def run_custom_protocol(pipette_type: 'StringSelection...'='p300-Single',
source_labware_type: 'StringSelection...'='trough-12row',
destination_labware_type: 'StringSelection...'='96-flat',
micro_liters: 'NumberSelection...'=1,
new_tip_type: 'StringSelection...'='once'):
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(
mount='right',
tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(
mount='right',
tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(
mount='right',
tip_racks=[tiprack])
else:
print('Unknown pipette type: ' + pipette_type)
return
source_container = labware.load(source_labware_type, '2')
destination_container = labware.load(destination_labware_type, '3')
source_wells = source_container.wells('A1')
destination_wells = destination_container.wells('A1')
pipette.distribute(
micro_liters,
source_wells,
destination_wells,
new_tip=new_tip_type)
def run_custom_protocol(
pipette_type: 'StringSelection...' = 'p300-Single',
dye_labware_type: 'StringSelection...' = 'trough-12row'):
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(mount='right', tip_racks=[tiprack])
if dye_labware_type == 'trough-12row':
dye_container = labware.load('trough-12row', '2')
else:
dye_container = labware.load('tube-rack-2ml', '2')
output = labware.load('96-flat', '3')
# Well Location set-up
dye1_wells = [
'C4', 'B4', 'A3', 'A2', 'B1', 'C1', 'D1', 'D2', 'E2', 'E1', 'F1', 'G1',
'H2', 'H3', 'G4', 'F4'
]
dye2_wells = [
'C5', 'C6', 'C7', 'C8', 'C9', 'B10', 'C11', 'D12', 'E12', 'F11', 'G10',
'E9', 'F9', 'F8', 'F7', 'F6', 'F5', 'G8'
]
dye2 = dye_container.wells('A1')
dye1 = dye_container.wells('A2')
pipette.distribute(50, dye1, output.wells(dye1_wells), new_tip='once')
pipette.distribute(50, dye2, output.wells(dye2_wells), new_tip='once')
def run_custom_protocol(
well_volume: float = 1.0,
pipette_type: StringSelection('p300-Single', 'p50-Single', 'p10-Single',
'p300-Multi', 'p50-Multi',
'p10-Multi') = 'p300-Single'):
pip_name = pipette_type.split('-') # Check which pipette type
if pipette_type == 'p300-Single':
pipette = instruments.P300_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
pipette = instruments.P50_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
pipette = instruments.P10_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p300-Multi':
pipette = instruments.P300_Multi(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p50-Multi':
pipette = instruments.P50_Multi(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p10-Multi':
pipette = instruments.P10_Multi(mount='left', tip_racks=[tiprack])
alternating_wells = []
for column in plate.cols():
if pip_name[1] == 'Multi':
alternating_wells.append(column.wells('A'))
alternating_wells.append(column.wells('B'))
else:
alternating_wells.append(column.wells('A', length=8, step=2))
alternating_wells.append(column.wells('B', length=8, step=2))
pipette.distribute(well_volume, trough.wells('A1'), alternating_wells)
def setup():
global header, p50, p300, stock_wells, tube_rack, df
df = np.genfromtxt('solutionmaker.csv',
delimiter=',',
skip_header=1,
missing_values='')
with open('solutionmaker.csv') as csvfile:
reader_object = csv.reader(csvfile)
header = [row for i_row, row in enumerate(reader_object) if i_row == 0]
(nrows, ncols) = df.shape
for n_row in range(nrows):
if (df[n_row, :].sum() > 1500):
raise ValueError(
'Individual wells will not tolerate addition of this much volume'
)
"""
The following are constants for instantiation (mm/sec or ul/sec)
-----------------------------------------
"""
XSPEED = 600
YSPEED = 600
ZSPEED = 125
P300_ASPIRATERATE = 150
P50_ASPIRATE = 25
P50_DISPENSERATE = 100
P300_DISPENSERATE = 600
"""
------------------------------------------
"""
# connects robot and sets robot settings
robot.home()
robot.connect()
robot.head_speed(x=XSPEED, y=YSPEED, z=ZSPEED)
# sets up labware and the layout of the experiment
m300rack_1 = containers.load('tiprack-200ul', '10', share='True')
m300rack_2 = containers.load('tiprack-200ul', '11', share='True')
stock_wells = []
slot_plate_wells = ['4', '5']
for slot in slot_plate_wells:
stock_wells.append(containers.load('plate_6_well', slot, share='True'))
stock_wells.append(containers.load('96-flat', '6', share='True'))
tube_rack = []
slots_tube_rack = ['1', '2', '3']
for slot in slots_tube_rack:
tube_rack.append(containers.load('4x6_Tube_rack', slot, share='True'))
# instantiates pipettes
p50 = instruments.P50_Single(mount="right",
tip_racks=[m300rack_1],
aspirate_flow_rate=P50_ASPIRATE,
dispense_flow_rate=P50_DISPENSERATE)
p300 = instruments.P300_Single(mount="left",
tip_racks=[m300rack_2],
aspirate_flow_rate=P300_ASPIRATERATE,
dispense_flow_rate=P300_DISPENSERATE)
def run_custom_protocol(pipette_type: 'StringSelection...'='p300-Single',
pipette_mount: 'StringSelection...'='right',
dye_labware_type: 'StringSelection...'='trough-12row'):
if pipette_mount == 'left' or pipette_mount == 'l':
mount_position = 'left'
elif pipette_mount == 'right' or pipette_mount == 'r':
mount_position = 'right'
else:
raise Exception(
"You can only mount the pipette on the 'left' or 'right' mount")
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(
mount=mount_position,
tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(
mount=mount_position,
tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(
mount=mount_position,
tip_racks=[tiprack])
if dye_labware_type == 'trough-12row':
dye_container = labware.load('trough-12row', '2')
elif dye_labware_type == '6-well-plate':
dye_container = labware.load('6-well-plate', '2')
else:
dye_container = labware.load('tube-rack-2ml', '2')
output = labware.load('96-flat', '3')
# Well Location set-up
dye1_wells = ['A5', 'A6', 'A8', 'A9', 'B4', 'B10', 'C3', 'C11', 'D3',
'D11', 'E3', 'E11', 'F3', 'F11', 'G4', 'G10',
'H5', 'H6', 'H7', 'H8', 'H9']
dye2_wells = ['C7', 'D6', 'D7', 'D8', 'E5', 'E6', 'E7', 'E8',
'E9', 'F5', 'F6', 'F7', 'F8', 'F9', 'G6', 'G7', 'G8']
dye2 = dye_container.wells('A1')
dye1 = dye_container.wells('A2')
pipette.distribute(
50,
dye1,
output.wells(dye1_wells),
new_tip='once')
pipette.distribute(
50,
dye2,
output.wells(dye2_wells),
new_tip='once')
def run_custom_protocol(
volumes_csv: FileInput = example_csv,
pipette_axis: StringSelection('B (left side)',
'A (right side)') = 'B (left side)',
pipette_model: StringSelection('p1000', 'p300', 'p50', 'p10') = 'p300',
source_plate_type: StringSelection('96-flat', '384-plate') = '96-flat',
destination_plate_type: StringSelection('96-flat',
'384-plate') = '96-flat',
tip_reuse: StringSelection('new tip each time',
'reuse tip') = 'new tip each time'):
pipette_max_vol = int(pipette_model[1:])
mount = 'right'
if pipette_axis[0] == 'B':
mount = 'left'
tiprack_slots = ['1', '4', '7', '10']
if pipette_max_vol == 300:
tipracks = [
labware.load('tiprack-200ul', slot) for slot in tiprack_slots
]
pipette = instruments.P300_Single(mount=mount, tip_racks=tipracks)
elif pipette_max_vol == 50:
tipracks = [
labware.load('tiprack-200ul', slot) for slot in tiprack_slots
]
pipette = instruments.P50_Single(mount=mount, tip_racks=tipracks)
elif pipette_max_vol == 10:
tipracks = [
labware.load('tiprack-200ul', slot) for slot in tiprack_slots
]
pipette = instruments.P10_Single(mount=mount, tip_racks=tipracks)
elif pipette_max_vol == 1000:
tipracks = [
labware.load('tiprack-200ul', slot) for slot in tiprack_slots
]
pipette = instruments.P1000_Single(mount=mount, tip_racks=tipracks)
data = [
[well, vol] for well, vol in
[row.split(',') for row in volumes_csv.strip().splitlines() if row]
]
source_plate = labware.load(source_plate_type, '2')
dest_plate = labware.load(destination_plate_type, '3')
tip_strategy = 'always' if tip_reuse == 'new tip each time' else 'once'
for well_idx, (source_well, vol) in enumerate(data):
if source_well and vol:
vol = float(vol)
pipette.transfer(vol,
source_plate.wells(source_well),
dest_plate.wells(well_idx),
new_tip=tip_strategy)
def test_set_flow_rate():
# Test new flow-rate functionality on all pipettes with different max vols
robot.reset()
p10 = instruments.P10_Single(mount='right')
p10.set_flow_rate(aspirate=10)
ul_per_mm = Pipette._p10_single_piecewise(p10, p10.max_volume, 'aspirate')
expected_mm_per_sec = round(10 / ul_per_mm, 6)
assert p10.speeds['aspirate'] == expected_mm_per_sec
p10.set_flow_rate(dispense=20)
ul_per_mm = Pipette._p10_single_piecewise(p10, p10.max_volume, 'dispense')
expected_mm_per_sec = round(20 / ul_per_mm, 6)
assert p10.speeds['dispense'] == expected_mm_per_sec
robot.reset()
p50 = instruments.P50_Single(mount='right')
p50.set_flow_rate(aspirate=50)
ul_per_mm = Pipette._p50_single_piecewise(p50, p50.max_volume, 'aspirate')
expected_mm_per_sec = round(50 / ul_per_mm, 6)
assert p50.speeds['aspirate'] == expected_mm_per_sec
p50.set_flow_rate(dispense=60)
ul_per_mm = Pipette._p50_single_piecewise(p50, p50.max_volume, 'dispense')
expected_mm_per_sec = round(60 / ul_per_mm, 6)
assert p50.speeds['dispense'] == expected_mm_per_sec
robot.reset()
p300 = instruments.P300_Single(mount='right')
p300.set_flow_rate(aspirate=300)
ul_per_mm = Pipette._p300_single_piecewise(p300, p300.max_volume,
'aspirate')
expected_mm_per_sec = round(300 / ul_per_mm, 6)
assert p300.speeds['aspirate'] == expected_mm_per_sec
p300.set_flow_rate(dispense=310)
ul_per_mm = Pipette._p300_single_piecewise(p300, p300.max_volume,
'dispense')
expected_mm_per_sec = round(310 / ul_per_mm, 6)
assert p300.speeds['dispense'] == expected_mm_per_sec
robot.reset()
p1000 = instruments.P1000_Single(mount='right')
p1000.set_flow_rate(aspirate=1000)
ul_per_mm = Pipette._p1000_piecewise(p1000, p1000.max_volume, 'aspirate')
expected_mm_per_sec = round(1000 / ul_per_mm, 6)
assert p1000.speeds['aspirate'] == expected_mm_per_sec
p1000.set_flow_rate(dispense=1100)
ul_per_mm = Pipette._p1000_piecewise(p1000, p1000.max_volume, 'dispense')
expected_mm_per_sec = round(1100 / ul_per_mm, 6)
assert p1000.speeds['dispense'] == expected_mm_per_sec
def run_custom_protocol(
pipette_axis: StringSelection(
'left', 'right')='left',
pipette_model: StringSelection(
'p10', 'p50', 'p300', 'p1000')='p300',
consolidate_volume: float=20.0,
source_container: StringSelection(
'96-flat', 'tube-rack-2ml')='96-flat',
number_of_source_wells: int=4,
destination_container: StringSelection(
'96-flat', 'tube-rack-2ml')='96-flat',
destination_well: str='A1',
tip_reuse_strategy: StringSelection(
'reuse one tip', 'new tip each time')='reuse one tip'):
pipette_max_vol = int(pipette_model[1:])
new_tip = 'always' if tip_reuse_strategy == 'new tip each time' else 'once'
tip_rack = labware.load(tiprack_from_pipette(pipette_max_vol), '1')
source = labware.load(source_container, '2')
dest = labware.load(destination_container, '3')
try:
dest_well = dest.wells(destination_well)
except ValueError:
raise RuntimeError(
'Invalid destination well "{}". Expected well name like A1, H11, '
.format(destination_well) + 'etc. The destination plate may not ' +
'have a well of that name (eg a 96-well plate has no well "T18")')
if pipette_model == 'p10':
pipette = instruments.P10_Single(
mount=pipette_axis,
tip_racks=[tip_rack])
elif pipette_model == 'p50':
pipette = instruments.P50_Single(
mount=pipette_axis,
tip_racks=[tip_rack])
elif pipette_model == 'p300':
pipette = instruments.P300_Single(
mount=pipette_axis,
tip_racks=[tip_rack])
else:
pipette = instruments.P1000_Single(
mount=pipette_axis,
tip_racks=[tip_rack])
pipette.consolidate(
consolidate_volume,
source[:number_of_source_wells],
dest_well,
new_tip=new_tip)
def run_custom_protocol(pipette_type: 'StringSelection...'='p300-Single',
dye_labware_type: 'StringSelection...'='trough-12row'):
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(
mount='left',
tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(
mount='left',
tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(
mount='left',
tip_racks=[tiprack])
if dye_labware_type == 'trough-12row':
dye_container = labware.load('trough-12row', '2')
else:
dye_container = labware.load('tube-rack-2ml', '2')
output = labware.load('96-flat', '3')
# Well Location set-up
dye1_wells = ['B2']
dye2_wells = ['A1','A2','A3','A4','A5','A6','A7','A8','A9','A10','A11','A12'
'B1','B6','B7', 'B12',
'C1','C3','C4','C5','C6','C7', 'C9', 'C10','C11','C12'
'D1','D3','D4','D5','D6','D7','D12',
'E1', 'E3', 'E4','E4','E5','E6','E7','E9','E10','E11','E12'
'F1','F3','F4','F5','F6','F7','F9','F10','F11','F12'
'G1','G6','G7','G9','G10','G11','G12'
'H1','H2','H3','H4','H5','H6','H7','H8','H9','H10','H11','H12'
]
dye2 = dye_container.wells('A1')
dye1 = dye_container.wells('A2')
pipette.distribute(
15,
dye1,
output.wells(dye1_wells),
new_tip='once')
pipette.distribute(
15,
dye2,
output.wells(dye2_wells),
new_tip='once')
def run_custom_protocol():
p50_single = instruments.P50_Single(mount='right', tip_racks=[tiprack])
transfer_volume = 50
initial_volume = 2000 # Initial volume held in source tube
source_tube = tube_rack_2ml.wells('D3')
destination_tube = tube_rack_2ml.wells('D4')
remaining_vol = 2000
height = 1 # Initial height within source tube
source_height_offset = 0.5 # Offset so that pipette tip is slightly submerged in source tube, not hovering at surface
source_height = height - source_height_offset
p50_single.pick_up_tip()
while remaining_vol > 0:
robot.comment(
str(source_height)) # Print out the current source_height
# This transfer command will start pipetting from the top of the source tube to the bottom of the destination
# tube, and will continue "tracking" the height of the two volumes in each tube
source = (source_tube,
source_tube.from_center(x=0, y=0, z=source_height)
) # locations are tuples
destination = (destination_tube,
destination_tube.from_center(x=0, y=0, z=-height)
) # locations are tuples
p50_single.transfer(transfer_volume,
source,
destination,
disposal_vol=0,
blow_out=True,
new_tip='never')
# Update height by subtracting ratio of transfer_vol:inital_vol, or set to bottom of tube is "below" bottom
if height > -1:
height -= (
transfer_volume / initial_volume
) * 2 # x2 because tube size is -1 to 1 i.e. a difference of 2
else:
height = -1
# Update source_height or set to bottom of tube
source_height = height - source_height_offset
if source_height < -1:
source_height = -1
# Update remaining volume
remaining_vol -= transfer_volume
def mount_pipette(pipette_type, mount, tiprack_slot):
if pipette_type == 'p10-single':
tip_rack = labware.load('tiprack-10ul', tiprack_slot)
pipette = instruments.P10_Single(mount=mount, tip_racks=[tip_rack])
elif pipette_type == 'p50-single':
tip_rack = labware.load('opentrons-tiprack-300ul', tiprack_slot)
pipette = instruments.P50_Single(mount=mount, tip_racks=[tip_rack])
elif pipette_type == 'p300-single':
tip_rack = labware.load('opentrons-tiprack-300ul', tiprack_slot)
pipette = instruments.P300_Single(mount=mount,
tip_racks=[tip_rack])
else:
tip_rack = labware.load('tiprack-1000ul', tiprack_slot)
pipette = instruments.P1000_Single(mount=mount,
tip_racks=[tip_rack])
return pipette
def run_custom_protocol(
pipette_type: StringSelection('p300-Single', 'p50-Single',
'p10-Single') = 'p300-Single',
dye_labware_type: StringSelection('trough-12row',
'tube-rack-2ml') = 'trough-12row'):
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(mount='right', tip_racks=[tiprack])
if dye_labware_type == 'trough-12row':
dye_container = labware.load('trough-12row', '2')
else:
dye_container = labware.load('tube-rack-2ml', '2')
output = labware.load('96-flat', '3')
# Well Location set-up
dye1_wells = [
'A5', 'A6', 'A8', 'A9', 'B4', 'B10', 'C3', 'C11', 'D3', 'D11', 'E3',
'E11', 'F3', 'F11', 'G4', 'G10', 'H5', 'H6', 'H7', 'H8', 'H9'
]
dye2_wells = [
'C7', 'D6', 'D7', 'D8', 'E5', 'E6', 'E7', 'E8', 'E9', 'F5', 'F6', 'F7',
'F8', 'F9', 'G6', 'G7', 'G8'
]
dye2 = dye_container.wells('A1')
dye1 = dye_container.wells('A2')
pipette.distribute(50, dye1, output.wells(dye1_wells), new_tip='once')
pipette.distribute(50, dye2, output.wells(dye2_wells), new_tip='once')
def run_custom_protocol(
volumes_csv: FileInput = example_csv,
pipette_mount: StringSelection('right', 'left') = 'right',
pipette_model: StringSelection('p300-Single', 'p50-Single',
'p10-Single') = 'p300-Single',
plate_type: StringSelection('96-flat', '384-plate') = '96-flat',
tip_reuse: StringSelection('new tip each time',
'reuse tip') = 'new tip each time'):
tipracks = [
labware.load('opentrons-tiprack-300ul', slot) for slot in tiprack_slots
]
if pipette_model == 'p300-Single':
pipette = instruments.P300_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_model == 'p50-Single':
pipette = instruments.P50_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_model == 'p10-Single':
tipracks = [
labware.load('tiprack-10ul', slot) for slot in tiprack_slots
]
pipette = instruments.P10_Single(mount=pipette_mount,
tip_racks=tipracks)
plate = labware.load(plate_type, '3')
volumes = [float(cell) for cell in well_csv_to_list(volumes_csv)]
for vol in volumes:
if 0 < vol < pipette.min_volume:
robot.comment(
'WARNING: volume {} is below pipette\'s minimum volume.'.
format(vol))
tip_strategy = 'always' if tip_reuse == 'new tip each time' else 'once'
pipette.transfer(volumes, source, plate, new_tip=tip_strategy)
# 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(mount='left', tip_racks=tipracks50)
p10 = instruments.P10_Single(mount='right', tip_racks=tipracks10)
def run_custom_protocol(number_of_samples: int = 24):
# define sample locations
samples = gDNA_plate.wells()[:number_of_samples]
if number_of_samples <= 24:
# index7 = 6
index5 = 4
output = [
well for col in gDNA_plate.cols('1', to='6')
for well in col.wells('A', to='D')
settling_time: float=5
drying_time: float=4
p50_type: 'StringSelection...'='p50_Single'
p50_mount: 'StringSelection...'='left'
# tipracks = labware.load('tiprack-starlab-S1120-9810', slot = 2)
tipracks = labware.load('opentrons_96_tiprack_300ul', 2)
p50_tips = labware.load('tiprack-starlab-S1120-2810', slot = 3)
p300 = instruments.P300_Multi(
mount=p300_mount,
tip_racks=[tipracks])
p50 = instruments.P50_Single(
mount=p50_mount,
tip_racks=[p50_tips])
# mode = p300_type.split('_')[1] # this is 'Multi'
### Here I'm not really sure whats going on. I think that this is is recording
# the potential locations for pipetting out from and to
col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0)
samples = [col for col in mag_plate.cols()[:col_num]]
#output = [col for col in output_plate.cols()[:col_num]]
# total_vol still needs to be specified
bead_volume = sample_volume*bead_ratio
total_vol = bead_volume + sample_volume + 4 # = 15ul of samples + 12 ul of beads + 5ul of excess
pipette_multi = instruments.P10_Multi(
mount=multi_pipette_mount,
tip_racks=tiprackmulti
)
pipette_multi.start_at_tip(tiprackmulti[0].well(tiprack_multi_startfrom))
pipette_multi.plunger_positions['drop_tip'] = -6
# single channel
if single_pipette_type == 'p50-Single': # this is mostly a type check
tipracksingle = [
labware.load(tiprack_single_type, tiprack_slot)
for tiprack_slot in tiprack_single_slots
]
pipette_single = instruments.P50_Single(
mount=single_pipette_mount,
tip_racks=tipracksingle
)
pipette_single.start_at_tip(tipracksingle[0].well(tiprack_single_startfrom))
pipette_single.plunger_positions['drop_tip'] = -6
# pdb.set_trace()
# container for controls
ctrl_src_container = labware.load(trough_type, trough_slot)
dmso_src_well = ctrl_src_container.wells(DMSO_source_well)
water_src_well = ctrl_src_container.wells(H2O_source_well)
# define library plate
lib_plate = labware.load(library_type, library_slot)
def run_custom_protocol(pipette_type: StringSelection(
'p300_Multi', 'p50_Single', 'p300_Single', 'p1000_Single', 'p10_Multi',
'p50_Multi', 'p10_Single') = 'p300_Multi',
pipette_mount: StringSelection('left',
'right') = 'left',
sample_number: int = 24,
sample_volume: float = 20,
bead_ratio: float = 1.8,
elution_buffer_volume: float = 200,
incubation_time: float = 1,
settling_time: float = 1,
drying_time: float = 5):
total_tips = sample_number * 8
tiprack_num = total_tips // 96 + (1 if total_tips % 96 > 0 else 0)
slots = ['3', '5', '6', '7', '8', '9', '10', '11'][:tiprack_num]
if pipette_type == 'p1000_Single':
tipracks = [labware.load('tiprack-1000ul', slot) for slot in slots]
pipette = instruments.P1000_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p300_Single':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P300_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p50_Single':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P50_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p10_Single':
tipracks = [labware.load('tiprack-10ul', slot) for slot in slots]
pipette = instruments.P10_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p10_Multi':
tipracks = [labware.load('tiprack-10ul', slot) for slot in slots]
pipette = instruments.P10_Multi(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p50_Multi':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P50_Multi(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p300_Multi':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P300_Multi(mount=pipette_mount,
tip_racks=tipracks)
mode = pipette_type.split('_')[1]
if mode == 'Single':
if sample_number <= 5:
reagent_container = labware.load('tube-rack-2ml', '4')
liquid_waste = labware.load('trough-12row', '5').wells('A12')
else:
reagent_container = labware.load('trough-12row', '4')
liquid_waste = reagent_container.wells('A12')
samples = [well for well in mag_plate.wells()[:sample_number]]
output = [well for well in output_plate.wells()[:sample_number]]
else:
reagent_container = labware.load('trough-12row', '4')
liquid_waste = reagent_container.wells('A12')
col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0)
samples = [col for col in mag_plate.cols()[:col_num]]
output = [col for col in output_plate.cols()[:col_num]]
# Define reagents and liquid waste
beads = reagent_container.wells(0)
ethanol = reagent_container.wells(1)
elution_buffer = reagent_container.wells(2)
# 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 + 5
# Mix beads and PCR samples
for target in samples:
pipette.pick_up_tip()
pipette.mix(5, mix_vol, beads)
pipette.transfer(bead_volume, beads, target, new_tip='never')
pipette.mix(10, mix_vol, target)
pipette.blow_out()
pipette.drop_tip()
# Incubate beads and PCR product at RT for 5 minutes
pipette.delay(minutes=incubation_time)
# Engagae MagDeck and incubate
mag_deck.engage()
pipette.delay(minutes=settling_time)
# Remove supernatant from magnetic beads
pipette.set_flow_rate(aspirate=25, dispense=150)
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 * 0.1
for cycle in range(2):
for target in samples:
pipette.transfer(200,
ethanol,
target,
air_gap=air_vol,
new_tip='once')
pipette.delay(minutes=1)
for target in samples:
pipette.transfer(200, target, liquid_waste, air_gap=air_vol)
# Dry at RT
pipette.delay(minutes=drying_time)
# Disengage MagDeck
mag_deck.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.pick_up_tip()
pipette.transfer(elution_buffer_volume,
elution_buffer,
target,
new_tip='never')
pipette.mix(20, mix_vol, target)
pipette.drop_tip()
# Incubate at RT for 3 minutes
pipette.delay(minutes=5)
# Engagae MagDeck for 1 minute and remain engaged for DNA elution
mag_deck.engage()
pipette.delay(minutes=settling_time)
# Transfer clean PCR product to a new well
for target, dest in zip(samples, output):
pipette.transfer(elution_buffer_volume, target, dest, blow_out=True)
def run_custom_protocol(pipette_type: StringSelection(
'p300_Multi', 'p50_Multi', 'p10_Multi', 'p1000_Single', 'p300_Single',
'p50_Single', 'p10_Single') = 'p300_Multi',
pipette_mount: StringSelection('left',
'right') = 'left',
sample_number: int = 16,
PCR_volume: float = 20,
bead_ratio: float = 1.8,
elution_buffer_volume: float = 20):
incubation_time = 300
settling_time = 50
drying_time = 5
total_tips = sample_number * 8
tiprack_num = total_tips // 96 + (1 if total_tips % 96 > 0 else 0)
slots = ['3', '5', '6', '8', '9', '10', '11'][:tiprack_num]
if pipette_type == 'p1000_Single':
tipracks = [labware.load('tiprack-1000ul', slot) for slot in slots]
pipette = instruments.P1000_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p300_Single':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P300_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p50_Single':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P50_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p10_Single':
tipracks = [labware.load('tiprack-10ul', slot) for slot in slots]
pipette = instruments.P10_Single(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p10_Multi':
tipracks = [labware.load('tiprack-10ul', slot) for slot in slots]
pipette = instruments.P10_Multi(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p50_Multi':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P50_Multi(mount=pipette_mount,
tip_racks=tipracks)
elif pipette_type == 'p300_Multi':
tipracks = [labware.load('tiprack-200ul', slot) for slot in slots]
pipette = instruments.P300_Multi(mount=pipette_mount,
tip_racks=tipracks)
mode = pipette_type.split('_')[1]
if mode == 'Single':
if sample_number <= 5:
reagent_container = labware.load('opentrons-tuberack-2ml-screwcap',
'7')
liquid_waste = labware.load('trough-12row', '5').wells('A12')
else:
reagent_container = labware.load('trough-12row', '7')
liquid_waste = reagent_container.wells('A12')
samples = [well for well in mag_plate.wells()[:sample_number]]
samples_top = [well.top() for well in samples]
output = [well for well in output_plate.wells()[:sample_number]]
else:
reagent_container = labware.load('trough-12row', '7')
liquid_waste = reagent_container.wells('A12')
col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0)
samples = [col for col in mag_plate.cols()[:col_num]]
samples_top = [well.top() for well in mag_plate.rows(0)[:col_num]]
output = [col for col in output_plate.cols()[:col_num]]
# Define reagents and liquid waste
beads = reagent_container.wells(0)
ethanol = reagent_container.wells(1)
elution_buffer = reagent_container.wells(2)
# Define bead and mix volume to resuspend beads
bead_volume = PCR_volume * bead_ratio
if mode == 'Single':
if bead_volume * sample_number > pipette.max_volume:
mix_vol = pipette.max_volume
else:
mix_vol = bead_volume * sample_number
else:
if bead_volume * col_num > pipette.max_volume:
mix_vol = pipette.max_volume
else:
mix_vol = bead_volume * col_num
total_vol = bead_volume + PCR_volume + 15
mix_voltarget = PCR_volume + 10
# Disengage MagDeck
mag_deck.disengage()
# Mix Speed
pipette.set_flow_rate(aspirate=180, dispense=180)
# Mix beads and PCR samples
for target in samples:
pipette.set_flow_rate(aspirate=180, dispense=180)
pipette.pick_up_tip()
# Slow down head speed 0.5X for bead handling
pipette.mix(25, mix_vol, beads)
max_speed_per_axis = {
'x': (50),
'y': (50),
'z': (50),
'a': (10),
'b': (10),
'c': (10)
}
robot.head_speed(combined_speed=max(max_speed_per_axis.values()),
**max_speed_per_axis)
pipette.set_flow_rate(aspirate=10, dispense=10)
pipette.transfer(bead_volume,
beads,
target,
air_gap=0,
new_tip='never')
pipette.set_flow_rate(aspirate=50, dispense=50)
pipette.mix(40, mix_voltarget, target)
pipette.blow_out()
max_speed_per_axis = {
'x': (600),
'y': (400),
'z': (100),
'a': (100),
'b': (40),
'c': (40)
}
robot.head_speed(combined_speed=max(max_speed_per_axis.values()),
**max_speed_per_axis)
pipette.drop_tip()
# Return robot head speed to the defaults for all axes
max_speed_per_axis = {
'x': (600),
'y': (400),
'z': (100),
'a': (100),
'b': (40),
'c': (40)
}
robot.head_speed(combined_speed=max(max_speed_per_axis.values()),
**max_speed_per_axis)
# Incubate beads and PCR product at RT for 5 minutes
robot.comment("Incubating the beads and PCR products at room temperature \
for 5 minutes. Protocol will resume automatically.")
pipette.delay(seconds=incubation_time)
# Engage MagDeck and Magnetize
robot._driver.run_flag.wait()
mag_deck.engage()
robot.comment("Delaying for " + str(settling_time) +
" seconds for beads to \
settle.")
pipette.delay(seconds=settling_time)
# Remove supernatant from magnetic beads
pipette.set_flow_rate(aspirate=25, dispense=120)
for target in samples:
pipette.transfer(total_vol,
target.bottom(0.7),
liquid_waste.top(),
blow_out=True)
# Wash beads twice with 70% ethanol
air_vol = pipette.max_volume * 0.1
for cycle in range(2):
pipette.pick_up_tip()
for target in samples_top:
pipette.transfer(185,
ethanol,
target,
air_gap=air_vol,
new_tip='never')
robot.comment("Delaying for 17 seconds.")
pipette.delay(seconds=17)
for target in samples:
if not pipette.tip_attached:
pipette.pick_up_tip()
pipette.transfer(195,
target.bottom(0.7),
liquid_waste.top(),
air_gap=air_vol,
new_tip='never')
pipette.drop_tip()
# Dry at RT
robot.comment("Drying the beads for " + str(drying_time) +
" minutes. Protocol \
will resume automatically.")
pipette.delay(minutes=drying_time)
# Disengage MagDeck
robot._driver.run_flag.wait()
mag_deck.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.pick_up_tip()
pipette.transfer(elution_buffer_volume,
elution_buffer,
target,
new_tip='never')
pipette.mix(45, mix_vol, target)
pipette.drop_tip()
# Incubate at RT for 3 minutes
robot.comment(
"Incubating at room temperature for 3 minutes. Protocol will \
resume automatically.")
pipette.delay(minutes=3)
# Engage MagDeck for 1 minute and remain engaged for DNA elution
robot._driver.run_flag.wait()
mag_deck.engage()
robot.comment("Delaying for " + str(settling_time) +
" seconds for beads to \
settle.")
pipette.delay(seconds=settling_time)
# Transfer clean PCR product to a new well
for target, dest in zip(samples, output):
pipette.transfer(elution_buffer_volume,
target.bottom(1),
dest.top(),
blow_out=True)
# Disengage MagDeck
mag_deck.disengage()
#### LABWARE SETUP ####
elution_plate_DNA = labware.load('96-flat', '3')
trough = labware.load('trough-12row', '2')
RNA_plate = labware.load('96-deep-well', '7')
mag_deck = modules.load('magdeck', '7')
temp_deck = modules.load('tempdeck', '10')
trash_box = labware.load('trash-box', '8')
tipracks_200 = [labware.load('tiprack-200ul', slot)
for slot in ['4','5','6','11']]
#### PIPETTE SETUP ####
p50 = instruments.P50_Single(
mount='right',
tip_racks=tipracks_200)
m300 = instruments.P300_Multi(
mount='left',
tip_racks=tipracks_200)
#### REAGENT SETUP
Elution_buffer = trough.wells('A4')
EtOH1 = trough.wells('A5')
EtOH2 = trough.wells('A6')
EtOH3 = trough.wells('A7')
EtOH4 = trough.wells('A8')
Wash = trough.wells('A9')
BufferC = trough.wells('A10')
#Left Mount
if current_pipettes[0] == 300:
#P300:
large_pipette = instruments.P300_Single(
mount="left",
dispense_flow_rate=P300_dispense_rate,
tip_racks=[m300rack],
trash_container=trash)
large_min_volume = P300_min_volume
if current_pipettes[0] == 50:
#P50:
if current_pipettes[0] > current_pipettes[1]:
large_pipette = instruments.P50_Single(
mount="left",
dispense_flow_rate=P50_dispense_rate,
tip_racks=[m50rack],
trash_container=trash)
large_min_volume = P50_min_volume
else:
small_pipette = instruments.P50_Single(
mount="left",
dispense_flow_rate=P50_dispense_rate,
tip_racks=[m50rack],
trash_container=trash)
if current_pipettes[0] == 10:
#P10:
small_pipette = instruments.P10_Single(
mount="left",
dispense_flow_rate=P10_dispense_rate,
# Labware and module initialization
if "eppendorf_rack" not in labware.list():
labware.create("eppendorf_rack",
grid=(12, 8),
spacing=(9, 9),
diameter=5,
depth=21,
volume=50)
plate = labware.load('eppendorf_rack', slot='8')
tiprack = labware.load('opentrons-tiprack-300ul', slot='6')
ninja = NinjaPCR(slot='10', simulating=robot.is_simulating())
primer_well = 'A2'
mm_well = 'B2'
dna_well = 'C2'
water_well = 'D2'
first_mix = 'A1'
second_mix = 'B1'
third_mix = 'C1'
pipette_l = instruments.P50_Single(mount='left', tip_racks=[tiprack])
args = [
plate, pipette_l, tiprack, ninja, primer_well, mm_well, dna_well,
water_well, first_mix, second_mix, third_mix
]
pcr(*args)
def run_custom_protocol(
pipette_type: 'StringSelection...' = 'p300-Single',
pipette_mount: 'StringSelection...' = 'right',
dye_labware_type: 'StringSelection...' = 'trough-12row',
tip_start_from: 'StringSelection...' = 'A1'):
if pipette_mount == 'left' or pipette_mount == 'l':
mount_position = 'left'
elif pipette_mount == 'right' or pipette_mount == 'r':
mount_position = 'right'
else:
raise Exception(
"You can only mount the pipette on the 'left' or 'right' mount")
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(mount=mount_position,
tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(mount=mount_position,
tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(mount=mount_position,
tip_racks=[tiprack])
if dye_labware_type == 'trough-12row':
dye_container = labware.load('trough-12row', '2')
elif dye_labware_type == '6-well-plate':
dye_container = labware.load('6-well-plate', '2')
else:
dye_container = labware.load('tube-rack-2ml', '2')
output = labware.load('96-flat', '3')
# Well Location set-up
pink_wells = [
'A3', 'A4', 'A5', 'A7', 'A8', 'A9', 'B2', 'B6', 'B10', 'C1', 'C11',
'D1', 'D11', 'E2', 'E10', 'F3', 'F4', 'F8', 'F9', 'G5', 'G7', 'H6'
]
light_pink_wells = [
'A2', 'A6', 'A10', 'B1', 'B11', 'C12', 'D12', 'E1', 'E11', 'F2', 'F10',
'G3', 'G4', 'G8', 'G9', 'H5', 'H7'
]
blue_wells = [
'C3', 'C4', 'C5', 'C8', 'C9', 'D5', 'D7', 'D8', 'E5', 'E6', 'E7'
]
light_blue_wells = ['D3']
water = dye_container.wells('A1')
pink_dye = dye_container.wells('A2')
blue_dye = dye_container.wells('A3')
pipette.start_at_tip(tiprack.well(tip_start_from))
# put water first
pipette.transfer(30,
water,
output.wells(light_pink_wells + light_blue_wells),
new_tip='once')
# pink
pipette.pick_up_tip()
pipette.transfer(50,
pink_dye,
output.wells(pink_wells),
new_tip='never',
trash=False)
wells_for_lighter_pink = [
well.top(-3) for well in output.wells(light_pink_wells)
]
pipette.transfer(20,
pink_dye,
wells_for_lighter_pink,
new_tip='never',
touch_tip=True,
trash=False)
print(pipette.current_tip())
# mixing step
for well_to_mix in light_pink_wells:
pipette.mix(4, 10, output.wells(well_to_mix))
pipette.drop_tip()
print(pipette.current_tip())
# blue
pipette.pick_up_tip()
pipette.transfer(50,
blue_dye,
output.wells(blue_wells),
new_tip='never',
trash='False')
pipette.transfer(20,
blue_dye,
output.wells(light_blue_wells).top(-3),
new_tip='never',
touch_tip=True,
trash=False)
print(pipette.current_tip())
# mixing step
pipette.mix(4, 10, output.wells(light_blue_wells))
pipette.drop_tip()
print(pipette.current_tip())
# sets up labware and the layout of the experiment
m300rack_1 = containers.load('tiprack-200ul', '10', share='True')
m300rack_2 = containers.load('tiprack-200ul', '11', share='True')
stock_wells = []
slot_plate_wells = ['4', '5']
for slot in slot_plate_wells:
stock_wells.append(containers.load('plate_6_well', slot, share='True'))
stock_wells.append(containers.load('96-flat', '6', share='True'))
tube_rack = []
slots_tube_rack = ['1', '2', '3']
for slot in slots_tube_rack:
tube_rack.append(containers.load('4x6_Tube_rack', slot, share='True'))
# instantiates pipettes
p50 = instruments.P50_Single(mount="right",
tip_racks=[m300rack_1],
aspirate_flow_rate=P50_ASPIRATE,
dispense_flow_rate=P50_DISPENSERATE)
p300 = instruments.P300_Single(mount="left",
tip_racks=[m300rack_2],
aspirate_flow_rate=P300_ASPIRATERATE,
dispense_flow_rate=P300_DISPENSERATE)
p50.transfer(100, stock_wells[0].wells('A1'), tube_rack[0].wells('A1'))
p300.transfer(100, stock_wells[1].wells('A1'), tube_rack[1].wells('A1'))
p300.transfer(100, stock_wells[2].wells('A1'), tube_rack[2].wells('A1'))
"""
# Uncomment for working on system
for stock_index, component in enumerate(header[0]):
for aliquot_index, volume in enumerate(df[:, stock_index]):
# logic for tube rack
aliquot_rem = aliquot_index % 24
def run_custom_protocol(
well_volume: float = 50.0,
reagent_well: StringSelection('A1', 'A2', 'A3', 'A4', 'A5', 'A6', 'A7',
'A8', 'A9', 'A10', 'A11', 'A12') = 'A1',
plate_starting_column: str = '1',
number_of_columns_to_fill: int = 24,
pipette_type: StringSelection('p300-Single', 'p50-Single',
'p10-Single', 'p300-Multi', 'p50-Multi',
'p10-Multi') = 'p50-Multi',
mix_reagent_before_transfer: StringSelection('True',
'False') = 'True'):
if int(plate_starting_column) <= 0 or int(plate_starting_column) > 24:
raise Exception("Plate starting column number must be 1-24.")
if (int(plate_starting_column) + number_of_columns_to_fill) > 25:
raise Exception("Number of columns to fill exceeds plate's limit.")
if mix_reagent_before_transfer == 'False':
mix_times = 0
else:
mix_times = 5
pip_name = pipette_type.split('-') # Check which pipette type
if pip_name[0] == 'p10':
tiprack = labware.load('tiprack-10ul', '1', 'p10rack')
else:
tiprack = labware.load('opentrons-tiprack-300ul', '1', 'p300rack')
if pip_name[0] != 'p10' and well_volume < 5:
raise Exception("Cannot transfer volume this small without p10.")
if pip_name[0] == 'p30' and well_volume < 30:
raise Exception("Cannot transfer volume this small with p300.")
if pipette_type == 'p300-Single':
pipette = instruments.P300_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
pipette = instruments.P50_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
pipette = instruments.P10_Single(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p300-Multi':
pipette = instruments.P300_Multi(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p50-Multi':
pipette = instruments.P50_Multi(mount='left', tip_racks=[tiprack])
elif pipette_type == 'p10-Multi':
pipette = instruments.P10_Multi(mount='left', tip_racks=[tiprack])
if pip_name[1] == 'Multi':
alternating_wells = []
for column in plate.cols(plate_starting_column, to='24'):
alternating_wells.append(column.wells('A'))
alternating_wells.append(column.wells('B'))
dests = alternating_wells[:number_of_columns_to_fill * 2]
else:
dests = plate.cols(plate_starting_column,
length=number_of_columns_to_fill)
pipette.distribute(well_volume,
trough.wells(reagent_well),
dests,
mix_before=(mix_times, pipette.max_volume))
plate_2 = labware.load('96-flat', '2')
plate_3 = labware.load('96-flat', '4')
plate_4 = labware.load('96-flat', '5')
plate_5 = labware.load('96-flat', '7')
plate_6 = labware.load('96-flat', '8')
"""
All four pipettes are loaded into the program, however the app will only
see pipettes that are currently being used.
"""
if pipette_type == 'p300_single':
pip = instruments.P300_Single(mount=mount, tip_racks=[tiprack1, tiprack2])
elif pipette_type == 'p10_single':
pip = instruments.P10_Single(mount=mount, tip_racks=[tiprack1, tiprack2])
elif pipette_type == 'p50_single':
pip = instruments.P50_Single(mount=mount, tip_racks=[tiprack1, tiprack2])
else:
raise ValueError("Incorrect pipette type.")
plates = [plate_1, plate_2, plate_3, plate_4, plate_5, plate_6]
volumes = [
VOLUME_ONE, VOLUME_TWO, VOLUME_THREE, VOLUME_FOUR, VOLUME_FIVE, VOLUME_SIX
]
"""
Helper functions
"""
def pre_wet(vol, well):
pip.aspirate(vol, well)
def run_custom_protocol(
pipette_type: 'StringSelection...' = 'p300-Single',
source_labware_type: 'StringSelection...' = 'tube-rack-80well'):
# Labware set-up
if pipette_type == 'p300-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P300_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p50-Single':
tiprack = labware.load('tiprack-200ul', '1')
pipette = instruments.P50_Single(mount='right', tip_racks=[tiprack])
elif pipette_type == 'p10-Single':
tiprack = labware.load('tiprack-10ul', '1')
pipette = instruments.P10_Single(mount='right', tip_racks=[tiprack])
source = labware.load(
source_labware_type,
'4') # Labware for stuff we're sucking in (tube-rack-80well)
plate = labware.load('96-flat',
'3') # Labware for stuff we're spitting out
liquid_waste = labware.load('trash-box', '9') # Liquid waste box
# Step 1: Add 100 uL of PBS into wells A2, B2, C2, D2... A12, B12, C12, D12
# NOTE: Our source of PBS is distributed across wells A1, A2, A3, and A4 in the source labware
pipette.pick_up_tip()
pbs_source_list = [
source.wells('A1'),
source.wells('A2'),
source.wells('A3'),
source.wells('A4')
]
pbs_src_index = 0
ul_pbs_elapsed = 0
pbs_source = pbs_source_list[pbs_src_index]
for row in plate.rows('A', to='D'):
for i in range(1, 12):
if ul_pbs_elapsed == 1200:
pbs_src_index += 1
ul_pbs_elapsed = 0
pbs_source = pbs_source_list[pbs_src_index]
pipette.aspirate(100, pbs_source)
ul_pbs_elapsed += 100
pipette.dispense(100, row[i])
pipette.drop_tip()
# Step 2: Add 200uL of fluorescein 1x stock solution into A1, B1, C1, D1
fluorescein_source = source.wells('A5')
destination_range = plate.wells('A1', 'B1', 'C1', 'D1')
pipette.transfer(200, fluorescein_source, destination_range)
# Step 3: Transfer 100 ul of fluorescein stock solution from A1 into A2, for A, B, C, D
pipette.transfer(100, plate.wells('A1'), plate.wells('A2'))
pipette.transfer(100, plate.wells('B1'), plate.wells('B2'))
pipette.transfer(100, plate.wells('C1'), plate.wells('C2'))
pipette.transfer(100, plate.wells('D1'), plate.wells('D2'))
# Step 4: Mixing A2 - A11 and A11 into waste, for rows A - D
for row in plate.rows('A', to='D'):
pipette.pick_up_tip()
for i in range(1, 11):
#pipette.pick_up_tip()
pipette.mix(3, 100, row[i])
pipette.aspirate(100, row[i])
if i < 10:
pipette.dispense(100, row[i + 1])
else:
pipette.dispense(100, liquid_waste)
pipette.drop_tip()
# Debug
for c in robot.commands():
print(c)
from opentrons import labware, instruments, modules
metadata = {
'protocolName': 'SPRI bead cleanups',
'author': 'James Kitson',
}
magdeck = modules.load('magdeck', '7')
tips50 = labware.load('tiprack-starlab-S1120-2810', '1')
pipette = instruments.P50_Single(mount='left', tip_racks=[tips50])
plate = labware.load('starlab-E1403-5200', '7', share=True)
plate2 = labware.load('starlab-E1403-5200', '9')
pipette.pick_up_tip()
pipette.transfer(10, plate2['A1'], plate2['A2'])
pipette.transfer(10, plate2['A1'], plate['A2'])
magdeck.engage(height=18)
pipette.delay(5)
magdeck.disengage()
magdeck.engage(height=16)
pipette.delay(5)
magdeck.disengage()
magdeck.engage(height=17)
pipette.delay(10)
magdeck.disengage()
magdeck.engage(height=18)
#num_chips = int(input('Number of chips to coat (1,2 or 3)'))
# labware
if 'ax_6' not in locals():
ax_6 = labware.load('ax6_5', '6')
if 'tiprack' not in locals():
tiprack = labware.load('opentrons-tiprack-300ul', '1')
if 'ep_rack' not in locals():
ep_rack = labware.load(
'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')
# pipettes
if 'pipette_300' not in locals():
pipette_300 = instruments.P300_Single(mount='left', tip_racks=[tiprack])
if 'pipette_50' not in locals():
pipette_50 = instruments.P50_Single(mount='right', tip_racks=[tiprack])
wells = [
"A1", "B1", "C1", "D1", "E1", "F1", "A2", "B2", "C2", "D2", "E2", "F2",
"A3", "B3", "C3", "D3", "E3", "F3"
]
#Keeping sanity on tips
piwells = [
"A1", "B1", "C1", "D1", "E1", "F1", "G1", "H1", "A2", "B2", "C2", "D2",
"E2", "F2", "G2", "H2", "A3", "B3", "C3", "D3", "E3", "F3", "G3", "H3",
"A4", "B4", "C4", "D4", "E4", "F4", "G4", "H4", "A5", "B5", "C5", "D5",
"E5", "F5", "G5", "H5", "A6", "B6", "C6", "D6", "E6", "F6", "G6", "H6",
"A7", "B7", "C7", "D7", "E7", "F7", "G7", "H7", "A8", "B8", "C8", "D8",
"E8", "F8", "G8", "H8", "A9", "B9", "C9", "D9", "E9", "F9", "G9", "H9",
"A10", "B10", "C10", "D10", "E10", "F10", "G10", "H10", "A11", "B11",
pipette_drugs = instruments.P10_Single(
mount=drugs_pipette_mount,
tip_racks=tiprackdrugs
)
pipette_drugs.start_at_tip(tiprackdrugs[0].well(tiprack_drugs_startfrom))
pipette_drugs.plunger_positions['drop_tip'] = -6
# single channel
if solvent_pipette_type == 'p50-Single': # this is mostly a type check
tipracksolvent = [
labware.load(tiprack_solvent_type, tiprack_slot)
for tiprack_slot in tiprack_solvent_slots
]
pipette_solvent = instruments.P50_Single(
mount=solvent_pipette_mount,
tip_racks=tipracksolvent
)
pipette_solvent.start_at_tip(tipracksolvent[0].well(tiprack_solvent_startfrom))
pipette_solvent.plunger_positions['drop_tip'] = -6
# pdb.set_trace()
# container for controls
ctrl_src_container = labware.load(trough_type, trough_slot)
dmso_src_well = ctrl_src_container.wells(DMSO_source_well)
water_src_well = ctrl_src_container.wells(H2O_source_well)
# define library plate
lib_plate = labware.load(library_type, library_slot)
# define destination for controls:
]
tiprack_p300s = [
labware.load(tiprack_type, slot_p300s) for slot_p300s in ['9']
]
rxn_plate = labware.load('384-corning-3702BC', '8')
nitrilase_samples = labware.load('opentrons-aluminum-block-2ml-eppendorf',
'10',
share=True)
reagent_rack = labware.load('opentrons-tuberack-15_50ml', '11')
substrate_rack = labware.load('opentrons-tuberack-2ml-eppendorf', '7')
ammonium_chloride = labware.load('opentrons-tuberack-15ml', '4')
liquid_trash = reagent_rack.wells('C1')
liquid_trash_2 = reagent_rack.wells('C2')
# instruments
p50s = instruments.P50_Single(mount="right", tip_racks=tiprack_p50s)
if tiprack_type == 'tiprack-200ul-VWR':
p300s = instruments.P300_Single(mount="left",
tip_racks=tiprack_p300s,
min_volume=10,
max_volume=200)
elif tiprack_type == 'opentrons-tiprack-300ul':
p300s = instruments.P300_Single(mount="left",
tip_racks=tiprack_p300s,
min_volume=30,
max_volume=300)
# protocol
def run_custom_protocol(phosphate_buffer_volume: float = 100,
water_volume: float = 100,
