def default_setup(self):
self.r_offset_cam = -0.1
self.t_offset_cam = 0
self.h_offset_cam = 2.5
self.trash = robot.fixed_trash()
self.tiprack = labware.load('tiprack-1000ul', 11)
plate_name = '3x2_plate_falcon'
if plate_name not in labware.list():
hydra_plate = labware.create(plate_name,
grid=(3, 2),
spacing=(39.24, 39.24),
diameter=35.71,
depth=17.65,
volume=3000)
self.plate_1 = labware.load(plate_name, '1')
self.plate_2 = labware.load(plate_name, '2')
self.plate_3 = labware.load(plate_name, '3')
self.plate_4 = labware.load(plate_name, '4')
self.plate_5 = labware.load(plate_name, '5')
self.plate_6 = labware.load(plate_name, '6')
self.plate_7 = labware.load(plate_name, '7')
self.plate_8 = labware.load(plate_name, '8')
self.plate_9 = labware.load(plate_name, '9')
self.plate_10 = labware.load(plate_name, '10')
self.pipette = instruments.P1000_Single('right',
tip_racks=[self.tiprack])
self.camera = instruments.P1000_Single('left')
def labware_setup(hardware):
from opentrons import containers, instruments
tip_racks = \
[containers.load('opentrons-tiprack-300ul', slot, slot)
for slot in ['1', '4']]
plates = \
[containers.load('96-flat', slot, slot) for slot in ['2', '5']]
p50 = instruments.P50_Multi(
mount='right', tip_racks=tip_racks)
p1000 = instruments.P1000_Single(
mount='left', tip_racks=tip_racks)
commands = [
{
'location': plates[0][0],
'instrument': p50
},
{
'location': plates[1]
},
{
'locations': [plates[0][0], plates[1]],
'instrument': p1000
}
]
return (p50, p1000), tip_racks, plates, commands
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 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
#After each ingredient is finished transferring, there is a key waiting for users to see the warnings or adding new ingredients
def waitForKey():
input('Press enter to continue...')
#prompt the users the number of slots for source ingredient
max_src_slot = int(input("Please input number of Plate Slot for ingredient: "))
#define the configuration of the experiment by telling the users where destination plates,source plates,tipracks are
max_dest_slot = 11 - max_src_slot - 1
min_dest_slot = max_src_slot + 2
tip_slot = max_src_slot + 1 #place the tip slot next to the src_plate
plate_containers = [None for x in range(11)] #create 11 arrays
print("Load tiprack-1000ul at slot no. ", (tip_slot))
#load 1000ul tips
tiprack1000ul = labware.load('tiprack-1000ul', str(tip_slot))
P1000 = instruments.P1000_Single(mount='right', tip_racks=[tiprack1000ul])
#######
## create and load customized 20ml scintillation vials plate
#for loop is written as if the plate cannot be found in the default labware list, the new labware will be created
plate_name = 'glass_20ml_v2_In'
if plate_name not in labware.list():
## create if not found
labware.create(
plate_name,
grid=(
3, 2
), #specify dimensions of the dimensions of the plates(columns,rows)
spacing=(33, 33), #distances (mm) between each (column, row)
diameter=16, #diameter (mm) of each well on the plate
depth=50, #height of each well (mm)
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)
from opentrons import labware, instruments
tips1000 = labware.load('opentrons-tiprack-1000ul', '1')
plate1 = labware.load('96-deep-well', '2')
pipette1000 = instruments.P1000_Single(mount='left', tip_racks=[tips1000])
pipette1000.transfer(100, plate1.well('A1'), plate1.well('B1'), touch_tip=True)
trash_box = labware.load('trash-box', '1')
mag_deck = modules.load('magdeck', '7')
sample_plate = labware.load('96-deep-well', '7', share=True)
temp_deck = modules.load('tempdeck', '10')
tipracks_200 = [labware.load('tiprack-200ul', slot)
for slot in ['4','5','6','11']]
tipracks_1000 = [labware.load('tiprack-1000ul', slot, share=True)
for slot in ['9']]
#### PIPETTE SETUP ####
s1000 = instruments.P1000_Single(
mount='right',
tip_racks=tipracks_1000)
m300 = instruments.P300_Multi(
mount='left',
tip_racks=tipracks_200)
#### REAGENT SETUP
Beads = trough.wells('A1')
Elution_buffer = trough.wells('A2')
Liquid_trash = trash_box.wells('A1')
Sample_buffer = buffer.wells('A1')
sys.path.append("/root")
import custom_labware
#### MODULES ####
#Source tubes (only load if mentioned in the map file)
tube_rack = labware.load('tube-rack-15_50ml', 7)
#Plate
buffer_plate = labware.load('96-deep-well', 8)
#### TIP RACKS ####
tiprack_1000 = labware.load('labsolute-tiprack-1000µl', '11')
#### PIPETTES ####
s1000 = instruments.P1000_Single(mount='left', tip_racks=[tiprack_1000])
#### LIQUID HANDLING ####
s1000.transfer(200,
tube_rack.wells('A3'),
buffer_plate.rows('1'),
blow_out=True,
touch_tip=True)
s1000.transfer(200,
tube_rack.wells('A3'),
buffer_plate.rows('2'),
blow_out=True,
touch_tip=True)
s1000.transfer(200,
tube_rack.wells('A3'),
buffer_plate.rows('3'),
plate_name = '3x2_plate_falcon'
if plate_name not in labware.list():
hydra_plate = labware.create(
plate_name,
grid=(3, 2),
spacing=(39.24, 39.24),
diameter=35.71,
depth=17.65,
volume=3000
)
plate_2 = labware.load(plate_name, '2')
tiprack = labware.load('tiprack-1000ul', 11)
pipette = instruments.P1000_Single('right', tip_racks=[tiprack])
pipette.pick_up_tip()
pipette.aspirate(100, plate_2.wells('A1'))
sleep(2)
h = 20
x_off = 34/2
y_off = 34/2
locations = [('A1', v(x_off, 0, h)), ('A1', v(0, y_off, h)),
('A2', v(x_off, 0, h)), ('A2', v(0, y_off, h)),
('A3', v(x_off, 0, h)), ('A3', v(0, y_off, h)),
('B1', v(x_off, 0, h)), ('B1', v(0, y_off, h)),
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()
tipracks_1000 = labware.load('tiprack-1000ul', '1', share=True)
#### PIPETTE SETUP ####
m300 = instruments.P300_Multi(
mount='left',
min_volume=30,
max_volume=300,
aspirate_flow_rate=100,
dispense_flow_rate=200,
tip_racks=[tipracks_300_1, tipracks_300_2, tipracks_300_3])
p1000 = instruments.P1000_Single(
mount='right',
aspirate_flow_rate=500,
dispense_flow_rate=500,
tip_racks=tipracks_1000)
#### REAGENT SETUP
Binding_buffer1 = trough.wells('A1')
Binding_buffer2 = trough.wells('A2')
Binding_buffer3 = trough.wells('A3')
Wash_1_1 = trough.wells('A4')
Wash_1_2 = trough.wells('A5')
Wash_2_1 = trough.wells('A6')
Wash_2_2 = trough.wells('A7')
Ethanol_1_1 = trough.wells('A8')
Ethanol_1_2 = trough.wells('A9')
tiprack_slots = ['10']
dest_plate = labware.load(destination_plate_type, '11')
# Set pipette type based on maximum volume
if pipette_max_vol == 300:
tipracks = [labware.load(tip_type, slot) for slot in tiprack_slots]
pipette = instruments.P300_Single(mount='left', tip_racks=tipracks)
elif pipette_max_vol == 50:
tipracks = [labware.load(tip_type, slot) for slot in tiprack_slots]
pipette = instruments.P50_Single(mount='left', tip_racks=tipracks)
elif pipette_max_vol == 10:
tipracks = [labware.load(tip_type, slot) for slot in tiprack_slots]
pipette = instruments.P10_Single(mount='left', tip_racks=tipracks)
elif pipette_max_vol == 1000:
tipracks = [labware.load(tip_type, slot) for slot in tiprack_slots]
pipette = instruments.P1000_Single(mount='left', tip_racks=tipracks)
# Sort the raw data into a list
data = [[slot, source_plate, source_well, vol]
for slot, source_plate, source_well, vol in
[row.split(',') for row in volumes_csv.strip().splitlines() if row]]
# Create a list to keep track of slots we've already used, incuding slots preallocated to tips and output plate
slot_list = ['10', '11']
for idx, (slot, source_plate, source_well, vol) in enumerate(data):
# Check we've not already filled the slot
if slot not in slot_list:
# Create the labware and add the slot to slot_list
vars()[source_plate] = labware.load(source_plate_type, str(slot),
str(source_plate))
from opentrons import labware, instruments, robot
robot.reset()
robot.home()
# DEFAULT PIPETTE FOR THIS IS THE P1000 - IF YOU NEED TO USE A DIFFERENT
#TIP YOU WILL NEED TO USE THE SWAPS IN "Walkthrough_Rate Calibration.ipynb"
#load labware
tiprack_1000 = labware.load("tiprack-1000ul", '1')
Stock1 = labware.load("vial-20ml", '2') #scintillation vials
vials = labware.load("vial-20ml", '3') #scintillation vials
trash = robot.fixed_trash
P1000 = instruments.P1000_Single(mount='right',
tip_racks=[tiprack_1000],
trash_container=trash)
robot.home()
P1000.pick_up_tip()
speeds = [.2, .4, .6, .8, 1]
pipette_amount = [600]
P1000.aspirate(Stock1('A1'))
P1000.dispense(Stock1('A1'))
P1000.aspirate(Stock1('A1'))
P1000.dispense(Stock1('A1'))
for counter, speed in enumerate(speeds, 0):
# distribution of the same amount at various speeds
P1000.distribute(pipette_amount,
