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sample_num: int=96,
old_media_volume: float=200,
trypsin_volume: float=200,
trypsin_wait_time: int=5,
wash_volume: float=200,
mix_times: int=3,
new_media_volume: float=200):
global pipette_m, pipette_s
# labware setup
old_plates = [labware.load(cell_container, '1')]
new_plates = [labware.load(cell_container, '2')]
pcr_plate = labware.load('96-PCR-tall', '3')
trough = labware.load('trough-12row', '4')
tuberack_15ml = labware.load('opentrons-tuberack-15ml', '5')
# reagent setup
trypsin = tuberack_15ml.wells('A1')
PBS = trough.wells('A1')
media = trough.wells('A4')
liquid_trash = trough.wells('A9', to='A12')
s_name = single_pipette_model.split('-')[0]
m_name = multi_pipette_model.split('-')[0]
# if using 24-well plate, only single channel pipette is loaded
if cell_container == '24-well-plate':
s_slots = ['6', '7', '8', '9', '10', '11']
else:
s_slots = ['10', '11']
m_slots = ['6', '7', '8', '9']
'author': 'Nick ',
'source': 'Custom Protocol Request'
}
# module
module = modules.load('tempdeck', '2')
strips = labware.load(
'opentrons-aluminum-block-PCR-strips-200ul',
'2',
share=True
)
module.set_temperature(4)
module.wait_for_temp()
# labware
tuberack = labware.load('tube-rack-2ml', '1')
tiprack = labware.load('tiprack-10ul', '4')
# pipettes
p10 = instruments.P10_Single(
mount='right',
tip_racks=[tiprack]
)
# reagent and PCR strip setup
h2o = tuberack.wells('A1')
primer1 = tuberack.wells('A2')
primer2 = tuberack.wells('A3')
dreamtaq_buffer = tuberack.wells('A4')
dNTP = tuberack.wells('A5')
dreamtaq_polymerase = tuberack.wells('A6')
mastermix = tuberack.wells('B1')
from opentrons import labware, instruments, modules, robot
# labware setup
mag_deck = modules.load('magdeck', '1')
mag_plate = labware.load('96-deep-well', '1', share=True)
plate = labware.load('96-deep-well', '2')
trough = labware.load('trough-12row', '3')
liquid_trash = labware.load('point', '4')
flat_plate = labware.load('96-flat', '5')
# reagent setup
RNase_A = trough.wells('A1')
solution_II = trough.wells('A2')
N3_buffer = trough.wells('A3')
LC_beads = trough.wells('A4')
ETR_bind_buffer = trough.wells('A5')
Mag_Bind_RQ = trough.wells('A6')
ETR_wash_buffer = trough.wells('A7')
VHB_buffer = trough.wells('A8')
SPM_wash_buffer = trough.wells('A9')
elution_buffer = trough.wells('A10')
# create labware
plate_name = 'Falcon-96-round'
if plate_name not in labware.list():
labware.create(
plate_name,
grid=(12, 8),
spacing=(9, 9),
diameter=6.35,
depth=10.59,
volume=320
)
# load labware and modules
tempdeck = modules.load('tempdeck', '1')
plate2 = labware.load(plate_name, '1', share=True)
plate1 = labware.load(plate_name, '2', 'plate 1')
plate3 = labware.load(plate_name, '3', 'plate 3')
trough = labware.load('trough-12row', '4')
tuberack = labware.load('opentrons-tuberack-2ml-eppendorf', '5')
tips = [labware.load('tiprack-10ul', slot) for slot in ['6', '7']]
# pipettes
p10 = instruments.P10_Single(mount='right', tip_racks=tips)
# setup wells
plate1_wells = [well for row in plate1.rows() for well in row]
plate2_wells = [well for row in plate2.rows() for well in row]
plate3_wells = [well for row in plate3.rows() for well in row]
tube = tuberack.wells('A1')
solution = trough.wells('A1')
sources = []
volumes = []
dests = []
mixes = []
plates = {}
for line in info_list[1:]:
if line[0] not in reagent_list.keys():
raise Exception('Source container in slot ' + line[0] +
' does not exist.')
else:
source = reagent_list[line[0]].wells(line[1])
volume = float(line[2])
if line[3] not in plates.keys():
plates[line[3]] = labware.load(
dest_plate, line[3], share=True)
if not line[5].lower().strip() == 'yes':
mixes.append("")
else:
mixes.append(True)
dest = plates[line[3]].wells(line[4])
sources.append(source)
volumes.append(volume)
dests.append(dest)
return sources, volumes, dests, mixes
from opentrons import labware, instruments
metadata = {
'protocolName': 'RBC Transfer',
'author': 'Alise ',
'source': 'Custom Protocol Request'
}
plate_name = 'omegaquant-96-well-plate'
if plate_name not in labware.list():
labware.create(
plate_name,
grid=(12, 8),
spacing=(9, 9),
diameter=9,
depth=30)
trough_name = 'glass-trough'
if trough_name not in labware.list():
labware.create(
trough_name,
grid=(1, 1),
spacing=(0, 0),
diameter=66,
depth=25)
from opentrons import labware, instruments
vol = 100 # in ul, can change
# tip rack for p300 pipette
tip300_rack = labware.load('tiprack-200ul', '1')
# 96 well plate
plate = labware.load('96-PCR-flat', '2')
cells = labware.load('tube-rack-2ml', '3')
# p100 (10 - 100 uL) (single)
p300 = instruments.P300_Single(
mount='right',
tip_racks=[tip300_rack])
p300.pick_up_tip()
# dilution steps
for col in cells.cols():
p300.transfer(vol, col[3:1:-1], col[2:0:-1])
# biofilm setup steps
for col in range(0, 6):
def run_custom_protocol(pipette_type: StringSelection(
'p10-single', 'p50-multi')='p10-single',
mm_volume: int=10,
titrator_volume: int=10,
dilution_volume: int=10):
experiment_plate = labware.load('384-plate', '3')
well_type = False # Variable showing Well object not list of wells
if pipette_type == 'p10-single':
# Use tuberack if p10 single pipette
tuberack = labware.load('opentrons-tuberack-2ml-eppendorf', '1')
master_mix = tuberack.wells('A1')
ab_titrator = tuberack.wells('B1')
well_type = True
tiprack = labware.load('tiprack-10ul', '2')
pipette = instruments.P10_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p50-multi':
# Use 96 flat if multichannel
reagent_plate = labware.load('96-flat', '1')
master_mix = reagent_plate.columns('1')
ab_titrator = reagent_plate.columns('2')
tiprack = labware.load('opentrons-tiprack-300ul', '2')
from opentrons import labware, instruments, robot
"""
Tagment Genomic DNA
Amplify Libraries
"""
# labware setup
gDNA_plate = labware.load('96-PCR-flat', '1')
out_plate = labware.load('96-PCR-flat', '2')
# out_plate = labware.load('biorad-hardshell-96-PCR', '2')
tuberack = labware.load('tube-rack-2ml', '5')
# reagent setup
atm = tuberack.wells('A1') # Amplicon Tagment Mix
td = tuberack.wells('B1') # Tagment DNA Buffer
nt = tuberack.wells('C1') # Neutralize Tagment Buffer
npm = tuberack.wells('D1') # Nextera PCR Master Mix
index_7 = tuberack.wells('A2', to='D4') # Index 1 (i7) adapters
index_5 = tuberack.wells('A5', to='D6') # Index 2 (i5) adapters
tipracks50 = [labware.load('tiprack-200ul', slot) for slot in ['3', '4']]
tipracks10 = [labware.load('tiprack-10ul', slot) for slot in ['6', '7']]
# pipette setup
p50 = instruments.P50_Single(
from opentrons import labware, instruments, robot, modules
from otcustomizers import StringSelection
metadata = {
'protocolName': 'BioFluid Mix and Transfer - Part 1/2',
'author': 'Chaz ',
'source': 'Custom Protocol Request'
}
# custom labware creation
cryo_container = 'custom_agilent_cryovial_container'
if cryo_container not in labware.list():
labware.create(
cryo_container,
grid=(5, 10),
spacing=(18.3, 18.3),
diameter=12,
depth=48,
volume=6000
)
centr_container = 'custom_centrifuge_tube_container'
if centr_container not in labware.list():
labware.create(
centr_container,
grid=(8, 12),
spacing=(9, 9),
diameter=5.5,