H7']} -#tiprack_num=1 - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - -final_assembly_dict={"A1": ["A7", "B7", "C7", "D7", "E7"], "B1": ["A7", "F7", "G7", "H7", "A8"], "C1": ["A7", "B8", "C8", "D8", "E8"]} -tiprack_num=1 -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - - -def run(protocol: protocol_api.ProtocolContext): - def final_assembly(final_assembly_dict, tiprack_num, tiprack_type=__LABWARES['96_tiprack_20ul']['id']): - # Constants, we update all the labware name in version 2 - #Tiprack - CANDIDATE_TIPRACK_SLOTS = ['3', '6', '9', '2', '5', '8', '11'] - PIPETTE_MOUNT = 'right' - #Plate of sample after purification - MAG_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_23']['id'] - MAG_PLATE_POSITION = '1' - #Tuberack - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - TUBE_RACK_POSITION = '7' - #Destination plate - DESTINATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_23']['id'] - #Temperature control plate - TEMPDECK_SLOT = '4' - TEMP = 20 - TOTAL_VOL = 15 - PART_VOL = 1.5 - MIX_SETTINGS = (1, 3) - tiprack_num=tiprack_num+1 - # Errors - sample_number = len(final_assembly_dict.keys()) - if sample_number > 96: - raise ValueError('Final assembly nummber cannot exceed 96.') - - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - tipracks = [protocol.load_labware(tiprack_type, slot) for slot in slots] - pipette = protocol.load_instrument(__LABWARES['p20_single']['id'], PIPETTE_MOUNT, tip_racks=tipracks) - - - # Define Labware and set temperature - magbead_plate = protocol.load_labware(MAG_PLATE_TYPE, MAG_PLATE_POSITION) - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - tempdeck = protocol.load_module('tempdeck', TEMPDECK_SLOT) - destination_plate = tempdeck.load_labware( - DESTINATION_PLATE_TYPE, TEMPDECK_SLOT) - tempdeck.set_temperature(TEMP) - - # Master mix transfers - final_assembly_lens = [] - for values in final_assembly_dict.values(): - final_assembly_lens.append(len(values)) - unique_assemblies_lens = list(set(final_assembly_lens)) - master_mix_well_letters = ['A', 'B', 'C', 'D'] - for x in unique_assemblies_lens: - master_mix_well = master_mix_well_letters[(x - 1) // 6] + str(x - 1) - destination_inds = [i for i, lens in enumerate(final_assembly_lens) if lens == x] - destination_wells = np.array([key for key, value in list(final_assembly_dict.items())]) - destination_wells = list(destination_wells[destination_inds]) - for destination_well in destination_wells:# make tube_rack_wells and destination_plate.wells in the same type - pipette.pick_up_tip() - pipette.transfer(TOTAL_VOL - x * PART_VOL, tube_rack.wells(master_mix_well), - destination_plate.wells(destination_well), new_tip='never')#transfer water and buffer in the pipette - - pipette.drop_tip() - - # Part transfers - for key, values in list(final_assembly_dict.items()): - for value in values:# magbead_plate.wells and destination_plate.wells in the same type - pipette.transfer(PART_VOL, magbead_plate.wells(value), - destination_plate.wells(key), mix_after=MIX_SETTINGS, - new_tip='always')#transfer parts in one tube - - tempdeck.deactivate() #stop increasing the temperature - - final_assembly(final_assembly_dict=final_assembly_dict, tiprack_num=tiprack_num)
--- a/test-data/dnabot_scripts/output/3_assembly_ot2_Thermocycler_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,107 +0,0 @@ -from opentrons import protocol_api -import numpy as np -# metadata -metadata = { -'protocolName': 'DNABOT Assembly Thermocycler', -'description': 'DNABOT Assembly Step3 with Thermocycler', -'apiLevel': '2.8' -} - -# It is possible to run 88 assemblies with this new module. The heat block module is removed. -# Assembly reactions is set up on thermocycler module. - - -# test dictionary can be used for simulation 3 or 88 assemblies -#final_assembly_dict={"A1": ['A7', 'B7', 'C7', 'F7'], "B1": ['A7', 'B7', 'D7', 'G7'], "C1": ['A7', 'B7', 'E7', 'H7']} -#tiprack_num=1 - -#final_assembly_dict={"A1": ["A7", "G7", "H7", "A8", "B8"], "B1": ["A7", "D8", "E8", "F8", "G8"], "C1": ["A7", "D8", "H7", "H8", "B9"], "D1": ["A7", "C9", "E9", "G9", "B8"], "E1": ["A7", "H9", "B10", "E9", "D10"], "F1": ["A7", "C9", "H8", "F10", "D10"], "G1": ["A7", "C9", "H10", "E8", "B9"], "H1": ["A7", "H9", "F8", "H10", "B11"], "A2": ["A7", "G7", "E8", "B10", "G8"], "B2": ["A7", "G7", "D11", "A8", "B9"], "C2": ["A7", "C9", "E9", "G9", "B9"], "D2": ["A7", "G7", "H7", "H8", "B8"], "E2": ["A7", "F11", "H11", "H7", "B12"], "F2": ["A7", "C9", "H8", "H11", "D10"], "G2": ["A7", "G7", "D11", "A8", "B8"], "H2": ["B7", "F11", "B10", "H10", "B11"], "A3": ["B7", "D8", "H7", "H8", "B8"], "B3": ["B7", "C9", "H10", "G9", "B8"], "C3": ["B7", "D12", "H8", "H11", "B11"], "D3": ["B7", "D12", "E9", "E8", "B8"], "E3": ["B7", "D12", "E9", "E8", "B9"], "F3": ["B7", "H9", "B10", "H10", "D10"], "G3": ["B7", "G7", "D11", "H8", "B8"], "H3": ["B7", "D12", "H10", "G9", "B9"], "A4": ["B7", "F11", "F10", "D11", "B12"], "B4": ["B7", "G7", "H7", "A8", "B9"], "C4": ["B7", "G7", "E8", "B10", "B12"], "D4": ["B7", "H9", "H11", "H7", "G8"], "E4": ["B7", "D8", "E8", "F8", "B12"], "F4": ["B7", "D12", "E9", "G9", "B8"], "G4": ["C7", "H9", "B10", "E9", "B11"], "H4": ["C7", "F11", "B10", "H10", "D10"], "A5": ["C7", "H9", "F8", "E9", "B11"], "B5": ["C7", "D12", "H8", "F10", "B11"], "C5": ["C7", "F11", "F8", "H10", "B11"], "D5": ["C7", "F11", "H11", "H7", "G8"], "E5": ["C7", "D8", "D11", "A8", "B9"], "F5": ["C7", "H9", "H11", "H7", "B12"], "G5": ["C7", "C9", "H10", "G9", "B9"], "H5": ["C7", "H9", "F10", "H7", "G8"], "A6": ["C7", "D12", "A8", "H11", "D10"], "B6": ["C7", "C9", "A8", "H11", "B11"], "C6": ["C7", "F11", "H11", "D11", "B12"], "D6": ["C7", "D8", "E8", "B10", "G8"], "E6": ["C7", "C9", "H8", "H11", "B11"], "F6": ["D7", "D8", "G9", "F8", "G8"], "G6": ["D7", "C9", "A8", "F10", "B11"], "H6": ["D7", "F11", "F10", "H7", "B12"], "A7": ["D7", "C9", "A8", "F10", "D10"], "B7": ["D7", "H9", "F8", "E9", "D10"], "C7": ["D7", "G7", "G9", "F8", "B12"], "D7": ["D7", "D12", "A8", "H11", "B11"], "E7": ["D7", "D12", "H10", "G9", "B8"], "F7": ["D7", "H9", "H11", "D11", "B12"], "G7": ["D7", "C9", "H8", "F10", "B11"], "H7": ["D7", "D8", "D11", "H8", "B8"], "A8": ["D7", "C9", "E9", "E8", "B9"], "B8": ["D7", "H9", "F10", "D11", "G8"], "C8": ["D7", "H9", "H11", "D11", "G8"], "D8": ["D7", "D12", "A8", "F10", "D10"], "E8": ["E7", "G7", "G9", "F8", "G8"], "F8": ["E7", "D12", "A8", "F10", "B11"], "G8": ["E7", "H9", "F10", "D11", "B12"], "H8": ["E7", "D8", "E8", "B10", "B12"], "A9": ["E7", "C9", "E9", "E8", "B8"], "B9": ["E7", "F11", "B10", "E9", "D10"], "C9": ["E7", "D12", "H8", "F10", "D10"], "D9": ["E7", "H9", "B10", "H10", "B11"], "E9": ["E7", "D8", "G9", "F8", "B12"], "F9": ["E7", "F11", "B10", "E9", "B11"], "G9": ["E7", "F11", "F8", "E9", "C11"], "H9": ["E7", "G7", "G9", "B10", "B12"], "A10": ["E7", "D8", "G9", "B10", "B12"], "B10": ["E7", "D8", "D11", "A8", "B8"], "C10": ["E7", "F11", "F10", "H7", "G8"], "D10": ["F7", "F11", "F8", "E9", "D10"], "E10": ["F7", "H9", "F10", "H7", "B12"], "F10": ["F7", "D12", "H10", "E8", "B9"], "G10": ["F7", "C9", "H10", "E8", "B8"], "H10": ["F7", "F11", "F8", "H10", "D10"], "A11": ["F7", "D12", "H10", "E8", "B8"], "B11": ["F7", "G7", "H7", "H8", "B9"], "C11": ["F7", "G7", "G9", "B10", "G8"], "D11": ["F7", "D12", "H8", "H11", "D10"], "E11": ["F7", "D9", "A8", "H11", "D10"], "F11": ["F7", "G7", "D11", "H8", "B9"], "G11": ["F7", "F11", "A12", "D11", "G8"], "H11": ["F7", "D8", "D11", "A9", "B9"]} -#tiprack_num=5 - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - -final_assembly_dict={"A1": ["A7", "B7", "C7", "D7", "E7"], "B1": ["A7", "F7", "G7", "H7", "A8"], "C1": ["A7", "B8", "C8", "D8", "E8"]} -tiprack_num=1 -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} - - -def run(protocol: protocol_api.ProtocolContext): - def final_assembly(final_assembly_dict, tiprack_num, tiprack_type=__LABWARES['96_tiprack_20ul']['id']): - # Constants, we update all the labware name in version 2 - #Tiprack - CANDIDATE_TIPRACK_SLOTS = ['2', '3', '5', '6', '9'] - PIPETTE_MOUNT = 'right' - #Plate of sample after purification - MAG_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_23']['id'] - MAG_PLATE_POSITION = '1' - #Tuberack - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - TUBE_RACK_POSITION = '4' - #Destination plate - DESTINATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_23']['id'] - TOTAL_VOL = 15 - PART_VOL = 1.5 - MIX_SETTINGS = (1, 3) - tiprack_num=tiprack_num+1 - # Errors - sample_number = len(final_assembly_dict.keys()) - if sample_number > 96: - raise ValueError('Final assembly nummber cannot exceed 96.') - - slots = CANDIDATE_TIPRACK_SLOTS[:tiprack_num] - tipracks = [protocol.load_labware(tiprack_type, slot) for slot in slots] - pipette = protocol.load_instrument(__LABWARES['p20_single']['id'], PIPETTE_MOUNT, tip_racks=tipracks) - - # Define Labware and set temperature - magbead_plate = protocol.load_labware(MAG_PLATE_TYPE, MAG_PLATE_POSITION) - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_POSITION) - - - #Thermocycler Module - tc_mod = protocol.load_module('Thermocycler Module') - destination_plate = tc_mod.load_labware(DESTINATION_PLATE_TYPE) - tc_mod.set_block_temperature(20) - - - # Master mix transfers - final_assembly_lens = [] - for values in final_assembly_dict.values(): - final_assembly_lens.append(len(values)) - unique_assemblies_lens = list(set(final_assembly_lens)) - master_mix_well_letters = ['A', 'B', 'C', 'D'] - - for x in unique_assemblies_lens: - master_mix_well = master_mix_well_letters[(x - 1) // 6] + str(x - 1) - destination_inds = [i for i, lens in enumerate(final_assembly_lens) if lens == x] - destination_wells = np.array([key for key, value in list(final_assembly_dict.items())]) - destination_wells = list(destination_wells[destination_inds]) - - pipette.pick_up_tip() - for destination_well in destination_wells:# make tube_rack_wells and destination_plate.wells in the same type - - pipette.transfer(TOTAL_VOL - x * PART_VOL, tube_rack.wells(master_mix_well), - destination_plate.wells(destination_well), new_tip='never')#transfer water and buffer in the pipette - - pipette.drop_tip() - - # Part transfers - for key, values in list(final_assembly_dict.items()): - for value in values:# magbead_plate.wells and destination_plate.wells in the same type - pipette.transfer(PART_VOL, magbead_plate.wells(value), - destination_plate.wells(key), mix_after=MIX_SETTINGS, - new_tip='always')#transfer parts in one tube - - - - #Thermocycler Module - tc_mod.close_lid() - tc_mod.set_lid_temperature(105) - tc_mod.set_block_temperature(50, hold_time_minutes=45, block_max_volume=15) - tc_mod.set_block_temperature(4, hold_time_minutes=2, block_max_volume=30) - # Increase the hold time at 4 C if necessary - tc_mod.set_lid_temperature(37) - tc_mod.open_lid() - - final_assembly(final_assembly_dict=final_assembly_dict, tiprack_num=tiprack_num)
--- a/test-data/dnabot_scripts/output/4_transformation_ot2_APIv1.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,318 +0,0 @@ -from opentrons import labware, instruments, modules, robot -import numpy as np - - -spotting_tuples=[(('A1', 'B1', 'C1'), ('A1', 'B1', 'C1'), (5, 5, 5))] -soc_well='A1' - - -def generate_transformation_wells(spotting_tuples): - """Evaluates spotting_tuples and returns transformation wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given - in the form: ((source wells), (target wells), (spotting volumes)). - Each unique transformation well is resuspended once prior to spotting. - - """ - wells = [] - for spotting_tuple in spotting_tuples: - for source_well in spotting_tuple[0]: - wells.append(source_well) - transformation_wells = [well for i, well in enumerate( - wells) if wells.index(well) == i] - return transformation_wells - - -def tiprack_slots( - spotting_tuples, - max_spot_vol=5): - """Calculates p10 and p300 tiprack slots required. - - Args: - spotting_tuples (list): Sets of spotting reactions are given - in the form: ((source wells), (target wells), (spotting volumes)). - Each unique transformation well is resuspended once prior to spotting. - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - # Reactions' number - transformation_reactions = len( - generate_transformation_wells(spotting_tuples)) - spotting_reactions = 0 - for spotting_tuple in spotting_tuples: - spots = np.array(spotting_tuple[2])/max_spot_vol - np.ceil(spots) - spotting_reactions = spotting_reactions + int(np.sum(spots)) - - # p10 tiprack slots - p10_tips = transformation_reactions + spotting_reactions - p10_tiprack_slots = p10_tips // 96 + 1 if p10_tips % 96 > 0 else p10_tips / 96 - - # p300 tiprack slots - p300_tips = transformation_reactions + spotting_reactions - p300_tiprack_slots = p300_tips // 96 + \ - 1 if p300_tips % 96 > 0 else p300_tips / 96 - return int(p10_tiprack_slots), int(p300_tiprack_slots) - - -def transformation_setup(transformation_wells): - """Sets up transformation reactions - - Args: - transformation_wells (list). - - """ - - # Constants - TEMP = 4 # Incubation temperature. - ASSEMBLY_VOL = 5 # Volume of final assembly added to competent cells. - MIX_SETTINGS = (4, 5) # Mix after setting during final assembly transfers. - INCUBATION_TIME = 20 # Cells and final assembly incubation time. - - # Set temperature deck to 4 °C and load competent cells - tempdeck.set_temperature(TEMP) - tempdeck.wait_for_temp() - robot.pause() - robot.comment('Load competent cells, uncap and resume run') - - # Transfer final assemblies - p10_pipette.transfer(ASSEMBLY_VOL, - assembly_plate.wells(transformation_wells), - transformation_plate.wells( - transformation_wells), new_tip='always', - mix_after=(MIX_SETTINGS)) - - # Incubate for 20 minutes and remove competent cells for heat shock - p10_pipette.delay(minutes=INCUBATION_TIME) - robot.pause() - robot.comment( - 'Remove transformation reactions, conduct heatshock and replace.') - - -def phase_switch(comment='Remove final assembly plate. Introduce agar tray and deep well plate containing SOC media. Resume run.'): - """Function pauses run enabling addition/removal of labware. - - Args: - comment (str): string to be displayed during run following pause. - - """ - robot.pause() - robot.comment(comment) - - -def outgrowth( - cols, - soc_well): - """Outgrows transformed cells. - - Args: - cols (list of str): list of cols in transformation plate containing samples. - soc_well (str): Well containing SOC media in relevant plate. - - """ - - # Constants - SOC_VOL = 125 - SOC_MIX_SETTINGS = (4, 50) - TEMP = 37 - OUTGROWTH_TIME = 60 - SOC_ASPIRATION_RATE = 25 - P300_DEFAULT_ASPIRATION_RATE = 150 - - # Define wells - transformation_cols = transformation_plate.cols(cols) - soc = soc_plate.wells(soc_well) - - # Add SOC to transformed cells - p300_pipette.set_flow_rate(aspirate=SOC_ASPIRATION_RATE) - p300_pipette.transfer(SOC_VOL, soc, transformation_cols, - new_tip='always', mix_after=SOC_MIX_SETTINGS) - p300_pipette.set_flow_rate(aspirate=P300_DEFAULT_ASPIRATION_RATE) - - # Incubate for 1 hour at 37 °C - tempdeck.set_temperature(TEMP) - tempdeck.wait_for_temp() - p300_pipette.delay(minutes=OUTGROWTH_TIME) - tempdeck.deactivate() - - -def spotting_cols(spotting_tuples): - """Evaluates spotting_tuples and returns unique cols (str) - associated with each spotting_tuple's source wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given - in the form: ((source wells), (target wells), (spotting volumes)). - Each unique transformation well is resuspended once prior to spotting. - - """ - cols_list = [] - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] - for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate( - source_wells_cols) if source_wells_cols.index(col) == i] - cols_list.append(unique_cols) - return cols_list - - -def spot_transformations( - spotting_tuples, - dead_vol=2, - spotting_dispense_rate=0.025, - stabbing_depth=10, - max_spot_vol=5): - """Spots transformation reactions. - - Args: - spotting_tuples (list): Sets of spotting reactions are given - in the form: ((source wells), (target wells), (spotting volumes)). - Each unique source well is resuspended once prior to spotting. - dead_vol (float): Dead volume aspirated during spotting. - spotting_dispense_rate (float): Rate p10_pipette dispenses at during spotting. - stabbing_depth (float): Depth p10_pipette moves into agar during spotting. - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - - def spot( - source, - target, - spot_vol): - """Spots an individual reaction using the p10 pipette. - - Args: - source (str): Well containing the transformation reaction to be spotted. - target (str): Well transformation reaction is to be spotted to. - spot_vol (float): Volume of transformation reaction to be spotted (uL). - - """ - # Constants - DEFAULT_HEAD_SPEED = {'x': 400, 'y': 400, - 'z': 125, 'a': 125} - SPOT_HEAD_SPEED = {'x': 400, 'y': 400, 'z': 125, - 'a': 125 // 4} - DISPENSING_HEIGHT = 5 - SAFE_HEIGHT = 15 # height avoids collision with agar tray. - - # Spot - p10_pipette.pick_up_tip() - p10_pipette.aspirate(spot_vol + dead_vol, source) - p10_pipette.move_to(target.top(SAFE_HEIGHT)) - p10_pipette.move_to(target.top(DISPENSING_HEIGHT)) - p10_pipette.dispense(volume=spot_vol, rate=spotting_dispense_rate) - robot.head_speed(combined_speed=max( - SPOT_HEAD_SPEED.values()), **SPOT_HEAD_SPEED) - p10_pipette.move_to(target.top(-1 * stabbing_depth)) - robot.head_speed(combined_speed=max( - DEFAULT_HEAD_SPEED.values()), **DEFAULT_HEAD_SPEED) - p10_pipette.move_to(target.top(SAFE_HEIGHT)) - - # Dispose of dead volume and tip - p10_pipette.dispense(dead_vol, spotting_waste) - p10_pipette.blow_out() - p10_pipette.drop_tip() - - def spot_tuple(spotting_tuple): - """Spots all reactions defined by the spotting tuple. Requires the function spot. - - Args: - spotting_tuple (tuple): Spotting reactions given in the form: (source wells), (target wells), (spotting volumes). - - """ - source_wells = spotting_tuple[0] - target_wells = spotting_tuple[1] - spot_vols = list(spotting_tuple[2]) - while max(spot_vols) > 0: - for index, spot_vol in enumerate(spot_vols): - if spot_vol == 0: - pass - else: - vol = spot_vol if spot_vol <= max_spot_vol else max_spot_vol - spot(transformation_plate.wells(source_wells[index]), - agar_plate.wells(target_wells[index]), vol) - spot_vols[index] = spot_vols[index] - vol - - # Constants - TRANSFORMATION_MIX_SETTINGS = [4, 50] - - # Spot transformation reactions - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] - for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate( - source_wells_cols) if source_wells_cols.index(col) == i] - for col in unique_cols: - p300_pipette.pick_up_tip() - p300_pipette.mix(TRANSFORMATION_MIX_SETTINGS[0], - TRANSFORMATION_MIX_SETTINGS[1], - transformation_plate.cols(col)) - p300_pipette.drop_tip() - spot_tuple(spotting_tuple) - - -# Run protocol - -# Constants -CANDIDATE_P10_SLOTS = ['9', '2', '5'] -CANDIDATE_P300_SLOTS = ['3', '6'] -P10_TIPRACK_TYPE = 'tiprack-10ul' -P300_TIPRACK_TYPE = 'opentrons_96_tiprack_300ul' -P10_MOUNT = 'right' -P300_MOUNT = 'left' -ASSEMBLY_PLATE_TYPE = '4ti-0960_FrameStar' -ASSEMBLY_PLATE_SLOT = '8' -TEMPDECK_SLOT = '10' -TRANSFORMATION_PLATE_TYPE = 'Eppendorf_30133366_plate_96' -SOC_PLATE_TYPE = '4ti0136_96_deep-well' -SOC_PLATE_SLOT = '7' -TUBE_RACK_TYPE = 'tube-rack_E1415-1500' -TUBE_RACK_SLOT = '11' -SPOTTING_WASTE_WELL = 'A1' -AGAR_PLATE_TYPE = 'Nunc_Omnitray' -AGAR_PLATE_SLOT = '1' - -# Tiprack slots -p10_p300_tiprack_slots = tiprack_slots(spotting_tuples) -p10_slots = CANDIDATE_P10_SLOTS[ - :p10_p300_tiprack_slots[0]] -p300_slots = CANDIDATE_P300_SLOTS[ - :p10_p300_tiprack_slots[1]] - -# Define labware -p10_tipracks = [labware.load(P10_TIPRACK_TYPE, slot) - for slot in p10_slots] -p300_tipracks = [labware.load(P300_TIPRACK_TYPE, slot) - for slot in p300_slots] -p10_pipette = instruments.P10_Single( - mount=P10_MOUNT, tip_racks=p10_tipracks) -p300_pipette = instruments.P300_Multi( - mount=P300_MOUNT, tip_racks=p300_tipracks) - -assembly_plate = labware.load(ASSEMBLY_PLATE_TYPE, ASSEMBLY_PLATE_SLOT) -tempdeck = modules.load('tempdeck', TEMPDECK_SLOT) -transformation_plate = labware.load(TRANSFORMATION_PLATE_TYPE, - TEMPDECK_SLOT, share=True) -soc_plate = labware.load(SOC_PLATE_TYPE, SOC_PLATE_SLOT) -tube_rack = labware.load(TUBE_RACK_TYPE, TUBE_RACK_SLOT) -spotting_waste = tube_rack.wells(SPOTTING_WASTE_WELL) -agar_plate = labware.load(AGAR_PLATE_TYPE, AGAR_PLATE_SLOT) - -# Register agar_plate for calibration -p10_pipette.transfer(1, agar_plate.wells( - 'A1'), agar_plate.wells('H12'), trash=False) -p10_pipette.start_at_tip(p10_tipracks[0][0]) - -# Run functions -transformation_setup(generate_transformation_wells(spotting_tuples)) -phase_switch() -spotting_tuples_cols = [col for cols in spotting_cols( - spotting_tuples) for col in cols] -unique_cols = [col for i, col in enumerate( - spotting_tuples_cols) if spotting_tuples_cols.index(col) == i] -outgrowth(unique_cols, soc_well=soc_well) -spot_transformations(spotting_tuples) - -for c in robot.commands(): - print(c) \ No newline at end of file
--- a/test-data/dnabot_scripts/output/4_transformation_ot2_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,422 +0,0 @@ -from opentrons import protocol_api -import numpy as np - - -# Rename to 'purification_template' and paste into 'template_ot2_scripts' folder in DNA-BOT to use - - -metadata = { - 'apiLevel': '2.8', - 'protocolName': 'Transformation', - 'description': 'Transformation reactions using an opentrons OT-2 for BASIC assembly.'} - -# Example output produced by DNA-BOT for a single construct, uncomment and run to test the template -#spotting_tuples=[(('A1','B1','C1'), ('A1','B1', 'C1'), (5,5,5))] -#soc_well='A1' - -# Example output produced by DNA-BOT for 88 constructs, uncomment and run to test the template -#spotting_tuples=[(('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1'), ('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2'), ('A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3'), ('A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4'), ('A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5'), ('A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6'), ('A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7'), ('A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8'), ('A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9'), ('A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10'), ('A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11'), ('A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11'), (5, 5, 5, 5, 5, 5, 5, 5))] -#soc_well='A1' - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -# __PARAMETERS={"purif_magdeck_height": {"value": 20.0}, "purif_wash_time": {"value": 0.5}, "purif_bead_ratio": {"value": 1.8}, "purif_incubation_time": {"value": 5.0}, "purif_settling_time": {"value": 2.0}, "purif_drying_time": {"value": 5.0}, "purif_elution_time": {"value": 2.0}, "transfo_incubation_temp": {"value": 4.0}, "transfo_incubation_time": {"value": 20.0}} - -spotting_tuples=[(('A1', 'B1', 'C1'), ('A1', 'B1', 'C1'), (5, 5, 5))] -soc_well='A1' -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -__PARAMETERS={"purif_magdeck_height": {"value": 20}, "purif_wash_time": {"value": 0}, "purif_bead_ratio": {"value": 1}, "purif_incubation_time": {"value": 5}, "purif_settling_time": {"value": 2}, "purif_drying_time": {"value": 5}, "purif_elution_time": {"value": 2}, "transfo_incubation_temp": {"value": 4}, "transfo_incubation_time": {"value": 20}} - - -def run(protocol: protocol_api.ProtocolContext): -# added run function for API version 2 - -# Constants - CANDIDATE_p20_SLOTS = ['9', '2', '5'] - CANDIDATE_P300_SLOTS = ['3', '6'] - p20_TIPRACK_TYPE = __LABWARES['96_tiprack_20ul']['id'] - # changed from 'tiprack-10ul' - P300_TIPRACK_TYPE = __LABWARES['96_tiprack_300ul']['id'] - P20_MOUNT = 'right' - P300_MOUNT = 'left' - ASSEMBLY_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - ASSEMBLY_PLATE_SLOT = '8' - - TRANSFORMATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - SOC_PLATE_TYPE = __LABWARES['96_deepwellplate_2ml']['id'] - SOC_PLATE_SLOT = '7' - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - TUBE_RACK_SLOT = '11' - SPOTTING_WASTE_WELL = 'A1' - AGAR_PLATE_TYPE = __LABWARES['agar_plate_step_4']['id'] - # changed from 'Nunc_Omnitray' - # it is a 1 well plate filled with agar; - # but for the Opentron to spot in the locations of a 96 wp, it is defined similar to a 96 wp - # was previously defined in add.labware.py, API version 2 doesn't support labware.create anymore - - - - # custom labware made using Opentron's Labware Creator: - # external dimensions: - # footprint length = 127.76 mm - # footrpint width = 85.48 mm - # footprint height = 15.70 mm - # taken from Thermofisher's documentation for Nunc Omnitray - # https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FD03023.pdf&title=VGVjaG5pY2FsIERhdGEgU2hlZXQ6IE51bmMgT21uaXRyYXk= - # well measurements - # depth = 0.01 mm - # diameter = 0.01 mm - # in old add.labware.py, they were defined as 0, but Labware Creator requires a value >0 - # spacing - # x-offset = 14.38 mm - # y-offset = 11.24 mm - # x-spacing = 9.00 mm - # y-spacing) = 9.00 mm - # taken from Nest 96 well plates - # https://labware.opentrons.com/nest_96_wellplate_100ul_pcr_full_skirt/ - # before using protocol, need to upload the 'nuncomnitray_96_wellplate_0.01ul.json' custom labware file into Opentrons app - - AGAR_PLATE_SLOT = '1' - - TEMPDECK_SLOT = '10' - - - - def generate_transformation_wells(spotting_tuples): - """ - Evaluates spotting_tuples and returns transformation wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - - """ - - wells = [] - for spotting_tuple in spotting_tuples: - for source_well in spotting_tuple[0]: - wells.append(source_well) - transformation_wells = [well for i, well in enumerate( - wells) if wells.index(well) == i] - return transformation_wells - - - def tiprack_slots(spotting_tuples, max_spot_vol=5): - """ - Calculates p20 and p300 tiprack slots required. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - - # Reactions' number - transformation_reactions = len(generate_transformation_wells(spotting_tuples)) - spotting_reactions = 0 - for spotting_tuple in spotting_tuples: - spots = np.array(spotting_tuple[2])/max_spot_vol - np.ceil(spots) - spotting_reactions = spotting_reactions + int(np.sum(spots)) - - # errrr should be fine lol # REMOVE - - # p20 tiprack slots - p20_tips = transformation_reactions + spotting_reactions - p20_tiprack_slots = p20_tips // 96 + 1 if p20_tips % 96 > 0 else p20_tips / 96 - - # p300 tiprack slots - p300_tips = transformation_reactions + spotting_reactions - p300_tiprack_slots = p300_tips // 96 + \ - 1 if p300_tips % 96 > 0 else p300_tips / 96 - return int(p20_tiprack_slots), int(p300_tiprack_slots) - - - def transformation_setup(transformation_wells): - """ - Sets up transformation reactions - - Args: - transformation_wells (list). - - """ - - # Constants - TEMP = __PARAMETERS['transfo_incubation_temp']['value'] # Incubation temperature. - ASSEMBLY_VOL = 5 # Volume of final assembly added to competent cells. - MIX_SETTINGS = (4, 5) # Mix after setting during final assembly transfers. - INCUBATION_TIME = __PARAMETERS['transfo_incubation_time']['value'] # Cells and final assembly incubation time. - - - - # Set temperature deck to 4 °C and load competent cells - tempdeck.set_temperature(TEMP) - # removed: tempdeck.wait_for_temp() - # API version2 automatically pauses execution until the set temperature is reached - # thus it no longer uses .wait_for_temp() - protocol.pause('Load competent cells, uncap and resume run') - - # Transfer final assemblies - p20_pipette.transfer(ASSEMBLY_VOL, - [assembly_plate.wells_by_name()[well_name] for well_name in transformation_wells], - [transformation_plate.wells_by_name()[well_name] for well_name in transformation_wells], - new_tip='always', - mix_after=(MIX_SETTINGS)) - - - # Incubate for 20 minutes and remove competent cells for heat shock - protocol.delay(minutes=INCUBATION_TIME) - - - protocol.pause('Remove transformation reactions, conduct heatshock and replace.') - - - def phase_switch(): - """ - Function pauses run enabling addition/removal of labware. - - """ - protocol.pause('Remove final assembly plate. Introduce agar tray and deep well plate containing SOC media. Resume run.') - - def outgrowth( - cols, - soc_well): - """ - Outgrows transformed cells. - - Args: - cols (list of str): list of cols in transformation plate containing samples. - soc_well (str): Well containing SOC media in relevant plate. - - """ - - # Constants - SOC_VOL = 125 - SOC_MIX_SETTINGS = (4, 50) - TEMP = 37 - OUTGROWTH_TIME = 60 - SOC_ASPIRATION_RATE = 25 - P300_DEFAULT_ASPIRATION_RATE = 150 - - # Define wells - transformation_cols = [transformation_plate.columns_by_name()[column] for column in cols] - - soc = soc_plate.wells(soc_well) - - # Add SOC to transformed cells - p300_pipette.flow_rate.aspirate = SOC_ASPIRATION_RATE - p300_pipette.transfer(SOC_VOL, soc, transformation_cols, - new_tip='always', mix_after=SOC_MIX_SETTINGS) - p300_pipette.flow_rate.aspirate = P300_DEFAULT_ASPIRATION_RATE - - # Incubate for 1 hour at 37 °C - tempdeck.set_temperature(TEMP) - - protocol.delay(minutes=OUTGROWTH_TIME) - - - tempdeck.deactivate() - - - def spotting_cols(spotting_tuples): - """ - Evaluates spotting_tuples and returns unique cols (str) associated with each spotting_tuple's source wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - - """ - cols_list = [] - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate(source_wells_cols) if source_wells_cols.index(col) == i] - cols_list.append(unique_cols) - return cols_list - - - def spot_transformations( - spotting_tuples, - dead_vol=1, - spotting_dispense_rate=0.025, - stabbing_depth=10, - max_spot_vol=5): - """ - Spots transformation reactions. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - dead_vol (float): Dead volume aspirated during spotting. - spotting_dispense_rate (float): Rate p20_pipette dispenses at during spotting. - stabbing_depth (float): Depth p20_pipette moves into agar during spotting. - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - - def spot( - source, - target, - spot_vol): - """ - Spots an individual reaction using the p20 pipette. - - Args: - source (str): Well containing the transformation reaction to be spotted. - target (str): Well transformation reaction is to be spotted to. - spot_vol (float): Volume of transformation reaction to be spotted (uL). - - """ - - # Constants - DEFAULT_HEAD_SPEED = {'x': 400, 'y': 400,'z': 125, 'a': 125} - SPOT_HEAD_SPEED = {'x': 400, 'y': 400, 'z': 125,'a': 125 // 4} - DISPENSING_HEIGHT = 5 - SAFE_HEIGHT = 7 # height avoids collision with agar tray. - - # Spot - p20_pipette.pick_up_tip() - p20_pipette.aspirate(spot_vol + dead_vol, source[0]) - # old code: - # p20_pipette.aspirate(spot_vol + dead_vol, source) - # returned type error because 'source' was a list containing one item (the well location) - # source[0] takes the location out of the list - - p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - p20_pipette.move_to(target[0].top(DISPENSING_HEIGHT)) - # old code: - # p20_pipette.move_to(target.top(SAFE_HEIGHT)) - # p20_pipette.move_to(target.top(DISPENSING_HEIGHT)) - # returned attribute error because 'target' was a list containing one item (the well location) - # target[0] takes the location out of the list - - p20_pipette.dispense(volume=spot_vol, rate=spotting_dispense_rate) - - protocol.max_speeds.update(SPOT_HEAD_SPEED) - # old code: - # robot.head_speed(combined_speed=max(SPOT_HEAD_SPEED.values()), **SPOT_HEAD_SPEED) - # robot.head_speed not used in API version 2 - # replaced with protocol.max_speeds - # new code no longer uses the lower value between combined speed or specified speed - # just uses each axis' specified speed directly - p20_pipette.move_to(target[0].top(-1 * stabbing_depth)) - # old code: - # p20_pipette.move_to(target.top(-1*stabbing_depth)) - # returns attribute error because 'target' was a list containing one item (the well location) - protocol.max_speeds.update(DEFAULT_HEAD_SPEED) - # old code: - # robot.head_speed(combined_speed=max(DEFAULT_HEAD_SPEED.values()), **DEFAULT_HEAD_SPEED) - # robot.head_speed not used in API version 2 - # replaced with protocol.max_speeds - # new code no longer uses the lower value between combined speed or specified speed - # just uses each axis' specified speed directly - p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - # old code: - # p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - # returns attribute error because 'target' was a list containing one item (the well location) - - - # the code below makes sure that the transformend cells are efficiently reaching to the agar surface - - p20_pipette.blow_out() - - protocol.delay(seconds=10) - - p20_pipette.blow_out() - - protocol.delay(seconds=10) - - # Dispose of dead volume and tip - p20_pipette.dispense(dead_vol, spotting_waste[0]) - - p20_pipette.blow_out() - # the simple .blow_out command blows out at current position (spotting waste) by defualt - # unlike blowout=true in complex commands, which by default will blow out in waste - - p20_pipette.drop_tip() - - def spot_tuple(spotting_tuple): - """ - Spots all reactions defined by the spotting tuple. Requires the function spot. - - Args: - spotting_tuple (tuple): Spotting reactions given in the form: (source wells), (target wells), (spotting volumes). - Each unique source well is resuspended once prior to spotting. - - """ - source_wells = spotting_tuple[0] - target_wells = spotting_tuple[1] - spot_vols = list(spotting_tuple[2]) - while max(spot_vols) > 0: - for index, spot_vol in enumerate(spot_vols): - if spot_vol == 0: - pass - else: - vol = spot_vol if spot_vol <= max_spot_vol else max_spot_vol - spot(source = transformation_plate.wells(source_wells[index]), target = agar_plate.wells(target_wells[index]), spot_vol = vol) - spot_vols[index] = spot_vols[index] - vol - - # Constants - TRANSFORMATION_MIX_SETTINGS = [4, 50] - - # Spot transformation reactions - # Each unique transformation well is resuspended once prior to spotting. - - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate(source_wells_cols) if source_wells_cols.index(col) == i] - for col in unique_cols: - p300_pipette.pick_up_tip() - p300_pipette.mix(TRANSFORMATION_MIX_SETTINGS[0], TRANSFORMATION_MIX_SETTINGS[1],transformation_plate.columns_by_name()[col][0]) - p300_pipette.drop_tip() - spot_tuple(spotting_tuple) - - #Tiprack slots - p20_p300_tiprack_slots = tiprack_slots(spotting_tuples) - p20_slots = CANDIDATE_p20_SLOTS[:p20_p300_tiprack_slots[0]] - p300_slots = CANDIDATE_P300_SLOTS[:p20_p300_tiprack_slots[1]] - # Define labware - p20_tipracks = [protocol.load_labware(p20_TIPRACK_TYPE, slot) for slot in p20_slots] - # changed to protocol.load_labware for API version 2 - p300_tipracks = [protocol.load_labware(P300_TIPRACK_TYPE, slot) for slot in p300_slots] - # changed to protocol.load_labware for API version 2 - p20_pipette = protocol.load_instrument(__LABWARES['p20_single']['id'], P20_MOUNT, tip_racks=p20_tipracks) - # changed to protocol.load_instrument for API version 2 - p300_pipette = protocol.load_instrument(__LABWARES['p300_multi']['id'], P300_MOUNT, tip_racks=p300_tipracks) - # changed to protocol.load_instrument for API version 2 - assembly_plate = protocol.load_labware(ASSEMBLY_PLATE_TYPE, ASSEMBLY_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - tempdeck = protocol.load_module('tempdeck', TEMPDECK_SLOT) - transformation_plate = tempdeck.load_labware(TRANSFORMATION_PLATE_TYPE, TEMPDECK_SLOT) - # changed to protocol.load_labware for API version 2 - # removed share=True, not required in API version 2 - # removed TEMPDECK_SLOT as it is loaded directly onto temperature module - soc_plate = protocol.load_labware(SOC_PLATE_TYPE, SOC_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_SLOT) - # changed to protocol.load_labware for API version 2 - spotting_waste = tube_rack.wells(SPOTTING_WASTE_WELL) - agar_plate = protocol.load_labware(AGAR_PLATE_TYPE, AGAR_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - - ### Run protocol - - - # Register agar_plate for calibration - p20_pipette.transfer(1, agar_plate.wells('A1'), agar_plate.wells('H12'), trash=False) - # removed: - # p20_pipette.start_at_tip(p20_tipracks[0][0]) - # pipette automatically starts from 'A1' tiprack location - # if re-adding, need to use p20.pipette.starting_tip() instead of p20.pipette.start_at_tip() - - - # Run functions - # Run functions - transformation_setup(generate_transformation_wells(spotting_tuples)) - phase_switch() - spotting_tuples_cols = [col for cols in spotting_cols(spotting_tuples) for col in cols] - unique_cols = [col for i, col in enumerate(spotting_tuples_cols) if spotting_tuples_cols.index(col) == i] - outgrowth(cols=unique_cols, soc_well=soc_well) - spot_transformations(spotting_tuples) - # Spot again to increase the chances of getting more colonies. Second spotting will only work for small number of assemblies where there is enough space on the deck for tipracks. - # protocol.pause('Let the spotted cells get dry') - # spot_transformations(spotting_tuples) - print(unique_cols)
--- a/test-data/dnabot_scripts/output/4_transformation_ot2_Thermocycler_APIv2.8.py Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,500 +0,0 @@ -from opentrons import protocol_api -import numpy as np - - -# Rename to 'purification_template' and paste into 'template_ot2_scripts' folder in DNA-BOT to use -# Tip rack positions are limited for this script, up to 48 transformations can be performed. - -metadata = { - 'apiLevel': '2.8', - 'protocolName': 'Transformation', - 'description': 'Transformation reactions using an opentrons OT-2 for BASIC assembly.'} - -# Example output produced by DNA-BOT for a single construct, uncomment and run to test the template -#spotting_tuples=[(('A1','B1','C1'), ('A1','B1', 'C1'), (8,8,8))] -#soc_well='A1' - -# Example output produced by DNA-BOT for 88 constructs, uncomment and run to test the template -#spotting_tuples=[(('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1'), ('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2'), ('A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3'), ('A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4'), ('A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5'), ('A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6'), ('A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7'), ('A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8'), ('A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9'), ('A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10'), ('A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10'), (5, 5, 5, 5, 5, 5, 5, 5)), (('A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11'), ('A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11'), (5, 5, 5, 5, 5, 5, 5, 5))] -#soc_well='A1' - -# __LABWARES is expected to be redefined by "generate_ot2_script" method -# Test dict -# __LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -# __PARAMETERS={"purif_magdeck_height": {"value": 20.0}, "purif_wash_time": {"value": 0.5}, "purif_bead_ratio": {"value": 1.8}, "purif_incubation_time": {"value": 5.0}, "purif_settling_time": {"value": 2.0}, "purif_drying_time": {"value": 5.0}, "purif_elution_time": {"value": 2.0}, "transfo_incubation_temp": {"value": 4.0}, "transfo_incubation_time": {"value": 20.0}} - -spotting_tuples=[(('A1', 'B1', 'C1'), ('A1', 'B1', 'C1'), (5, 5, 5))] -soc_well='A1' -__LABWARES={"p20_single": {"id": "p20_single_gen2"}, "p300_multi": {"id": "p300_multi_gen2"}, "mag_deck": {"id": "magdeck"}, "96_tiprack_20ul": {"id": "opentrons_96_tiprack_20ul"}, "96_tiprack_300ul": {"id": "opentrons_96_tiprack_300ul"}, "24_tuberack_1500ul": {"id": "e14151500starlab_24_tuberack_1500ul"}, "96_wellplate_200ul_pcr_step_14": {"id": "4ti0960rig_96_wellplate_200ul"}, "96_wellplate_200ul_pcr_step_23": {"id": "4ti0960rig_96_wellplate_200ul"}, "agar_plate_step_4": {"id": "4ti0960rig_96_wellplate_200ul"}, "12_reservoir_21000ul": {"id": "4ti0131_12_reservoir_21000ul"}, "96_deepwellplate_2ml": {"id": "4ti0136_96_wellplate_2200ul"}} -__PARAMETERS={"purif_magdeck_height": {"value": 20}, "purif_wash_time": {"value": 0}, "purif_bead_ratio": {"value": 1}, "purif_incubation_time": {"value": 5}, "purif_settling_time": {"value": 2}, "purif_drying_time": {"value": 5}, "purif_elution_time": {"value": 2}, "transfo_incubation_temp": {"value": 4}, "transfo_incubation_time": {"value": 20}} - - -def run(protocol: protocol_api.ProtocolContext): -# added run function for API version 2 - - # Constants - CANDIDATE_p20_SLOTS = ['3'] - CANDIDATE_P300_SLOTS = ['6'] - P20_TIPRACK_TYPE = __LABWARES['96_tiprack_10ul']['id'] - P300_TIPRACK_TYPE = __LABWARES['96_tiprack_300ul']['id'] - P20_MOUNT = 'right' - P300_MOUNT = 'left' - ASSEMBLY_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - ASSEMBLY_PLATE_SLOT = '2' - - TRANSFORMATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - SOC_PLATE_TYPE = __LABWARES['96_deepwellplate_2ml']['id'] - # changed from '4ti0136_96_deep-well' - SOC_PLATE_SLOT = '5' - TUBE_RACK_TYPE = __LABWARES['24_tuberack_1500ul']['id'] - # changed from 'tube-rack_E1415-1500' - TUBE_RACK_SLOT = '9' - SPOTTING_WASTE_WELL = 'A1' - AGAR_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - # changed from 'Nunc_Omnitray' - # it is a 1 well plate filled with agar; - # but for the Opentron to spot in the locations of a 96 wp, it is defined similar to a 96 wp - # was previously defined in add.labware.py, API version 2 doesn't support labware.create anymore - - # !!! CURRENT PLATE IS A PLACEHOLDER FOR RUNNING SIMMULATION WITHOUT CUSTOM LABWARE!!! - # !!! name made with Opentron Labware Creator = 'nuncomnitray_96_wellplate_0.01ul' !!!! - - - # custom labware made using Opentron's Labware Creator: - # external dimensions: - # footprint length = 127.76 mm - # footrpint width = 85.48 mm - # footprint height = 15.70 mm - # taken from Thermofisher's documentation for Nunc Omnitray - # https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FD03023.pdf&title=VGVjaG5pY2FsIERhdGEgU2hlZXQ6IE51bmMgT21uaXRyYXk= - # well measurements - # depth = 0.01 mm - # diameter = 0.01 mm - # in old add.labware.py, they were defined as 0, but Labware Creator requires a value >0 - # spacing - # x-offset = 14.38 mm - # y-offset = 11.24 mm - # x-spacing = 9.00 mm - # y-spacing) = 9.00 mm - # taken from Nest 96 well plates - # https://labware.opentrons.com/nest_96_wellplate_100ul_pcr_full_skirt/ - # before using protocol, need to upload the 'nuncomnitray_96_wellplate_0.01ul.json' custom labware file into Opentrons app - - AGAR_PLATE_SLOT = '1' - - TEMPDECK_SLOT = '4' - - - def generate_transformation_wells(spotting_tuples): - """ - Evaluates spotting_tuples and returns transformation wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - - """ - - wells = [] - for spotting_tuple in spotting_tuples: - for source_well in spotting_tuple[0]: - wells.append(source_well) - transformation_wells = [well for i, well in enumerate( - wells) if wells.index(well) == i] - return transformation_wells - - - def tiprack_slots(spotting_tuples, max_spot_vol=5): - """ - Calculates p20 and p300 tiprack slots required. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - - # Reactions' number - transformation_reactions = len(generate_transformation_wells(spotting_tuples)) - spotting_reactions = 0 - for spotting_tuple in spotting_tuples: - spots = np.array(spotting_tuple[2])/max_spot_vol - np.ceil(spots) - spotting_reactions = spotting_reactions + int(np.sum(spots)) - - # errrr should be fine lol # REMOVE - - # p20 tiprack slots - p20_tips = transformation_reactions + spotting_reactions - p20_tiprack_slots = p20_tips // 96 + 1 if p20_tips % 96 > 0 else p20_tips / 96 - - # p300 tiprack slots - p300_tips = transformation_reactions + spotting_reactions - p300_tiprack_slots = p300_tips // 96 + \ - 1 if p300_tips % 96 > 0 else p300_tips / 96 - return int(p20_tiprack_slots), int(p300_tiprack_slots) - - - def transformation_setup(transformation_wells): - """ - Sets up transformation reactions - - Args: - transformation_wells (list). - - """ - - # Constants - TEMP = __PARAMETERS['transfo_incubation_temp']['value'] # Incubation temperature. - ASSEMBLY_VOL = 5 # Volume of final assembly added to competent cells. - MIX_SETTINGS = (4, 5) # Mix after setting during final assembly transfers. - INCUBATION_TIME = __PARAMETERS['transfo_incubation_time']['value'] # Cells and final assembly incubation time. - - - - # Set temperature deck to 4 °C and load competent cells - tempdeck.set_temperature(TEMP) - # removed: tempdeck.wait_for_temp() - # API version2 automatically pauses execution until the set temperature is reached - # thus it no longer uses .wait_for_temp() - protocol.pause('Load competent cells, uncap and resume run') - # old code: - # robot.pause() - # robot.comment('Load competent cells, uncap and resume run') - # API version 2 uses 'protocol.' instead of 'robot.' and combines '.pause' and '.comment' - - # Transfer final assemblies - p20_pipette.transfer(ASSEMBLY_VOL, - [assembly_plate.wells_by_name()[well_name] for well_name in transformation_wells], - [transformation_plate.wells_by_name()[well_name] for well_name in transformation_wells], - new_tip='always', - mix_after=(MIX_SETTINGS)) - # old code: - # p20_pipette.transfer(ASSEMBLY_VOL, - # assembly_plate.wells(transformation_wells), - # transformation_plate.wells(transformation_wells), - # new_tip='always', - # mix_after=(MIX_SETTINGS)) - # .wells() doesn't take lists as arguements, newer wells_by_name() returns a dictionary - - - # Incubate for 20 minutes and remove competent cells for heat shock - protocol.delay(minutes=INCUBATION_TIME) - # old code: - # p20_pipette.delay(minutes=INCUBATION_TIME) - # API version 2 no longer has .delay() for pipettes, it uses protocol.delay() to pause the entire protocol - - protocol.pause('Get ready for heat shock when thermocycler reaches to 42 C.') - # old code: - # robot.pause() - # robot.comment('Remove transformation reactions, conduct heatshock in the next heat block and and return the plate.') - # API version 2 uses 'protocol.' instead of 'robot.' and combines '.pause' and '.comment' - - def heat_shock(): - - - #Thermocycler Module - tc_mod = protocol.load_module('Thermocycler Module') - # Destination Plates - DESTINATION_PLATE_TYPE = __LABWARES['96_wellplate_200ul_pcr_step_14']['id'] - # Loads destination plate onto Thermocycler Module - destination_plate = tc_mod.load_labware(DESTINATION_PLATE_TYPE) - tc_mod.set_block_temperature(42, hold_time_minutes=1, block_max_volume=180) - protocol.pause('Place the competent cells on thermocycler and resume run to conduct heat shock.') - protocol.delay(seconds=45) - - - - - def phase_switch(): - """ - Function pauses run enabling addition/removal of labware. - - """ - protocol.pause('Return the transformants to heat block. Remove final assembly plate. Introduce agar tray and deep well plate containing SOC media. Resume run.') - # old code: - # def phase_switch(comment='Remove final assembly plate. Introduce agar tray and deep well plate containing SOC media. Resume run.'): - # robot.pause() - # robot.comment(comment) - # API version 2 uses 'protocol.' instead of 'robot.' and combines '.pause' and '.comment' - - - def outgrowth( - cols, - soc_well): - """ - Outgrows transformed cells. - - Args: - cols (list of str): list of cols in transformation plate containing samples. - soc_well (str): Well containing SOC media in relevant plate. - - """ - - # Constants - SOC_VOL = 125 - SOC_MIX_SETTINGS = (4, 50) - TEMP = 37 - OUTGROWTH_TIME = 60 - SOC_ASPIRATION_RATE = 25 - P300_DEFAULT_ASPIRATION_RATE = 150 - - # Define wells - transformation_cols = [transformation_plate.columns_by_name()[column] for column in cols] - # old code: - # transformation_cols = transformation_plate.cols(cols) - # API version 2 labware use .columns attribute, not .cols - # but .columns() doesn't take lists as arguements, newer columns_by_name() returns a dictionary - - soc = soc_plate.wells(soc_well) - - # Add SOC to transformed cells - p300_pipette.flow_rate.aspirate = SOC_ASPIRATION_RATE - # old code: - # p300_pipette.set_flow_rate(aspirate=SOC_ASPIRATION_RATE) - # flow rates are set directly in API version 2, brackets not required - p300_pipette.transfer(SOC_VOL, soc, transformation_cols, - new_tip='always', mix_after=SOC_MIX_SETTINGS) - p300_pipette.flow_rate.aspirate = P300_DEFAULT_ASPIRATION_RATE - # old code: - # p300_pipette.set_flow_rate(aspirate=P300_DEFAULT_ASPIRATION_RATE) - # API version 2 labware use .columns attribute, not .cols - - # Incubate for 1 hour at 37 °C - tempdeck.set_temperature(TEMP) - # removed: tempdeck.wait_for_temp() - # API version2 automatically pauses execution until the set temperature is reached - # thus it no longer uses .wait_for_temp() - - protocol.delay(minutes=OUTGROWTH_TIME) - # old code: - # p300_pipette.delay(minutes=OUTGROWTH_TIME) - # API version 2 no longer has .delay() for pipettes, it uses protocol.delay() to pause the entire protocol - - tempdeck.deactivate() - - - - - - def spotting_cols(spotting_tuples): - """ - Evaluates spotting_tuples and returns unique cols (str) associated with each spotting_tuple's source wells. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - - """ - cols_list = [] - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate(source_wells_cols) if source_wells_cols.index(col) == i] - cols_list.append(unique_cols) - return cols_list - - - def spot_transformations( - spotting_tuples, - dead_vol=1, - spotting_dispense_rate=0.025, - stabbing_depth=10, - max_spot_vol=5): - """ - Spots transformation reactions. - - Args: - spotting_tuples (list): Sets of spotting reactions are given in the form: ((source wells), (target wells), (spotting volumes)). - dead_vol (float): Dead volume aspirated during spotting. - spotting_dispense_rate (float): Rate p20_pipette dispenses at during spotting. - stabbing_depth (float): Depth p20_pipette moves into agar during spotting. - max_spot_vol (float): Maximum volume that is spotted per spot reaction. - - """ - - def spot( - source, - target, - spot_vol): - """ - Spots an individual reaction using the p20 pipette. - - Args: - source (str): Well containing the transformation reaction to be spotted. - target (str): Well transformation reaction is to be spotted to. - spot_vol (float): Volume of transformation reaction to be spotted (uL). - - """ - - # Constants - DEFAULT_HEAD_SPEED = {'x': 400, 'y': 400,'z': 125, 'a': 125} - SPOT_HEAD_SPEED = {'x': 400, 'y': 400, 'z': 125,'a': 125 // 4} - DISPENSING_HEIGHT = 5 - SAFE_HEIGHT = 7 # height avoids collision with agar tray. - - # Spot - p20_pipette.pick_up_tip() - p20_pipette.aspirate(spot_vol + dead_vol, source[0]) - # old code: - # p20_pipette.aspirate(spot_vol + dead_vol, source) - # returned type error because 'source' was a list containing one item (the well location) - # source[0] takes the location out of the list - - p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - p20_pipette.move_to(target[0].top(DISPENSING_HEIGHT)) - # old code: - # p20_pipette.move_to(target.top(SAFE_HEIGHT)) - # p20_pipette.move_to(target.top(DISPENSING_HEIGHT)) - # returned attribute error because 'target' was a list containing one item (the well location) - # target[0] takes the location out of the list - - p20_pipette.dispense(volume=spot_vol, rate=spotting_dispense_rate) - - protocol.max_speeds.update(SPOT_HEAD_SPEED) - # old code: - # robot.head_speed(combined_speed=max(SPOT_HEAD_SPEED.values()), **SPOT_HEAD_SPEED) - # robot.head_speed not used in API version 2 - # replaced with protocol.max_speeds - # new code no longer uses the lower value between combined speed or specified speed - # just uses each axis' specified speed directly - p20_pipette.move_to(target[0].top(-1 * stabbing_depth)) - # old code: - # p20_pipette.move_to(target.top(-1*stabbing_depth)) - # returns attribute error because 'target' was a list containing one item (the well location) - protocol.max_speeds.update(DEFAULT_HEAD_SPEED) - # old code: - # robot.head_speed(combined_speed=max(DEFAULT_HEAD_SPEED.values()), **DEFAULT_HEAD_SPEED) - # robot.head_speed not used in API version 2 - # replaced with protocol.max_speeds - # new code no longer uses the lower value between combined speed or specified speed - # just uses each axis' specified speed directly - - #Make sure that the transformed cells drops on the agar plate - - p20_pipette.blow_out() - - protocol.delay(seconds=10) - - p20_pipette.blow_out() - - protocol.delay(seconds=10) - - p20_pipette.blow_out() - - protocol.delay(seconds=10) - - p20_pipette.blow_out() - - - - p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - # old code: - # p20_pipette.move_to(target[0].top(SAFE_HEIGHT)) - # returns attribute error because 'target' was a list containing one item (the well location) - - - # the code below makes sure that the transformend cells are efficiently reaching to the agar surface - - - - # Dispose of dead volume and tip - p20_pipette.dispense(dead_vol, spotting_waste[0]) - # old code: - # p20_pipette.dispense(dead_vol, spotting_waste) - # returns type error because 'target' was a list containing one item (the well location) - - p20_pipette.blow_out() - # the simple .blow_out command blows out at current position (spotting waste) by defualt - # unlike blowout=true in complex commands, which by default will blow out in waste - - p20_pipette.drop_tip() - - def spot_tuple(spotting_tuple): - """ - Spots all reactions defined by the spotting tuple. Requires the function spot. - - Args: - spotting_tuple (tuple): Spotting reactions given in the form: (source wells), (target wells), (spotting volumes). - Each unique source well is resuspended once prior to spotting. - - """ - source_wells = spotting_tuple[0] - target_wells = spotting_tuple[1] - spot_vols = list(spotting_tuple[2]) - while max(spot_vols) > 0: - for index, spot_vol in enumerate(spot_vols): - if spot_vol == 0: - pass - else: - vol = spot_vol if spot_vol <= max_spot_vol else max_spot_vol - spot(source = transformation_plate.wells(source_wells[index]), target = agar_plate.wells(target_wells[index]), spot_vol = vol) - spot_vols[index] = spot_vols[index] - vol - - # Constants - TRANSFORMATION_MIX_SETTINGS = [4, 50] - - # Spot transformation reactions - # Each unique transformation well is resuspended once prior to spotting. - - for spotting_tuple in spotting_tuples: - source_wells_cols = [source_well[1:] for source_well in spotting_tuple[0]] - unique_cols = [col for i, col in enumerate(source_wells_cols) if source_wells_cols.index(col) == i] - for col in unique_cols: - p300_pipette.pick_up_tip() - p300_pipette.mix(TRANSFORMATION_MIX_SETTINGS[0], TRANSFORMATION_MIX_SETTINGS[1],transformation_plate.columns_by_name()[col][0]) - # old code: - # p300_pipette.mix(TRANSFORMATION_MIX_SETTINGS[0], TRANSFORMATION_MIX_SETTINGS[1],transformation_plate.cols(col)) - # .columns aka .cols doesn't take lists anymore - # replaced with .columns_by_name - # .mix only takes one location, not several locations - # added [0] to specify only the wells in row A - # is identical for the protocol, as this is using a multi-channel pipette - p300_pipette.drop_tip() - spot_tuple(spotting_tuple) - - - # Tiprack slots - - p20_p300_tiprack_slots = tiprack_slots(spotting_tuples) - p20_slots = CANDIDATE_p20_SLOTS[:p20_p300_tiprack_slots[0]] - p300_slots = CANDIDATE_P300_SLOTS[:p20_p300_tiprack_slots[1]] - - # Define labware - p20_tipracks = [protocol.load_labware(P20_TIPRACK_TYPE, slot) for slot in p20_slots] - # changed to protocol.load_labware for API version 2 - p300_tipracks = [protocol.load_labware(P300_TIPRACK_TYPE, slot) for slot in p300_slots] - # changed to protocol.load_labware for API version 2 - p20_pipette = protocol.load_instrument(__LABWARES['p20_single']['id'], P20_MOUNT, tip_racks=p20_tipracks) - # changed to protocol.load_instrument for API version 2 - p300_pipette = protocol.load_instrument(__LABWARES['p300_multi']['id'], P300_MOUNT, tip_racks=p300_tipracks) - # changed to protocol.load_instrument for API version 2 - - assembly_plate = protocol.load_labware(ASSEMBLY_PLATE_TYPE, ASSEMBLY_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - tempdeck = protocol.load_module('tempdeck', TEMPDECK_SLOT) - transformation_plate = tempdeck.load_labware(TRANSFORMATION_PLATE_TYPE, TEMPDECK_SLOT) - # changed to protocol.load_labware for API version 2 - # removed share=True, not required in API version 2 - # removed TEMPDECK_SLOT as it is loaded directly onto temperature module - soc_plate = protocol.load_labware(SOC_PLATE_TYPE, SOC_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - tube_rack = protocol.load_labware(TUBE_RACK_TYPE, TUBE_RACK_SLOT) - # changed to protocol.load_labware for API version 2 - spotting_waste = tube_rack.wells(SPOTTING_WASTE_WELL) - agar_plate = protocol.load_labware(AGAR_PLATE_TYPE, AGAR_PLATE_SLOT) - # changed to protocol.load_labware for API version 2 - - - ### Run protocol - - - - - - # Run functions - transformation_setup(generate_transformation_wells(spotting_tuples)) - heat_shock() - phase_switch() - spotting_tuples_cols = [col for cols in spotting_cols(spotting_tuples) for col in cols] - unique_cols = [col for i, col in enumerate(spotting_tuples_cols) if spotting_tuples_cols.index(col) == i] - outgrowth(cols=unique_cols, soc_well=soc_well) - spot_transformations(spotting_tuples) - print(unique_cols)
--- a/test-data/dnabot_scripts/output/metainformation/dataset_4472_clip_run_info.csv Tue Dec 14 14:46:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -MASTER_MIX -Component,Volume (uL) -"Promega T4 DNA Ligase buffer, 10X",45.0 -Water,232.5 -NEB BsaI-HFv2,15.0 -Promega T4 DNA Ligase,7.5 - -SOURCE_PLATES -Deck position,Source plate,Path -2,dataset_4475.dat,/galaxy/database/files/004/dataset_4475.dat -5,dataset_4476.dat,/galaxy/database/files/004/dataset_4476.dat - -CLIP_REACTIONS -prefixes,parts,suffixes,number,mag_well -LMS-P,BASIC_SEVA_37_CmR-p15A.1,LMP-S,1,"('A7',)" -LMP-P,PJ23104_BASIC,U1-S,1,"('B7',)" -U1-RBS2-P,D5AP78,U3-S,1,"('C7',)" -U3-RBS3-P,Q1XBU4,U2-S,1,"('D7',)" -U2-RBS1-P,O66129,LMS-S,1,"('E7',)" -LMP-P,PJ23101_BASIC,U1-S,1,"('F7',)" -U1-RBS1-P,D2WKD9,U2-S,1,"('G7',)" -U2-RBS3-P,O48935,U3-S,1,"('H7',)" -U3-RBS1-P,O66952,LMS-S,1,"('A8',)" -LMP-P,PJ23104_BASIC,U2-S,1,"('B8',)" -U2-RBS2-P,P48537,U3-S,1,"('C8',)" -U3-RBS2-P,O07333,U1-S,1,"('D8',)" -U1-RBS2-P,Q9C446,LMS-S,1,"('E8',)" -