def run(protocol: protocol_api.ProtocolContext):
"""
Dilute samples in a fixed or varying rates
or transfer samples to different tubes.
"""
# =============================================================================
# LOADING LABWARE AND PIPETTES=================================================
# =============================================================================
##### Loading pipettes and tips
tips_20 = []
tips_200 = []
if tips_20_needed > 0:
tips_20_1 = protocol.load_labware(
'opentrons_96_filtertiprack_20ul',
11,
'tips_20_1')
tips_20.append(tips_20_1)
tips_20_2 = protocol.load_labware(
'opentrons_96_filtertiprack_20ul',
10,
'tips_20_2')
tips_20.append(tips_20_2)
if tips_20_needed > 96:
tips_20_3 = protocol.load_labware(
'opentrons_96_filtertiprack_20ul',
7,
'tips_20_3')
tips_20.append(tips_20_3)
if tips_20_needed > 192:
tips_20_4 = protocol.load_labware(
'opentrons_96_filtertiprack_20ul',
8,
'tips_20_4')
tips_20.append(tips_20_4)
elif tips_200_needed > 0:
tips_200_1 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
8,
'tips_200_1')
tips_200.append(tips_200_1)
elif tips_200_needed > 0:
tips_200_1 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
7,
'tips_200_1')
tips_200.append(tips_200_1)
tips_200_2 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
8,
'tips_200_2')
tips_200.append(tips_200_2)
else:
tips_200_1 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
11,
'tips_200_1')
tips_200.append(tips_200_1)
tips_200_2 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
10,
'tips_200_2')
tips_200.append(tips_200_2)
if tips_200_needed > 96:
tips_200_3 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
7,
'tips_200_3')
tips_200.append(tips_200_3)
if tips_200_needed > 192:
tips_200_4 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul',
8,
'tips_200_4')
tips_200.append(tips_200_4)
##### Loading pipettes
if tips_20_needed > 0:
p20 = protocol.load_instrument(
'p20_single_gen2',
'left',
tip_racks = tips_20)
if tips_200_needed > 0:
p300 = protocol.load_instrument(
'p300_single_gen2',
'right',
tip_racks = tips_200)
##### Loading labware
if sample_tubes == 'plate_96':
if sample_racks >= 1:
sample_source_1 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
1,
'sample_source_1')
if sample_racks >= 2:
sample_source_2 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
4,
'sample_source_2')
if sample_racks >= 3:
sample_source_3 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
2,
'sample_source_3')
if sample_tubes == 'tubes_1.5mL':
if sample_racks >= 1:
sample_source_1 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
1,
'sample_source_1')
if sample_racks >= 2:
sample_source_2 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
2,
'sample_source_2')
if sample_racks >= 3:
sample_source_3 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
4,
'sample_source_3')
if sample_racks >= 4:
sample_source_4 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
5,
'sample_source_4')
if dilution_tubes == 'plate_96':
if dilution_racks >= 1:
dilution_dest_1 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
6,
'dilution_dest_1')
if dilution_racks >= 2:
dilution_dest_2 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
3,
'dilution_dest_2')
if dilution_racks >= 3:
dilution_dest_3 = protocol.load_labware(
'biorad_96_wellplate_200ul_pcr',
5,
'dilution_dest_3')
if dilution_tubes == 'tubes_1.5mL':
if dilution_racks >= 1:
dilution_dest_1 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
6,
'dilution_dest_1')
if dilution_racks >= 2:
dilution_dest_2 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
3,
'dilution_dest_2')
if dilution_racks >= 3:
dilution_dest_3 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
5,
'dilution_dest_3')
if dilution_racks >= 4:
dilution_dest_4 = protocol.load_labware(
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
2,
'dilution_dest_4')
if simulate:
with open("labware/pcrstrips_96_wellplate_200ul/"
"pcrstrips_96_wellplate_200ul.json") as labware_file:
labware_def_pcrstrips = json.load(labware_file)
if sample_tubes == 'PCR_strips':
if sample_racks >= 1:
sample_source_1 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
1,
'sample_source_1')
if sample_racks >= 2:
sample_source_2 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
4,
'sample_source_2')
if sample_racks >= 3:
sample_source_3 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
2,
'sample_source_3')
if sample_racks >= 4:
sample_source_4 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
5,
'sample_source_4')
if dilution_tubes == 'PCR_strips':
if dilution_racks >= 1:
dilution_dest_1 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
3,
'dilution_dest_1')
if dilution_racks >= 2:
dilution_dest_2 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
6,
'dilution_dest_2')
if dilution_racks >= 3:
dilution_dest_3 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
5,
'dilution_dest_3')
if dilution_racks >= 4:
dilution_dest_4 = protocol.load_labware_from_definition(
labware_def_pcrstrips,
2,
'dilution_dest_4')
with open("labware/eppendorfscrewcap_15_tuberack_5000ul/"
"eppendorfscrewcap_15_tuberack_5000ul.json") as labware_file:
labware_def_5mL = json.load(labware_file)
tubes_5mL = protocol.load_labware_from_definition(
labware_def_5mL,
9,
'5mL_tubes')
else:
if sample_tubes == 'PCR_strips':
if sample_racks >= 1:
sample_source_1 = protocol.load_labware(
'pcrstrips_96_wellplate_200ul',
1,
'sample_source_1')
if sample_racks >= 2:
sample_source_2 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
4,
'sample_source_2')
if sample_racks >= 3:
sample_source_3 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
2,
'sample_source_3')
if sample_racks >= 4:
sample_source_4 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
5,
'sample_source_4')
if dilution_tubes == 'PCR_strips':
if dilution_racks >= 1:
dilution_dest_1 = protocol.load_labware(
'pcrstrips_96_wellplate_200ul',
3,
'dilution_dest_1')
if dilution_racks >= 2:
dilution_dest_2 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
6,
'dilution_dest_2')
if dilution_racks >= 3:
dilution_dest_3 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
5,
'dilution_dest_3')
if dilution_racks >= 4:
dilution_dest_4 = protocol.load_labwware(
'pcrstrips_96_wellplate_200ul',
2,
'dilution_dest_4')
tubes_5mL = protocol.load_labware(
'eppendorfscrewcap_15_tuberack_5000ul',
9,
'tubes_5mL')
##### MB: I think this can be removed... but not completely sure because I
#don't know why it was her ein the first place.
# # Setting sample_source
# if sample_racks == 1:
# sample_source_1 = sample_source_1
# elif sample_racks == 2:
# sample_source_1 = sample_source_1
# sample_source_2 = sample_source_2
# elif sample_racks == 3:
# sample_source_1 = sample_source_1
# sample_source_2 = sample_source_2
# sample_source_3 = sample_source_3
# elif sample_racks == 4:
# sample_source_1 = sample_source_1
# sample_source_2 = sample_source_2
# sample_source_3 = sample_source_3
# sample_source_4 = sample_source_4
# # Setting dilution_dest
# if dilution_racks == 1:
# dilution_dest_1 = dilution_dest_1
# elif dilution_racks == 2:
# dilution_dest_1 = dilution_dest_1
# dilution_dest_2 = dilution_dest_2
# elif dilution_racks == 3:
# dilution_dest_1 = dilution_dest_1
# dilution_dest_2 = dilution_dest_2
# dilution_dest_3 = dilution_dest_3
# elif dilution_racks == 4:
# dilution_dest_1 = dilution_dest_1
# dilution_dest_2 = dilution_dest_2
# dilution_dest_3 = dilution_dest_3
# dilution_dest_4 = dilution_dest_4
# =============================================================================
# SETTING LOCATIONS#!!!========================================================
# =============================================================================
##### Setting starting tip
if tips_20_needed > 0:
p20.starting_tip = tips_20_1.well(starting_tip_p20)
if tips_200_needed > 0:
p300.starting_tip = tips_200_1.well(starting_tip_p200)
## The starting_tip is the location of first pipette tip in the box ##
##### Setting tube locations
sample_wells = []
if sample_tubes == 'PCR_strips':
columns_odd = ['1','3','5','7','9','11']
sample_columns = []
if sample_racks >= 1:
sample_columns_1 = (
([sample_source_1.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in sample_columns_1:
sample_columns.append(column)
if sample_racks >= 2:
sample_columns_2 = (
([sample_source_2.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in sample_columns_2:
sample_columns.append(column)
if sample_racks >= 3:
sample_columns_3 = (
([sample_source_3.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in sample_columns_3:
sample_columns.append(column)
if sample_racks >= 4:
sample_columns_4 = (
([sample_source_4.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in sample_columns_4:
sample_columns.append(column)
for column in sample_columns:
for well in column:
sample_wells.append(well)
##makes a list of all wells in 1,2,3 or 4 full plates of PCR strips##
else:
if sample_racks == 1:
for well in sample_source_1.wells():
sample_wells.append(well)
if sample_racks == 2:
for well in sample_source_1.wells():
sample_wells.append(well)
for well in sample_source_2.wells():
sample_wells.append(well)
if sample_racks == 3:
for well in sample_source_1.wells():
sample_wells.append(well)
for well in sample_source_2.wells():
sample_wells.append(well)
for well in sample_source_3.wells():
sample_wells.append(well)
if sample_racks == 4:
for well in sample_source_1.wells():
sample_wells.append(well)
for well in sample_source_2.wells():
sample_wells.append(well)
for well in sample_source_3.wells():
sample_wells.append(well)
for well in sample_source_4.wells():
sample_wells.append(well)
dilution_wells = []
if dilution_tubes == 'PCR_strips':
columns_odd = ['1','3','5','7','9','11']
dilution_columns = []
if dilution_racks >= 1:
dilution_columns_1 = (
([dilution_dest_1.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in dilution_columns_1:
dilution_columns.append(column)
if dilution_racks >= 2:
dilution_columns_2 = (
([dilution_dest_2.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in dilution_columns_2:
dilution_columns.append(column)
if dilution_racks >= 3:
dilution_columns_3 = (
([dilution_dest_3.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in dilution_columns_3:
dilution_columns.append(column)
if dilution_racks >= 4:
dilution_columns_4 = (
([dilution_dest_4.columns_by_name()[column_name]
for column_name in columns_odd]))
for column in dilution_columns_4:
dilution_columns.append(column)
for column in dilution_columns:
for well in column:
dilution_wells.append(well)
##makes a list of all wells in 1,2,3 or 4 full plates of PCR strips##
else:
if dilution_racks == 1:
for well in dilution_dest_1.wells():
dilution_wells.append(well)
if dilution_racks == 2:
for well in dilution_dest_1.wells():
dilution_wells.append(well)
for well in dilution_dest_2.wells():
dilution_wells.append(well)
if dilution_racks == 3:
for well in dilution_dest_1.wells():
dilution_wells.append(well)
for well in dilution_dest_2.wells():
dilution_wells.append(well)
for well in dilution_dest_3.wells():
dilution_wells.append(well)
if dilution_racks == 4:
for well in dilution_dest_1.wells():
dilution_wells.append(well)
for well in dilution_dest_2.wells():
dilution_wells.append(well)
for well in dilution_dest_3.wells():
dilution_wells.append(well)
for well in dilution_dest_4.wells():
dilution_wells.append(well)
sample_wells = sample_wells[:number_of_samples]
dilution_wells = dilution_wells[:number_of_samples]
## cuts off the list after certain number of samples ##
# =============================================================================
# MESSAGE AT THE START=========================================================
# =============================================================================
if len([x for x in water_volumes if x > 0]) > 0:
protocol.pause("I need "+ str(water_tubes) + " tube(s) with 5mL of water.")
# =============================================================================
# ALIQUOTING WATER=============================================================
# =============================================================================
##### Variables for volume tracking and aliquoting
if len([x for x in water_volumes if x > 0]) > 0:
counter = 0 # to count how many tubes already emptied
source = tubes_5mL.wells()[counter]
destination = dilution_wells
container = 'tube_5mL'
start_height = vt.cal_start_height(container, 4800)
current_height = start_height
for i, (well, water_vol) in enumerate(zip(destination, water_volumes)):
## aliquot water in the correct wells, for each well do the following:
if water_vol > 0:
dispension_vol = water_vol
aspiration_vol = dispension_vol + (dispension_vol/100*2)
if i == 0:
if len([x for x in water_volumes[i:i+15] if x < 20]) > 0:
p20.pick_up_tip()
if len([x for x in water_volumes[i:i+15] if x >= 20]) > 0:
p300.pick_up_tip()
## If we are at the first well, start by picking up a tip
elif i % 16 == 0:
try:
p20.drop_tip()
except:
pass
try:
p300.drop_tip()
except:
pass
## Then, after every 16th well, try to drop tip
if len([x for x in water_volumes[i:i+15] if x < 20]) > 0:
p20.pick_up_tip()
if len([x for x in water_volumes[i:i+15] if x >= 20]) > 0:
p300.pick_up_tip()
## Pick up new tip if needed in next 16
current_height, pip_height, bottom_reached = vt.volume_tracking(
container, dispension_vol, current_height)
## call volume_tracking function, obtain current_height,
## pip_height and whether bottom_reached.
if bottom_reached:
## continue with next tube, reset vt
current_height = start_height
current_height, pip_height, bottom_reached = (
vt.volume_tracking(
container, dispension_vol, current_height))
counter = counter + 1
source = tubes_5mL.wells()[counter]
aspiration_location = source.bottom(current_height)
protocol.comment(
"Continue with tube " + str(counter + 1) + " of water")
else:
aspiration_location = source.bottom(pip_height)
## Set the location of where to aspirate from.
if aspiration_vol > 20:
water_pipette = p300
else:
water_pipette = p20
## What pipette to use
#### The actual aliquoting of water
water_pipette.aspirate(aspiration_vol, aspiration_location)
## Aspirate the amount specified in aspiration_vol from the
## location specified in aspiration_location.
water_pipette.dispense(dispension_vol, well)
## Dispense the amount specified in dispension_vol to the
## location specified in well (looping through plate)
water_pipette.dispense(10, aspiration_location)
## Alternative for blow-out, make sure the tip doesn't fill
## completely when using a disposal volume by dispensing some
## of the volume after each pipetting step. (blow-out too many
## bubbles)
try:
p20.drop_tip()
except:
pass
try:
p300.drop_tip()
except:
pass
## when entire plate is full, try to drop tip
# =============================================================================
# DILUTING SAMPLES=============================================================
# =============================================================================
for sample_well, dilution_well, sample_vol, water_vol in zip(
sample_wells, dilution_wells, sample_volumes, water_volumes):
## Combine each sample with a dilution_well and a destination well ##
if sample_vol > 17:
sample_pipette = p300
else:
sample_pipette = p20
sample_pipette.pick_up_tip()
## p20 picks up tip from location of specified starting_tip ##
## or following ##
sample_pipette.aspirate(sample_vol, sample_well)
## aspirate sample_volume_dil = volume for dilution from sample ##
sample_pipette.dispense(sample_vol, dilution_well)
## dispense sample_volume_dil = volume for dilution into dil_well ##
if water_vol > 0:
sample_pipette.mix(3, sample_vol + 3, dilution_well)
## pipette up&down 3x to get everything from the tip ##
sample_pipette.dispense(20, dilution_well)
## instead of blow-out
sample_pipette.drop_tip()
## Drop tip in trashbin on 12. ##
# =============================================================================
