def run_custom_protocol(
left_pipette: StringSelection('p10-single', 'P50-single',
'p300-single', 'p1000-single',
'none') = 'p50-single',
right_pipette: StringSelection('p10-single', 'P50-single',
'p300-single', 'p1000-single',
'none') = 'p300-single',
master_mix_csv: FileInput = mastermix_csv_example):
if left_pipette == right_pipette and left_pipette == 'none':
raise Exception('You have to select at least 1 pipette.')
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
# labware setup
labware.load('opentrons-tuberack-2ml-eppendorf', '1')
labware.load('opentrons-tuberack-2ml-screwcap', '2')
trough = labware.load('trough-12row', '3')
# instrument setup
pipette_l = mount_pipette(left_pipette, 'left',
'5') if 'none' not in left_pipette else None
pipette_r = mount_pipette(right_pipette, 'right',
'6') if 'none' not in right_pipette else None
# determine which pipette has the smaller volume range
if pipette_l and pipette_r:
if left_pipette == right_pipette:
pip_s = pipette_l
pip_l = pipette_r
else:
if pipette_l.max_volume < pipette_r.max_volume:
pip_s, pip_l = pipette_l, pipette_r
else:
pip_s, pip_l = pipette_r, pipette_l
else:
pipette = pipette_l if pipette_l else pipette_r
# destination
mastermix_dest = trough.wells('A1')
info_list = [
cell for line in master_mix_csv.splitlines() if line
for cell in [line.split(',')]
]
for line in info_list[1:]:
source = robot.deck.children_by_name[line[1]][0].wells(line[2])
vol = float(line[3])
if pipette_l and pipette_r:
if vol <= pip_s.max_volume:
pipette = pip_s
else:
pipette = pip_l
pipette.transfer(vol, source, mastermix_dest)
from opentrons import labware, instruments, modules, robot
"""
Clean Up Libraries
"""
# labware setup
mag_deck = modules.load('magdeck', '4')
# mag_plate = labware.load('96-PCR-flat', '4', share=True)
mag_plate = labware.load('biorad-hardshell-96-PCR', '4', share=True)
in_plate = labware.load('96-PCR-flat', '5')
out_plate = labware.load('96-PCR-flat', '1')
# out_plate = labware.load('biorad-hardshell-96-PCR', '2')
trough = labware.load('trough-12row', '2')
liquid_trash = trough.wells('A12')
# reagent setup
rsb = trough.wells('A1') # resuspension buffer
beads = trough.wells('A2') # AMPure XP beads
ethanol = trough.wells('A3') # 80% ethanol
tipracks50 = [labware.load('tiprack-200ul', slot) for slot in ['6', '7', '8']]
# pipette setup
p50 = instruments.P50_Single(mount='left', tip_racks=tipracks50)
def run_custom_protocol(number_of_samples: int = 24,
PCR_product_volume: float = 50,
bead_ratio: float = 1.8,
dry_time: int = 15):
if number_of_samples <= 24:
labware_plate.wells(to_wells[i]),
air_gap=20,
new_tip='never',
blow_out=True,
)
# mix_after=(5))
else:
p10.transfer(
vols[i],
labware_plate.wells(from_wells[i]),
labware_plate.wells(to_wells[i]),
air_gap=20,
new_tip='never',
blow_out=True,
)
# mix_after=(5))
# Labware:
plate = labware.load('96-flat', '1')
p300_tip_rack = labware.load('opentrons_96_tiprack_300ul', '4')
p10_tip_rack = labware.load('opentrons_96_tiprack_10ul', '3')
p300 = instruments.P300_Single(mount='left', tip_racks=[p300_tip_rack])
p10 = instruments.P10_Single(mount='right', tip_racks=[p10_tip_rack])
smart_transfer([2, 7, 15, 200], plate, ['A1', 'A1', 'A1', 'A1'],
['B1', 'C1', 'D1', 'E1'])
for c in robot.commands():
print(c)
return (pipette)
# =============================== Load labware ===============================
tip_name = 'Biozym-tiprack-200ul' # Add Biozym 200 ul tiprack to labware library
if tip_name not in labware.list():
custom_tip = labware.create(
tip_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=5.23, # diameter (mm) of each well on the plate
depth=50, # depth (mm) of each well on the plate
volume=200)
tiprack = labware.load(tip_name, '9') # Load tiprack
trough = labware.load('opentrons_6_tuberack_falcon_50ml_conical',
'1') # Load reservoir
pipette = instruments.P300_Single(mount='right',
tip_racks=[tiprack],
max_volume=200) # Load pipette
# =========================== Set source locations ============================
EmptyFalcon = trough.wells(
'B1') #50 ml falcon left EMPTY for dispension of water
WaterFalcon = trough.wells(
'B2'
# -*- coding: utf-8 -*-
"""
@author: Allan Li, Sunnie Ma
"""
import opentrons
from opentrons import labware, instruments, robot
#This is the radius of the dish in centermeters
radius = 4.5
tiprack = labware.load('tiprack-10ul', '1')
bacteria = labware.load('96-flat', '4')
dish = labware.load('96-PCR-flat', '5')
p = instruments.P300_Single(mount='right', tip_racks=[tiprack])
dishInfo = dish.wells('A1').top()[0]
n = radius / 5
center_x = dish.wells('A1').top()[1][0]
center_y = dish.wells('A1').top()[1][1] - 40
z = dish.wells('A1').top()[1][2] - 3
#adjust the coordinates of the dish
#function that moves to a specific point of the dish
def move(x, y):
x = n * x
'H10',
'A11',
'B11',
'C11',
'D11',
'E11',
'F11',
'G11',
'H11',
'A12',
'B12',
'C12',
'D12',
]
water_rack = labware.load('tube-rack-2ml', '5')
gDNA_plate = labware.load('96-flat', '2')
dest_plate = labware.load('96-flat', '1')
water = water_rack.wells('A1')
tiprack_10 = [labware.load('tiprack-10ul', slot) for slot in ['6', '7']]
p10 = instruments.P10_Single(mount='right', tip_racks=tiprack_10)
p10.pick_up_tip()
p10.transfer(Vol,
water,
dest_plate.wells(dest_well),
blow_out=True,
new_tip='never')
p10.drop_tip()
stamp_tiprack,
grid = (4,1),
spacing = (10,10),
diameter = 5,
depth = 5)
paper_sheet = "paper-sheet"
if paper_sheet not in labware.list():
labware.create(
paper_sheet,
grid = (4,1),
spacing = (12,30),
diameter = 5,
depth = 2)
stamps = labware.load(stamp_tiprack, slot=6)
wax = labware.load('agilent_1_reservoir_290ml', slot=10)
paper = labware.load(paper_sheet, slot=1)
pipette = instruments.P300_Single(mount='left')
pipette.pick_up_tip(location=stamps.wells('A1'))
for i in range(1,5):
pipette.move_to(wax.wells('A1').top(20))
pipette.aspirate(30)
pipette.move_to(wax.wells('A1').top(-2))
pipette.dispense(30)
pipette.move_to(wax.wells('A1').top(20))
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,
diameter=5.50, # diameter (mm) of each well on the plate (here width at top!!)
depth=15.00, # depth (mm) of each well on the plate
volume=200) # as per manufacturer's website
print('Wells in 96WP PCR Thermo Fisher:')
for well in custom_plate.wells():
print(well)
############################ define labware
# i.e. translate user-friendly parameters into opentrons language
# pipette and tiprack
# multi channel
if multi_pipette_type == 'p10-Multi':
tiprackdrugs = [labware.load(tiprackdrugs_type, slot) \
for slot in tiprackdrugs_slots]
pipette_multi = instruments.P10_Multi(
mount=multi_pipette_mount,
tip_racks=tiprackdrugs)
pipette_multi.start_at_tip(tiprackdrugs[0].well(tiprackdrugs_startfrom))
pipette_multi.plunger_positions['drop_tip'] = -6
# faster dispense
pipette_multi.set_speed(dispense=pipette_multi.speeds['dispense']*4)
# translate the drugs mapping dict in robot language
# load source plate first
src_plate = labware.load(drugs_source_type, drugs_source_slot)
src_wells = [well.bottom(frombottom_off) for well in src_plate.rows('A')]
wells_mapping = {}
for key, value in drugs_mapping.items():
elif speed_conf ==1:
speed_set = medium_speed
elif speed_conf ==2:
speed_set = slow_speed
robot.head_speed(combined_speed=max(speed_set.values()),**speed_set)
#Number of chips to coat
#num_chips = int(input('Number of chips to coat (1,2 or 3)'))
num_chips = int(args.integers[1])
#this variable when change to something other that None allows the while loop to be broken.
rotate_st = None;
# Import labware
#ax-6 definition
if 'ax_6' not in locals():
ax_6 = labware.load('ax6_5','6')
#tiprack
if 'tiprack' not in locals():
tiprack = labware.load('opentrons-tiprack-300ul', '1')
#eppendorf rack
if 'ep_rack' not in locals():
ep_rack = labware.load('opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap','4')
# Import pipette definitions
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])
#This function stores the current tip that the robot will use and can reset the pipette wells or display the current tip.
from opentrons import labware, instruments
metadata = {
'protocolName':
'Dilute extracted DNA',
'author':
'James Kitson',
'description':
'A series of commands to dilute the extracted DNA obtained through the spin column extraction proceedure'
}
# get the plates loaded
DNA_plate1 = labware.load('starlab-E2896-0600', '4', 'input DNA plate')
#DNA_plate2 = labware.load('starlab-E2896-0600', '5', 'input DNA plate')
diluted_DNA_plate1 = labware.load('starlab-E1403-0100', '7',
'diluted_DNA plate')
#diluted_DNA_plate2 = labware.load('starlab-E1403-0100', '8', 'diluted_DNA plate')
Tris_plate = labware.load('starlab-E2896-0220', '9', 'Tris plate')
# load the tips
tips_10 = labware.load('tiprack-starlab-S1120-3810', '1')
tips_300 = labware.load('tiprack-starlab-S1120-9810', '3')
# set pipettes
pipette300 = instruments.P300_Multi(mount='left', tip_racks=[tips_300])
pipette10 = instruments.P10_Multi(mount='right', tip_racks=[tips_10])
# set the dilution parameters
final_volume: float = 200
from opentrons import labware, instruments, modules, robot
from opentrons.data_storage import database
from time import sleep
sample = labware.load('96-flat', slot=3)
tiprack = labware.load('opentrons-tiprack-300ul', slot=9)
tiprack_l = labware.load('opentrons-tiprack-300ul', slot=5)
# [2] Pipettes
pipette_r = instruments.P50_Multi(mount='right', tip_racks=[tiprack])
pipette_l = instruments.P300_Single(mount='left', tip_racks=[tiprack_l])
pipette_l.transfer(100, sample.wells('A1'), sample.wells('A3'))
pipette_l.transfer(100, sample.wells('B1'), sample.wells('B3'))
pipette_l.transfer(100, sample.wells('C1'), sample.wells('C3'))
pipette_r.transfer(50, sample.wells('A3'), sample.wells('A4'))
pipette_r.transfer(50, sample.wells('A3'), sample.wells('A5'))
pipette_r.transfer(50, sample.wells('A1'), sample.wells('A6'))
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=5.23, # diameter (mm) of each well on the plate
depth=50, # depth (mm) of each well on the plate
volume=200)
plate_name = 'biolector-flower-plate-48-well'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of labware
grid=(8, 6), # amount of (columns, rows)
spacing=(13, 13), # distances (mm) between each (column, row)
diameter=10.85, # diameter (mm) of each well on the plate
depth=33, # depth (mm) of each well on the plate
volume=3200)
tiprack = labware.load(tip_name, '9') # Load tiprack
trough = labware.load('opentrons_6_tuberack_falcon_50ml_conical',
'6') # Load reservoir
troughCell = labware.load('opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical',
'5')
pipette = instruments.P300_Single(mount='right',
tip_racks=[tiprack],
max_volume=200) # Load pipette
plate = labware.load(plate_name, '3') # Load wellplate
# =========================== Set source locations ============================
from opentrons import robot, labware, instruments
metadata = {
'protocolName': 'Tube Distribution Test: Fill 384 and transfer to 4*96',
'author': 'Amhed Vargas <*****@*****.**>',
'source': 'KAUST - OT-2 Protocols'
}
###Robot speed
robot.head_speed(x=100, y=100, z=100, a=125, b=50, c=50)
##Labware
#Tips
#p300rack = labware.load('opentrons_96_tiprack_300ul', '9')
p10rack1 = labware.load('tiprack-10ul', '1')
p10rack2 = labware.load('tiprack-10ul', '2')
#p10rack3 = labware.load('opentrons_96_tiprack_10ul', '4')
#p10rack4 = labware.load('opentrons_96_tiprack_10ul', '5')
#Plates
p384plate = labware.load('384-plate', '3')
p96plateA = labware.load('96-PCR-tall', '10')
p96plateB = labware.load('96-PCR-tall', '7')
#p96plateC = labware.load('biorad_96_wellplate_200ul_pcr', '11')
#p96plateD = labware.load('biorad_96_wellplate_200ul_pcr', '8')
#Samples
sample_tubes = labware.load('opentrons-tuberack-2ml-eppendorf', '6')
metadata = {
'protocolName':
'D-Rex Inital Extraction',
'author':
'Jacob Agerbo Rasmussen <*****@*****.**>',
'version':
'1.0',
'date':
'2019/03/28',
'description':
'Automation of D-Rex RNA and DNA seperation for extraction protocol of stool samples in SHIELD',
}
#### LABWARE SETUP ####
trough = labware.load('trough-12row', '2')
RNA_plate = labware.load('96-deep-well', '1')
mag_deck = modules.load('magdeck', '7')
sample_plate = labware.load('96-deep-well', '7', share=True)
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
transfer_list_of_volumes(Q, starting_well_plate,
starting_well_number, reagent_volume[0])
moves = transfer_list_of_volumes(H, starting_well_plate,
starting_well_number,
reagent_volume[1])
i += moves
return
#Import Dependencies
from opentrons import labware, instruments, robot
import numpy as np
################################################################################
#Importing labware
tiprack_300 = labware.load(
"opentrons-tiprack-300ul",
'10') # 300ul tips can be used for P300 and P50 pipettes
tiprack_300_2 = labware.load("opentrons-tiprack-300ul", '11') # Second tiprack
stock = labware.load("trough-12row", '2') # 12 well resovoir for stocks
A_96_well = labware.load("96-flat", '8') # Using 4, 96 wellplates labeled A-D
B_96_well = labware.load("96-flat", '9')
C_96_well = labware.load("96-flat", '5')
D_96_well = labware.load("96-flat", '6')
trash = robot.fixed_trash
################################################################################
#Importing pipettes
P300 = instruments.P300_Single(
mount='left', tip_racks=[tiprack_300],
trash_container=trash) # Volume range = 30-300uL
P50 = instruments.P50_Single(mount='right',
depth=35, # depth (mm) of each well on the plate
volume=350000)
#### LABWARE SETUP ####
temp_deck_1 = tempdeck.TempDeck()
temp_deck_2 = tempdeck.TempDeck()
temp_deck_1._port = '/dev/ttyACM0'
temp_deck_2._port = '/dev/ttyACM1'
if not robot.is_simulating():
temp_deck_1.connect()
temp_deck_2.connect()
temp_deck1 = modules.load('tempdeck', '7')
Cold_plate = labware.load('biorad-hardshell-96-PCR', '7', share=True)
# trough = labware.load('trough-12row', '2')
# Trash = labware.load('One-Column-reservoir','3')
temp_deck2 = modules.load('tempdeck', '10')
temp_plate = labware.load('biorad-hardshell-96-PCR', '10', share=True)
#mag_deck = modules.load('magdeck', '7')
#mag_plate = labware.load('biorad-hardshell-96-PCR', '7', share=True)
tipracks_10 = [
labware.load('tiprack-10ul', slot, share=True) for slot in ['8', '5', '4']
]
tipracks_200 = [
labware.load('tiprack-200ul', slot, share=True) for slot in ['9', '11']
]
#Python 3.6.4
#Please keep the author(s) attached to the code segment for traceability, if changes are made please append the authour list and modify the timestamp #
#####################################################################################################################################
#The input from the code must be in list within a list, the sublist must contain the appropriate float type value and no whitespaces
#####################################################################################################################################
from opentrons import labware, instruments, robot, modules # Import all opentrons API
from sqlite3 import IntegrityError # Import sqlite3 for custom container support
#####################################################################################################################################
#####################################################################################################################################
# LOADED LABWARE
TempDeck = modules.load('tempdeck', '6') # Loads TempDeck
tiprack200_1 = labware.load('opentrons-tiprack-300ul', '9')
Compcells1 = labware.load('96-flat', '6', "compcells1", share=True)
trash = robot.fixed_trash # Specify trash
Culture = labware.load(
'duran_100', '4') # Chilledflask_100 and duran_250 are custom containers
Buffers = labware.load('96-deep-well', '3')
#####################################################################################################################################
#####################################################################################################################################
# LOADED PIPETTES
# CAN CHANGE IF NEEDED
P300 = instruments.P300_Single( # Import Pipette, set aspiration/dispense rates and equip with rack
mount='right',
aspirate_flow_rate=200,
dispense_flow_rate=200,
from opentrons import labware, instruments
p300rack = labware.load('tiprack-200ul', '11', 'p300rack')
trough = labware.load('trough-12row', '10', 'trough')
plate = labware.load('96-PCR-flat', '4', 'plate')
top_plate = labware.load('96-PCR-flat', '5', 'top_plate')
liquid_trash = labware.load('trash-box', '3')
p300_multi = instruments.P300_Multi(
tip_racks=[p300rack],
mount='right'
)
# Reagent locations in trough:
# trough row 1 = buffer
# trough row 2 = Ph-Ch-Iso-Amyl mix
# trough row 3 = isopropanol
# trough row 4 = ethanol
# Transfer 300uL of L buffer from trough to 96 well deep plate with same tips
p300_multi.transfer(300, trough('A1'), plate.cols('1', to='12'))
# Transfer 180uL of Ph-Ch-Iso-Amyl mixture to 96 well deep plate
p300_multi.transfer(180, trough('A2'), plate.cols('1', to='12'))
# Transfer top layer (200uL) from 96 well deep plate to new 96 deep well plate
top_source = [col[0].top(-2) for col in plate.cols('1', to='12')]
p300_multi.transfer(
200, top_source, top_plate.cols())
#Last modified: 19:43, 12/10/18
#Python 3.6.4
#Please keep the author(s) attached to the code segment for traceability, if changes are made please append the authour list and modify the timestamp
#####################################################################################################################################
#The input from the code must be in list within a list, the sublist must contain the appropriate float type value and no whitespaces
from opentrons import labware, robot, instruments, modules # Import all opentrons API
from sqlite3 import IntegrityError # Import sqlite3 for custom container support
#####################################################################################################################################
#####################################################################################################################################
# LOADED LABWARE
TempDeck = modules.load('tempdeck', '6') # Loads TempDeck
Tiprack10uL = labware.load('tiprack-10ul', '11')
Tiprack300uL = labware.load('opentrons-tiprack-300ul', '9')
Compcells = labware.load('96-flat', '6', "compcells1",
share=True) # Competent Cells
trash = robot.fixed_trash
DNA = labware.load('tube-rack-2ml', '10') # Plasmid/DNA wanted to transform
SOB = labware.load(
'duran_100',
'7') # Recovery media, SOB strongly recommended for E. coli DH5a
#####################################################################################################################################
#####################################################################################################################################
# LOADED PIPETTES
# CAN CHANGE IF NEEDED
P300 = instruments.P300_Single(mount='right',
return(pipette)
# =============================== Load labware ===============================
tip_name = 'Biozym-tiprack-200ul' # Add Biozym 200 ul tiprack to labware library
if tip_name not in labware.list():
custom_tip = labware.create(
tip_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=5.23, # diameter (mm) of each well on the plate
depth=50, # depth (mm) of each well on the plate
volume=200)
tiprack = labware.load(tip_name, '9', label="tiprack") # Load tiprack
trough = labware.load('opentrons_6_tuberack_falcon_50ml_conical', '6', label= "source") # Load reservoir
plate = labware.load('corning_96_wellplate_360ul_flat', '3', label="wellplate") # Load wellplate
pipette = instruments.P300_Single(mount='right', tip_racks=[tiprack], max_volume=200) # Load pipette
# =========================== Set source locations ============================
DyeSource = trough.wells("A1") #50 ml falcon with dye added as baseline and gradient
pipette.start_at_tip(tiprack['A1'])
from opentrons import robot, labware, instruments
# labware setup
block = labware.load('nest_96_wellplate_100ul_pcr_full_skirt', '2')
plates = [
labware.load('nest_96_wellplate_100ul_pcr_full_skirt', slot)
for slot in ['3', '4', '5', '6', '7', '8', '9', '10', '11']
]
tiprack = labware.load('opentrons-tiprack-10ul', '1')
# instrument setup
# p300 = instruments.P20_Single(
# mount='left',
# tip_racks=[tiprack])
# initialize pipettes
p20 = instruments.P20_Single_GEN2(mount='right', tip_racks=[tiprack])
def run_custom_protocol(transfer_volume: float = 100,
number_of_plates: int = 9,
discard_tip: 'StringSelection...' = 'False'):
if discard_tip == 'False':
discard_tip = False
else:
discard_tip = True
for index, source in enumerate(block.wells()):
dest = [plate.wells(index) for plate in plates[:number_of_plates]]
p20.distribute(transfer_volume,
TRANSFORMATION_PLATE_TYPE = 'Eppendorf_30133366_plate_96'
SOC_PLATE_TYPE = '4ti0136_96_deep-well'
SOC_PLATE_SLOT = '7'
TUBE_RACK_TYPE = 'tube-rack_E1415-1500'
TUBE_RACK_SLOT = '11'
SPOTTING_WASTE_WELL = 'A1'
AGAR_PLATE_TYPE = 'Nunc_Omnitray'
AGAR_PLATE_SLOT = '1'
# Tiprack slots
p10_p300_tiprack_slots = tiprack_slots(spotting_tuples)
p10_slots = CANDIDATE_P10_SLOTS[:p10_p300_tiprack_slots[0]]
p300_slots = CANDIDATE_P300_SLOTS[:p10_p300_tiprack_slots[1]]
# Define labware
p10_tipracks = [labware.load(P10_TIPRACK_TYPE, slot) for slot in p10_slots]
p300_tipracks = [labware.load(P300_TIPRACK_TYPE, slot) for slot in p300_slots]
p10_pipette = instruments.P10_Single(mount=P10_MOUNT, tip_racks=p10_tipracks)
p300_pipette = instruments.P300_Multi(mount=P300_MOUNT,
tip_racks=p300_tipracks)
assembly_plate = labware.load(ASSEMBLY_PLATE_TYPE, ASSEMBLY_PLATE_SLOT)
tempdeck = modules.load('tempdeck', TEMPDECK_SLOT)
transformation_plate = labware.load(TRANSFORMATION_PLATE_TYPE,
TEMPDECK_SLOT,
share=True)
soc_plate = labware.load(SOC_PLATE_TYPE, SOC_PLATE_SLOT)
tube_rack = labware.load(TUBE_RACK_TYPE, TUBE_RACK_SLOT)
spotting_waste = tube_rack.wells(SPOTTING_WASTE_WELL)
agar_plate = labware.load(AGAR_PLATE_TYPE, AGAR_PLATE_SLOT)
spacing=(8.99, 8.99), # distances (mm) between each (column, row)
diameter=7.57, # diameter (mm) of each well on the plate (here width at bottom)
depth=10.35, # depth (mm) of each well on the plate
volume=650) # this is the actual volume as per specs, not a "volume of work"
print('Wells in 96WP Whatman:')
for well in custom_plate.wells():
print(well)
############################ define labware
# pipette and tiprack
# single channel
if single_pipette_type == 'p10-Single':
tipracks_single = [labware.load(tiprack_type_single, tiprack_slot) \
for tiprack_slot in tiprack_slots_single]
pipette_single = instruments.P10_Single(
mount=single_pipette_mount,
tip_racks=tipracks_single)
pipette_single.start_at_tip(tipracks_single[0].well(tip_start_from_single))
pipette_single.plunger_positions['drop_tip'] = -6
# multi channel
if multi_pipette_type == 'p10-Multi':
tipracks_multi = [labware.load(tiprack_type_multi, tiprack_slot) \
for tiprack_slot in tiprack_slots_multi]
pipette_multi = instruments.P10_Multi(
mount=multi_pipette_mount,
tip_racks=tipracks_multi)
pipette_multi.start_at_tip(tipracks_multi[0].well(tip_start_from_multi))
if '96-well-plate-sqfb-whatman' not in labware.list():
custom_plate = labware.create(
'96-well-plate-sqfb-whatman', # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(8.99, 8.99), # distances (mm) between each (column, row)
diameter=7.57, # diameter (mm) of each well on the plate (here width at bottom)
depth=10.35, # depth (mm) of each well on the plate
volume=650) # this is the actual volume as per specs, not a "volume of work"
for well in custom_plate.wells():
print(well)
############################ define labware
# pipette and tiprack
if pipette_type == 'p10-Single':
tipracks = [labware.load(tiprack_type, tiprack_slot) for tiprack_slot in tiprack_slots]
pipette = instruments.P10_Single(
mount=pipette_mount,
tip_racks=tipracks)
pipette.start_at_tip(tipracks[0].well(tip_start_from))
elif pipette_type == 'p10-Multi':
tipracks = [labware.load(tiprack_type, tiprack_slot) for tiprack_slot in tiprack_slots]
pipette = instruments.P10_Multi(
mount=pipette_mount,
tip_racks=tipracks)
pipette.start_at_tip(tipracks[0].cols(tip_start_from))
pipette.plunger_positions['drop_tip'] = -6
# container for the drugs
src_container = labware.load(source_type, source_slot)
# where water, op50, and dmso are in the source container
depth=15.00, # depth (mm) of each well on the plate
volume=200) # as per manufacturer's website
print('Wells in 96WP PCR Thermo Fisher:')
for well in custom_plate.wells():
print(well)
############################ define labware
# i.e. translate user-friendly parameters into opentrons language
# pipette and tiprack
# multi channel
if drugs_pipette_type == 'p10-Single': # this is mostly a check
tiprackdrugs = [
labware.load(tiprack_drugs_type, tiprack_slot)
for tiprack_slot in tiprack_drugs_slots
]
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)
depth=15.00, # depth (mm) of each well on the plate
volume=200) # as per manufacturer's website
print('Wells in 96WP PCR Thermo Fisher:')
for well in custom_plate.wells():
print(well)
############################ define labware
# i.e. translate user-friendly parameters into opentrons language
# pipette and tiprack
# multi channel
if multi_pipette_type == 'p10-Multi': # this is mostly a check as we don't own other multichannel pipettes (and to not have swapped single/multi)
tiprackmulti = [
labware.load(tiprack_multi_type, tiprack_slot)
for tiprack_slot in tiprack_multi_slots
]
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)
try:
self.rack[i][j + n - 1]
except IndexError:
continue
tips = self.rack[i][j:j + n]
if any(x is None for x in tips):
continue
else:
for t in range(n):
self.rack[i][j + t] = None
tip_name = tips[-1]
print("\nTaking {} tips".format(n))
return self.tiprack.wells(tip_name)
tube_rack_2ml = labware.load('storeylab-2ml-coldrack1', '7')
tube_rack_15ml = labware.load('opentrons-tuberack-15_50ml', '10')
small_reagent_plate = labware.load('PCR-strip-tall', '8')
pcr_plate1 = labware.load('96-flat', '4')
pcr_plate2 = labware.load('96-flat', '5')
pcr_plate3 = labware.load('96-flat', '6')
tiprack1 = labware.load('opentrons-tiprack-300ul', '11')
tiprack2 = labware.load('opentrons-tiprack-300ul', '9')
tiprack2_tracker = TipTracker(tiprack=tiprack2)
TOTAL_VOL = 20.0
CDNA_VOL = 5.0
WATER_PER_WELL = 12.115 - CDNA_VOL
assert WATER_PER_WELL >= 0, "Water per well is less than 0"
5.50, # diameter (mm) of each well on the plate (here width at top!!)
depth=15.00, # depth (mm) of each well on the plate
volume=200) # as per manufacturer's website
print('Wells in 96WP PCR Thermo Fisher:')
for well in custom_plate.wells():
print(well)
############################ define labware
# i.e. translate user-friendly parameters into opentrons language
# pipette and tiprack
# multi channel
if multi_pipette_type == 'p10-Multi': # this is mostly a check as we don't own other multichannel pipettes (and to not have swapped single/multi)
tiprackdrugs = [labware.load(tiprackdrugs_type, slot) \
for slot in tiprackdrugs_slots]
pipette_multi = instruments.P10_Multi(mount=multi_pipette_mount,
tip_racks=tiprackdrugs)
pipette_multi.start_at_tip(tiprackdrugs[0].well(tiprackdrugs_startfrom))
pipette_multi.plunger_positions['drop_tip'] = -6
# faster dispense
pipette_multi.set_speed(dispense=pipette_multi.speeds['dispense'] * 4)
# I only associated the "drugs" tiprack to the pipette as this is the one I want to handle authomatically
# I'll manually handle pipetting water
# container for water
water_src_container = labware.load(H2O_source_type, H2O_source_slot)
water_src_well = water_src_container.wells(H2O_source_well)
# tiprack for water
tiprackwater = labware.load(tiprackH2O_type, tiprackH2O_slot)
custom_plate_name = 'tulio96'
if custom_plate_name not in labware.list():
labware.create(custom_plate_name,
grid=(12, 8),
spacing=(8.3, 8.3),
diameter=8.3,
depth=42,
volume=2000)
# name of you labware
# number of (columns, rows)
# distances (mm) between each (column, row)
# diameter (mm) of each well
# depth (mm) of each well
# volume (μL) of each well
tiprack = labware.load('opentrons-tiprack-300ul', slot='1')
pool_source = labware.load('tulio96', '7')
pool_slice = labware.load('tulio96', '10')
trash = labware.load('trash-box', '12', share=True)
pipette = instruments.P50_Single(mount='right',
tip_racks=[tiprack],
trash_container=trash)
for pool in pool_dict.keys():
for single_slice in slice_dict[pool]:
pipette.pick_up_tip()
pipette.transfer(200, pool_source.wells(single_slice),
pool_slice.wells(pool_dict[pool][0]))
#pipette.drop_tip(trash)
