def __init__(self,
simulating = True,
slot = '10',
name = 'ninjapcr',
connection_mode = 'external_wifi',
ssid = None,
psk = None,
lw_name = None):
if connection_mode not in CONNECTION_MODES:
raise ValueError(f'Invalid connection mode: {connection_mode}')
self.simulating = simulating
self.local_url = f'http://{name}.local'
self.net_ssid = ssid
self.net_psk = psk
self.connected = False
self.connection_mode = connection_mode
# Define and load associated labware
if lw_name not in labware.list():
labware.create(
lw_name, # Labware Name
grid=(4, 4), # Amount of (columns, rows)
spacing=(9, 9), # Distances (mm) between each (column, row)
diameter=2, # Diameter (mm) of each well on the plate
depth=20, # Depth (mm) of each well on the plate
volume=50)
self.labware = labware.load(lw_name, slot=slot)
def loadPlate():
if CUSTOM_PLATE not in labware.list():
labware.create(
CUSTOM_PLATE, # name of labware
grid=(12, 8), # number of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=5.49, # diameter (mm) of each well
depth=16.4, # depth (mm) of each well
volume=100) # volume (µL) of each well
def test_labware_create(dummy_db):
from opentrons import labware
lw_name = '15-well-plate'
if lw_name in labware.list():
database.delete_container(lw_name)
n_cols = 5
n_rows = 3
col_space = 12
row_space = 18
diameter = 5
height = 20
volume = 3.14 * (diameter / 2.0)**2
res = labware.create(lw_name, (n_cols, n_rows), (col_space, row_space),
diameter, height, volume)
lw = database.load_container(lw_name)
database.delete_container(lw_name)
assert len(lw.wells()) is n_cols * n_rows
for well in lw.wells():
name = well.get_name()
assert res[name].coordinates() == well.coordinates()
for prop in ['height', 'diameter']:
assert res[name].properties[prop] == well.properties[prop]
assert lw.well("B5").coordinates() == ((n_cols - 1) * col_space, row_space,
0)
assert lw.well("C3").coordinates() == (2 * col_space, 0, 0)
assert lw.well(2).get_name() == 'C1'
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 test_labware_create(dummy_db):
n_cols = 6
n_rows = 4
x_dist = 19.6
y_dist = 19.6
radius = 5.65
depth = 84
lw = labware.create(
'testing-lw',
grid=(n_cols, n_rows),
spacing=(x_dist, y_dist), # distances (mm) between each (column, row)
diameter=radius * 2,
depth=depth)
row_a_center = ((n_rows - 1) * y_dist) + radius
col_1_center = radius
row_d_center = radius
col_6_center = ((n_cols - 1) * x_dist) + radius
expected = {
'A1': (col_1_center, row_a_center, depth),
'D1': (col_1_center, row_d_center, depth),
'A6': (col_6_center, row_a_center, depth),
'D6': (col_6_center, row_d_center, depth)
}
labware_coords = lw.coordinates() # currently (0, 0, 0)
def top(well):
wc = well.coordinates()
wt = well.top()[1]
return labware_coords + wc + wt
actual = {key: top(lw[key]) for key in expected.keys()}
for key in expected.keys():
assert expected[key] == actual[key]
destination_OP50_rows = ['D','E','F']
compound_volumes = [3, 5, 10]
water_volumes = [5, 10]
destination_water_cols = [['1','2','3','4'],
['5','6','7','8']]
agar_thickness = +3 # mm from the bottom of the well
############################# define custom multiwell plates
if '48-well-plate-sarsted' not in labware.list():
custom_plate = labware.create(
'48-well-plate-sarsted', # name of you labware
grid=(8, 6), # specify amount of (columns, rows)
spacing=(12.4, 12.4), # distances (mm) between each (column, row)
diameter=10, # diameter (mm) of each well on the plate
depth=17.05, # depth (mm) of each well on the plate
volume=500) # Sarsted had a "volume of work"
for well in custom_plate.wells():
print(well)
############################ define labware
# pipette and tiprack
if pipette_type == 'p10-Single':
tiprack = labware.load(tiprack_type, tiprack_slot)
pipette = instruments.P10_Single(
mount=pipette_mount,
tip_racks=[tiprack])
pipette.start_at_tip(tiprack.well(tip_start_from))
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)
volume=20000 #maximum volume that can be put for each well (um)
)
for slot in range(max_src_slot):
plate_containers[slot] = labware.load(plate_name, str(slot + 1))
print("Load experiment destination plate tuberack: ", plate_name, " for ",
10 - max_src_slot, " slot")
dest_slot_start = max_src_slot + 1
#print out the slot no. so users know where to put plates in which slot
for slot in range(dest_slot_start, 11):
print("Load ", plate_name, " at slot no. ", (slot + 1))
plate_containers[slot] = labware.load(plate_name, str(slot + 1))
from opentrons import labware, instruments, robot
from sqlite3 import IntegrityError
###################################################################################
# CREATE YOUR LABWARE BELOW
# TO LOAD LABWARE, RUN THIS CODE WITH YOUR SPECIFICATIONS
# ONCE LOADED, LABWARE WILL BE SAVED TO THE OT-2
# LOAD YOUR PROTOCOL AND THE CUSTOM LABWARE WILL BE RECOGNISED
###################################################################################
try:
Universals_Cold_Box = labware.create(
'Universals_Cold_Box',
grid=(5,3),
spacing=(25,25),
diameter=20,
depth=105,
volume=20000
)
except IntegrityError:
pass
###################################################################################
###################################################################################
# PASTE YOUR CREATED LABWARE BELOW
###################################################################################
# This did not work when I tried, may work again with update (Matt)
# Temp_96flat = Tempdeck + standard 96 well plate
# TempDeck_96-flat = labware.create(
REPLACE = False
#define a dict of custom plates. Can add as many as necessary
custom_plates = dict()
custom_plates['CCL_ARTBot_canvas'] = dict(grid=(1, 1),
spacing=(0, 0),
diameter=60,
depth=13,
volume=100)
custom_plates['falcon_6_wellplate_15.5ml_flat'] = dict(grid=(3, 2),
spacing=(39.3, 39.3),
diameter=34.75,
depth=18,
volume=15500)
custom_plates['nunc_8_wellplate_flat'] = dict(grid=(4, 2),
spacing=(31, 40.5),
diameter=31,
depth=13.3,
volume=13000)
for plate_name in custom_plates:
if plate_name in labware.list():
if REPLACE:
database.delete_container(plate_name)
else:
continue
labware.create(plate_name, **custom_plates[plate_name])
'mix_repetitions': MIX_REPETITIONS,
'new_tip': NEW_TIP
}
metadata = {
'protocolName': 'RNA Extraction v0.1',
'author': 'Neil MacKenzie, Eyal Kazin <*****@*****.**>',
'source': 'Testing' #'Custom Protocol Request'
}
# create custom labware
plate_name = 'MidSci-96-Well'
if plate_name not in labware.list():
labware.create(plate_name,
grid=(12, 8),
spacing=(9, 9),
diameter=5,
depth=21,
volume=200)
# labware
trough = labware.load('trough-12row', '2', 'trough')
fresh_plate = labware.load(plate_name, '3', 'fresh plate')
tips = [
labware.load('opentrons-tiprack-300ul', str(slot))
for slot in range(4, 10)
]
print('-' * 50)
print('Make sure the `tips` make sense!')
print(tips)
print('-' * 50)
drugs_mapping[(drugs_source_slot, ds)] = (src_cols, dst_cols)
# print out drugs_mapping:
for key, value in drugs_mapping.items():
_src_slot, _dst_slot = key
_src_cols, _dst_cols = value
for _src_col, _dst_col in zip(_src_cols, _dst_cols):
print('slot {0} col {1} --> slot {2} col {3}'.format(_src_slot, _src_col, _dst_slot, _dst_col))
############################# define custom multiwell plates
if '96-well-plate-pcr-thermofisher' not in labware.list():
custom_plate = labware.create(
'96-well-plate-pcr-thermofisher', # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9.00, 9.00), # distances (mm) between each (column, row)
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':
redefine = False
if redefine is True:
from opentrons.data_storage import database
database.delete_container('3x2_plate')
database.delete_container('3x2_plate_eppendorf')
database.delete_container('3x2_plate_corning')
database.delete_container('3x2_plate_falcon')
# 6-well plate custom entry
plate_name = '3x2_plate_eppendorf'
if plate_name not in labware.list():
hydra_plate = labware.create(
plate_name,
grid=(3, 2),
spacing=(38, 40),
diameter=35,
depth=17,
volume=3000
)
plate_name = '3x2_plate_corning'
if plate_name not in labware.list():
hydra_plate = labware.create(
plate_name,
grid=(3, 2),
spacing=(39.12, 39.12),
diameter=34.8,
depth=17.4,
volume=16800
)
from opentrons import labware, instruments, robot
from otcustomizers import FileInput, StringSelection
reservoir_name = 'biotix-resevoir'
if reservoir_name not in labware.list():
labware.create(reservoir_name,
grid=(1, 1),
spacing=(0, 0),
diameter=72,
depth=23)
tiprack_slots = ['1', '4', '7', '10']
resevoir = labware.load(reservoir_name, '2')
source = resevoir.wells('A1')
trash = robot.fixed_trash[0]
example_csv = """
90,168,187,13,70,189,196,93
56,197,147,139,74,61,44,157
106,198,45,6,46,113,111,33
28,143,185,17,199,155,78,93
185,96,60,105,143,151,18,102
139,48,111,68,179,126,59,172
111,25,84,12,63,31,34,8
24,128,106,88,124,65,133,26
61,71,109,84,85,62,89,168
58,101,121,5,122,88,27,59
43,16,156,175,190,41,78,8
66,60,164,129,106,7,198,195
"""
# plate layout by column:
# column 1: PBS for equilibration volume: 1.0 mL
# 2: sample containing Fc volume: ? >200 uL
# 3: PBS wash volume: 1.0 mL
# 4: acetate pH 6.0 wash volume: 1.0 mL
# 5: acetate pH 3.5 elution buffer volume: 60 uL
# 6: neutralization buffer volume: as needed to aspirate 6 uL
# create custom plate
custom_plate_name = 'VWR_SBS_96_well_1.2mL_plate'
if custom_plate_name not in labware.list():
labware.create(
custom_plate_name, # name of you labware
grid=(12, 8), # number of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=8.24, # x dimension of well ** crude hack to tell API that it is a round well since x-size throws error **
# y-size=8.24, # y dimension of well
depth=24.63, # depth (mm) of each well
volume=1200) # volume (µL) of each well
plate = labware.load(custom_plate_name, slot='2')
tiprack = labware.load('opentrons_96_tiprack_300ul', '3')
# pipettes
pipette = instruments.P300_Multi(
mount='right',
aspirate_flow_rate=8,
dispense_flow_rate=8,
blow_out_flow_rate=16,
tip_racks=[tiprack]) # *** DO NOT CALL (tiprack) in pipette.pick_up_tip() command *** !!!
import time
import math
from opentrons import robot, instruments, labware, modules
COLD_BLOCK = '96-PCR-tall-cold-block'
try:
labware.create(COLD_BLOCK,
grid=(12, 8),
spacing=(9, 9),
diameter=5,
depth=15.4,
volume=200)
except:
print("Using existing labware definition for {0}".format(COLD_BLOCK))
# Up to 48 rxns per run (4 spots on agar per rxn)
# Multichannel p300, single channel p10
# This protocol is optimized for maximum walkaway time
num_rxns = len(combinations_to_make)
num_plates = math.ceil(num_rxns / 24)
# Load in 96-well PCR plate (96-PCR-flat) on temp deck for moclos, transformation, and outgrowth.
temp_deck = modules.load('tempdeck', '10')
reaction_plate = labware.load('96-PCR-tall', '10', share=True)
available_deck_slots = ['11', '8', '7', '5', '4', '2', '1']
# Load in 1 10ul tiprack and 2 300ul tipracks
tr_10 = [labware.load('tiprack-10ul', '3'), labware.load('tiprack-10ul', '6')]
from opentrons import labware
metadata = {
'protocolName':
'Create_labware_Starlab',
'author':
'James Kitson <*****@*****.**>',
'description':
'A list of the labware create commands for standard ThermoFisher consumables'
}
#######################################
############## Microplates ############
#######################################
# Black Thermo micro plates compatible with the Scorpion plate stacker and plate reader
plate_name = 'Thermo-237108'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=7.1, # diameter (mm) of each well on the plate
depth=11.2, # depth (mm) of each well on the plate
volume=250)
'author':
'Jacob Agerbo Rasmussen <*****@*****.**>',
'version':
'1.0',
'date':
'2019/07/04',
'description':
'End Repair of Automated single tube library preperation after Carøe et al. 2017',
}
#### LOADING CUSTOM LABWARE ####
plate_name = 'chill_rack_96'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(12, 12), # distances (mm) between each (column, row)
diameter=6.4, # diameter (mm) of each well on the plate
depth=15, # depth (mm) of each well on the plate
volume=200)
plate_name = '1ml_Covaris'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=5.2, # diameter (mm) of each well on the plate
depth=18.6, # depth (mm) of each well on the plate
volume=1000)
plate_name = 'One-Column-reservoir'
pipette.transfer(100, md_well, td_lab.wells('B3'))
pipette.blow_out(td_lab.wells('B3'))
# (45) Repeat
# (46) Add 600 ul from A1 to magdeck
pipette.transfer(600, td_lab.wells('A1'), md_well)
mix(5,300,md_well)
magdeck.disengage()
plate_eppendorf = 'Eppendorf_Samples'
if plate_eppendorf not in labware.list():
Eppendorf = labware.create(
plate_eppendorf,
grid = (8,4),
spacing = (15,20),
diameter = 10,
depth = 35,
volume = 100)
magdeck_plate = 'MagDeck_24'
if magdeck_plate not in labware.list():
labware.create(
magdeck_plate,
grid = (6,4),
spacing = (18, 18),
diameter = 10,
depth = 41,
volume = 1500)
_new_fillvol = fillvol #save the updated fillvol as _new_fillvol to use further
#cited from "pipette.transfer"
pipette._run_transfer_plan(tips, plan, **kwargs)
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_10_tuberack_falcon_4x50ml_6x15ml_conical',
'6') # Load reservoir
pipette = instruments.P300_Single(mount='right',
tip_racks=[tiprack],
max_volume=200) # Load pipette
plate = labware.load("flowerplate_48_wellplate_3200ul", '3') # Load wellplate
assay_start = 2 #The start of the column of 384 well plates I want to dispense TE into.
assay_end = 48 #The end of the column I want to disepnse TE
assay_1_start = 2
assay_2_start = 22
sample_1_start = 0 #the column of 384 well plate where the sample was first dispensed into.
sample_1_end = 11 #the column of 384 well plate where the sample was last dispensed into.
sample_2_start = 0 #the column of 384 well plate where the sample from plate 2 was first dispensed into.
sample_2_end = 11 #the column of 384 well plate where the sample from plate 2 was last dispensed into.
plate_name = 'epMotion_10mL'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of you labware
grid=(7, 1), # specify amount of (columns, rows)
spacing=(17.5, 0), # distances (mm) between each (column, row)
diameter=5, # diameter (mm) of each well on the plate
depth=30, # depth (mm) of each well on the plate
volume=10000)
PG = labware.load('epMotion_10mL', '11', 'PG')
plate_384 = labware.load('corning_384_wellplate_112ul_flat', '2', 'plate')
sample_1 = labware.load('biorad_96_wellplate_200ul_pcr', '3')
sample_2 = labware.load('biorad_96_wellplate_200ul_pcr', '6')
tiprack_200 = labware.load('tiprack-200ul', '1', 'p200rack')
tiprack_10_1 = labware.load('opentrons_96_tiprack_10ul', '4')
tiprack_10_2 = labware.load('opentrons_96_tiprack_10ul', '7')
P10_8 = instruments.P10_Multi(mount='left',
print('Tips used so far: %d' % tc)
return
#%% LABWARE
# Source plate
src_plate = labware.load(source_type, source_slot)
# Destination plates
if '96-well-plate-sqfb-whatman' not in labware.list():
# Define custom 96WP Whatman plates
custom_plate = labware.create(
'96-well-plate-sqfb-whatman', # Name of labware
grid=(12, 8), # Specify number of (columns, rows)
spacing=(8.99, 8.99), # Distance (mm) between each (column, row)
diameter=7.57, # Diameter (mm) of each well on the plate
depth=10.35, # Depth (mm) of each well on the plate
volume=650) # Volume of well as per specs (not 'working volume')
print('Wells in 96WP Whatman:')
for well in custom_plate.wells():
print(well)
dst_plates = [labware.load(destination_type, dst_slot) for dst_slot in\
destination_slots]
#%% PIPETTES
# Multi-channel pipette + tip rack
if multi_pipette_type == 'p50-Multi':
tipracks_multi = [labware.load(tiprack_type_multi, tiprack_slot)\
'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap',
slot='7' & '8' & '9')
trashBox = labware.load('trash-box', slot='12')
pipette10 = instruments.P10_Single(mount='left',
tip_racks=[p10Rack],
trash_container=trashBox)
pipette300 = instruments.P300_Single(mount='right',
tip_racks=[p200Rack],
trash_container=trashBox)
custom_plate_name = 'greiner_384'
labware.create(
custom_plate_name,
grid=(24, 16),
spacing=(4.5, 4.5),
diameter=(4),
depth=(5.5),
volume=(20),
)
greiner380 = labware.load(custom_plate_name, slot='1')
# MMX (6.840 mL) was prepared by hand and split in to 6 tubes (1.14 mL)
tubeOTDBMMx = ['A1', 'A2', 'A3', 'A4', 'A5', 'A6']
#tubeOTDB = ['A1']
#tubeNTPs = ['A2']
#tubeT7RNApol = ['A3']
#tubeDFHBI = ['A4']
tubeWater = ['B1', 'B2', 'B3']
#tubeCFSMG1655 = ['B1']
#tubeCFSCH34 = ['B2']
# metals to be used
tubeCu = ['B4']
from opentrons import labware, instruments, modules, robot
from time import sleep
from subprocess import Popen
import os
metadata = {
'protocolName': 'Dar cera, pulir cera',
'description': 'Applies wax to paper sheets using a custom stamp',
'source': 'https://github.com/Zildj1an/SELEX'
}
stamp_tiprack = "wax-stamp-tiprack"
if stamp_tiprack not in labware.list():
labware.create(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=7)
wax = labware.load('agilent_1_reservoir_290ml', slot=4)
paper = labware.load(paper_sheet, slot=1)
#Small volume condition (is the volume less than or equal to this value?)
small_condition = 6 #ul
###### END OF USER INPUT #######
###Settings
from opentrons import containers, instruments, robot, labware
from opentrons.data_storage import database
from sqlite3 import IntegrityError
import math
#Creating P50 Tiprack
try:
custom_container = labware.create(
'tiprack-Fisher200ul', # name of your container. For a tiprack, must start with 'tiprack'
grid=(12, 8), # specify amount of (columns, rows)
spacing=(8.5, 8.5), # distances (mm) between each (column, row)
diameter=6.0,
depth=60) # depth (mm) of each tip on the rack
except IntegrityError:
pass
#Creating aluminum plate container
try:
custom_container = labware.create(
'full_alumina', # name of your container
grid=(8, 8), # specify amount of (columns, rows)
spacing=(10, 12), # distances (mm) between each (column, row)
diameter=0.5, # diameter (mm) of each well on the plate
depth=25) # depth (mm) of each well on the plate
except IntegrityError:
pass
#trashBox = labware.load('trash-box', slot='12')
pipette10 = instruments.P10_Single(
mount='left',
tip_racks=[p10Rack] #, trash_container=trashBox
)
pipette300 = instruments.P300_Single(
mount='right', #tip_racks=[p200Rack]#, trash_container=trashBox
)
#Defining 384 well plate
custom_plate_name = 'greiner_384'
if custom_plate_name not in labware.list():
labware.create(custom_plate_name,
grid=(24, 16),
spacing=(4.5, 4.5),
diameter=4,
depth=5.5,
volume=20)
greiner380 = labware.load(custom_plate_name, slot='1')
# MMX (6.840 mL) was prepared by hand and split in to 6 tubes (1.14 mL)
tubeOTDBMMx = ['A1', 'A2', 'A3', 'A4', 'A5', 'A6']
#tubeOTDB = ['A1']
#tubeNTPs = ['A2']
#tubeT7RNApol = ['A3']
#tubeDFHBI = ['A4']
tubeWater = ['B1', 'B2', 'B3', 'B4']
#tubeCFSMG1655 = ['B1']
#tubeCFSCH34 = ['B2']
# metals to be used
#tubeCu = ['B4']
from opentrons import labware, instruments, robot
microplate_name = 'greiner-384-square-1'
if microplate_name not in labware.list():
labware.create(microplate_name,
grid=(24, 16),
spacing=(4.5, 4.5),
diameter=3.7,
depth=11.5)
# labware setup
destination = protocol.load_labware(microplate_name, '2', 'Destination')
destination.properties['height'] = 14.5
master = protocol.load_labware(microplate_name, '1', 'Master')
master.properties['height'] = 14.5
control_1 = protocol.load_labware(microplate_name, '3', 'Control 1')
control_1.properties['height'] = 14.5
control_2 = protocol.load_labware(microplate_name, '5', 'Control 2')
control_2.properties['height'] = 14.5
tipracks = [
protocol.load_labware('tiprack-10ul', str(slot))
for slot in ['4', '6', '7', '8']
]
# instruments setup
m10 = instruments.P10_Multi(mount='left', tip_racks=tipracks)
m10.set_flow_rate(aspirate=10, dispense=200)
from opentrons import labware, instruments
metadata = {
'protocolName': 'Create_labware_Starlab',
'author': 'James Kitson <*****@*****.**>',
'description': 'A list of the labware create commands for standard Starlab consumables'
}
#######################################
######## PCR plates and strips ########
#######################################
# Starlab 1000ul RPT filter tips - cat no. S1182-1830 without tips - USED AS TRASH TROUGH
plate_name = 'trash-starlab-S1182-1830'
if plate_name not in labware.list():
custom_plate = labware.create(
plate_name, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=8, # diameter (mm) of each well on the plate
depth=90.3, # depth (mm) of tiprack and holder
volume=100000)
### makes sure to remove trash-tiprack-starlab-S1182-1830'
from opentrons import labware, instruments, modules, robot
if '4ti0131_trough-12' not in labware.list():
custom_plate = labware.create('4ti0131_trough-12',
grid=(12, 1),
spacing=(9, 0),
diameter=8.25,
depth=39.22,
volume=21000)
robot.comment('4ti0131_trough-12 added to labware database')
else:
robot.comment(
'4ti0131_trough-12 already exists in the OT2 database and has not been updated. Refer to Opentrons API and Custom_labware.csv'
)
if '4ti0136_96_deep-well' not in labware.list():
custom_plate = labware.create('4ti0136_96_deep-well',
grid=(12, 8),
spacing=(9, 9),
diameter=8.2,
depth=39.15,
volume=2200)
robot.comment('4ti0136_96_deep-well added to labware database')
else:
robot.comment(
'4ti0136_96_deep-well already exists in the OT2 database and has not been updated. Refer to Opentrons API and Custom_labware.csv'
)
if 'Nunc_Omnitray' not in labware.list():
custom_plate = labware.create('Nunc_Omnitray',
grid=(12, 8),
# print out drugs_mapping:
for key, value in drugs_mapping.items():
_src_slot, _dst_slot = key
_src_cols, _dst_cols = value
for _src_col, _dst_col in zip(_src_cols, _dst_cols):
print('slot {0} col {1} --> slot {2} col {3}'.format(
_src_slot, _src_col, _dst_slot, _dst_col))
############################# define custom multiwell plates
if '48-well-plate-sarsted' not in labware.list():
custom_plate = labware.create(
'48-well-plate-sarsted', # name of you labware
grid=(8, 6), # specify amount of (columns, rows)
spacing=(12.4, 12.4), # distances (mm) between each (column, row)
diameter=10, # diameter (mm) of each well on the plate
depth=17.05, # depth (mm) of each well on the plate
volume=500) # Sarsted had a "volume of work"
print('Wells in 48WP Sarsted:')
for well in custom_plate.wells():
print(well)
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)
}]
}
robot._driver.turn_off_rail_lights()
thermocycler.wait_for_program(PROGRAM)
robot.home()
# Run PCR as an independent protocol
# 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'