def test_containers_create(self):
import os
import json
from opentrons import Robot
container_name = 'plate_for_testing_containers_create'
containers.create(name=container_name,
grid=(8, 12),
spacing=(9, 9),
diameter=4,
depth=8,
volume=1000)
p = containers.load(container_name, 'A1')
self.assertEquals(len(p), 96)
self.assertEquals(len(p.rows), 12)
self.assertEquals(len(p.cols), 8)
self.assertEquals(p.get_parent(), Robot.get_instance().deck['A1'])
self.assertEquals(p['C3'], p[18])
self.assertEquals(p['C3'].max_volume(), 1000)
for i, w in enumerate(p):
self.assertEquals(w, p[i])
# remove the file if we only created it for this test
should_delete = False
with open(environment.get_path('CONTAINERS_FILE')) as f:
created_containers = json.load(f)
del created_containers['containers'][p.get_name()]
if not len(created_containers['containers'].keys()):
should_delete = True
if should_delete:
os.remove(environment.get_path('CONTAINERS_FILE'))
def getEquipment():
equipment = {}
containers.create('heating-block-3x4',
grid=(3, 4),
spacing=(22.3, 22.3),
diameter=17,
depth=45)
equipment['InputsC1'] = containers.load('heating-block-3x4', 'C1')
containers.create('heating-block-3x4',
grid=(3, 4),
spacing=(22.3, 22.3),
diameter=17,
depth=45)
equipment['MixingD1'] = containers.load('heating-block-3x4', 'D1')
equipment['OutputD2'] = containers.load('96-flat', 'D2')
equipment['TouchC2'] = containers.load('96-flat', 'C2')
containers.create('1000tiprack2',
grid=(7, 5),
spacing=(10.3, 18.6),
diameter=9,
depth=56)
equipment['1000tiprack'] = containers.load('1000tiprack2', 'B2')
equipment['100TiprackB1'] = containers.load('tiprack-1000ul', 'B1')
equipment['TrashA1'] = containers.load('trash-box', 'A1')
equipment['pd1000'] = instruments.Pipette(
name='pd1000',
axis='b',
max_volume=1000,
min_volume=100,
channels=1,
aspirate_speed=800,
dispense_speed=1200,
trash_container=equipment['TrashA1'])
equipment['pd100'] = instruments.Pipette(
name='pd100',
axis='a',
max_volume=100,
min_volume=10,
channels=1,
aspirate_speed=600,
dispense_speed=1000,
trash_container=equipment['TrashA1'])
return (equipment)
lines = open(input_file).readlines()
header = lines[0].rstrip().split(",")
out_d = {}
for head in header:
out_d[head] = []
for line in lines[1:]:
spl_line = line.rstrip().split(",")
for i, head in enumerate(header):
out_d[head].append(spl_line[i])
df = DataFrame(out_d, len(lines[1:]))
return df
containers.create(
"Starlab_96_Square_2mL", # name of you container
grid=(8, 12), # 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=45) # depth (mm) of each well on the plate
# CSV file data
stock_reagent_df = read_csv(
r"C:\Users\opentrons\protocols\GitHub_repos\OT1-coding\urea_phip_triple_reaction\csv\stock_reagents.csv"
)
solvent_df = read_csv(
r"C:\Users\opentrons\protocols\GitHub_repos\OT1-coding\urea_phip_triple_reaction\csv\solvents.csv"
)
"""Function that does two liquid handling transfers. First it will dilute a solid reagent in a big trough to the right concentration.
(Up to 2 reagents). Second, it will transfer the reagent from the big trough to the Fluix 24 vial rack, using the volume from the csv file
It requires 2 csv files. The first is the solvent csv, the second the custom made stock reagent csv."""
from opentrons import robot, containers, instruments
from itertools import chain
# ~~~~~~~~~~~ SET UP ~~~~~~~~~~
#max_speed_per_axis = { # Head Speed
# 'x': 2000, 'y': 1000, 'z':500, 'a':500, 'b':500, 'c':200}
#robot.head_speed(
# combined_speed=max(max_speed_per_axis.values()), **max_speed_per_axis)
tipracks = [containers.load('tiprack-200ul', slot) for slot in ['D2', 'E2']]
## Tyler's custom 8-trough container (treated as 4, because of the way BD made them)
containers.create('trough-8row',
grid=(8, 4),
spacing=(9, 30),
diameter=6,
depth=35)
## Axygen 96-well deep plate (1.1 ml)
containers.create('96-deep-well-Axygen',
grid=(8, 12),
spacing=(9, 9),
diameter=6,
depth=43)
## VWR 1.2-ml sample tubes
containers.create('96-sample-tubes',
grid=(8, 12),
spacing=(9, 9),
diameter=6,
from opentrons import containers containers.create( '96-really-deep', grid=(8,12), spacing=(9,9), depth=39, diameter=9, volume=2000)
from opentrons import containers, instruments
containers.create(
'tube-rack-4ml', # name of you container
grid=(6, 8), # specify amount of (columns, rows)
spacing=(13.25, 13.5), # distances (mm) between (column, row)
diameter=6.5, # diameter (mm) of each well on the plate
depth=44) # depth (mm) of each well on the plate
containers.create(
'reservoir-2', # name of you container
grid=(1, 2), # specify amount of (columns, rows)
spacing=(0, 54), # distances (mm) between each (column, row)
diameter=6.5, # diameter (mm) of each well on the plate
depth=39.22) # depth (mm) of each well on the plate
tube_B2 = containers.load('tube-rack-4ml', 'B2', 'tube-rack-B2')
WP_500ul = containers.load('96-PCR-flat', 'C1', 'output 1')
resevoir = containers.load('reservoir-2', 'B1', 'resevoir')
tube_C2 = containers.load('tube-rack-4ml', 'C2', 'tube-rack-C2')
tube_D2 = containers.load('tube-rack-4ml', 'D2', 'tube-rack-D2')
WP_1ml = containers.load('96-PCR-flat', 'E1', 'output 2')
all_dest_wells = WP_500ul.wells(0, length=80) + WP_1ml.wells(0, length=48)
all_source_wells = tube_B2.wells(0, length=40) \
+ tube_C2.wells(0, length=40) + tube_D2.wells()
all_dest_rows = WP_500ul.rows(0, length=12) + WP_1ml.rows(0, length=12)
## Code to make a PCR master mix and distribute it between wells of a 96-well plate
from opentrons import robot, containers, instruments
#Define containers
source_tubes = containers.load('tube-rack-2ml', 'E3', 'tube_rack')
output = containers.load('96-PCR-flat', 'C1', 'output')
p200rack = containers.load('tiprack-200ul', 'A1', 'p200_rack')
trash = containers.load('trash-box', 'A3')
#Create 6x12 p20 tip rack container
containers.create('tiprack-200ul-6x12',
grid=(6, 12),
spacing=(9, 9),
diameter=5,
depth=60)
p20rack = containers.load('tiprack-200ul-6x12', 'B2', 'p20_rack')
#Create 3x6 2ml tube rack for DNA samples
containers.create('3x6-tube-rack-2ml',
grid=(3, 6),
spacing=(19.5, 19.5),
diameter=9.5,
depth=40)
DNA_rack = containers.load('3x6-tube-rack-2ml', 'C3', 'DNA_rack')
#Define pipettes
p20 = instruments.Pipette(trash_container=trash,
## Code to test dual pipetting capabilities of opentrons
from opentrons import robot, containers, instruments
source_tubes = containers.load('tube-rack-2ml', 'D2', 'tube rack')
output = containers.load('96-PCR-flat', 'C1', 'output')
containers.create('7x12_tiprack',
grid=(7, 12),
spacing=(9, 9),
diameter=5,
depth=60)
p200rack = containers.load('7x12_tiprack', 'A1', 'p200-rack')
p200 = instruments.Pipette(tip_racks=[p200rack],
min_volume=20,
max_volume=200,
axis="b")
for i in range(10):
p200.pick_up_tip()
p200.return_tip()
from otcustomizers import FileInput, StringSelection
from opentrons import containers, instruments
containers.create(
'FluidX_96_small', # name of you container
grid=(8, 12), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=6, # diameter (mm) of each well on the plate
depth=20)
containers.create(
'FluidX_24_9ml', # name of you container
grid=(6, 8), # specify amount of (columns, rows)
spacing=(18, 18), # distances (mm) between each (column, row)
diameter=13, # diameter (mm) of each well on the plate
depth=83) # depth (mm) of each well on the plate
tiprack = containers.load("tiprack-1000ul", "B3")
plate_96 = containers.load("FluidX_96_small", "B2", label="FluidX_96_small")
plate_24 = containers.load('FluidX_24_9ml', "B2", label="FluidX_24_9ml")
source = containers.load("trough-12row", "D2")
trash = containers.load("trash-box", 'C3')
# Define the pipettes
p1000 = instruments.Pipette(
name="eppendorf1000",
axis="a",
trash_container=trash,
tip_racks=[tiprack],
max_volume=1000,
min_volume=10,
tubes_overflow = containers.load(
'96-deep-well',
'B2',
'b2qubit_tubes',
)
trash = containers.load(
'point',
'A3',
'a3trash',
)
containers.create(
'15ml-short-tube',
grid=(1, 1),
spacing=(20, 20),
diameter=18,
depth=105,
)
solution = containers.load(
'15ml-short-tube',
'B1',
'15mltube',
)
standards = containers.load(
'96-deep-well',
'B1',
'b1p5tube',
)
from opentrons import containers, instruments
wash_volume = 6000
containers.create(
'2x3_plate', # name of you container
grid=(2, 3), # specify amount of (columns, rows)
spacing=(39, 24.9), # distances (mm) between each (column, row)
diameter=35.58, # diameter (mm) of each well on the plate
depth=16.5 # depth (mm) of each well on the plate
)
culture_plate = containers.load('2x3_plate', 'C1')
trash = containers.load('trash-box', 'A3')
p1000rack1 = containers.load('tiprack-1000ul', 'A1')
p1000rack2 = containers.load('tiprack-1000ul', 'A2')
trough = containers.load('trough-12row', 'C2')
p1000 = instruments.Pipette(
name="p1000",
axis="a",
min_volume=100,
max_volume=1000,
trash_container=trash,
tip_racks=[p1000rack1, p1000rack2]
)
PBS_wash = trough['A1']
culture_medium = trough['A2']
dest_wells = [
from opentrons import containers, instruments, robot
import math
containers.create(
'trough-7row', # name of you container
grid=(1, 7), # specify amount of (columns, rows)
spacing=(0, 18.21), # distances (mm) between each (column, row)
diameter=2.46, # diameter (mm) of each well on the plate
depth=40)
"""
Column A
"""
tiprack = containers.load('tiprack-200ul', 'A1', 'Tip M')
tiprack2 = containers.load('tiprack-200ul', 'A2', 'Tip N')
tiprack3 = containers.load('tiprack-200ul', 'A3', 'Tip O')
"""
Column B
"""
tiprack4 = containers.load('tiprack-200ul', 'B1', 'Tip J')
trough = containers.load('trough-7row', 'B2')
tiprack5 = containers.load('tiprack-200ul', 'B3', 'Tip L')
"""
Column C
"""
tiprack6 = containers.load('tiprack-200ul', 'C1', 'Tip G')
cleanup_plate = containers.load('384-plate', 'C2')
tiprack7 = containers.load('tiprack-200ul', 'C3', 'Tip I')
"""
Column D
from opentrons import containers, instruments
# the number of plates with 19 mm diameter wells
# num19plates = 1 # change here
# the number of plates with 32 mm diameter wells
# num32plates = 1 # change here
# time to create liquid flow
time = 45 # change here
containers.create(
'2x3_MaxwellPlate19mm', # name of you container
grid=(2, 3), # specify amount of (columns, rows)
spacing=(38.4, 38.4), # distances (mm) between each (column, row)
diameter=19, # diameter (mm) of each well on the plate
depth=8) # depth (mm) of each well on the plate
containers.create(
'2x3_MaxwellPlate32mm', # name of you container
grid=(2, 3), # specify amount of (columns, rows)
spacing=(38.4, 38.4), # distances (mm) between each (column, row)
diameter=32, # diameter (mm) of each well on the plate
depth=8) # depth (mm) of each well on the plate
# HACK: need to explicitly load each container like this
# instead of using a for loop, so that deck map can be parsed out
# for protocol library
# smallplates = []
# largeplates = []
from opentrons import robot, containers, instruments
#containers.create(
# "tiprack-300ul_storm2", # name of you container
# grid=(8, 12), # specify amount of (columns, rows)
# spacing=(9, 9), # distances (mm) between each (column, row)
# diameter=4, # diameter (mm) of each well on the plate
# depth=60) # depth (mm) of each well on the plate
#containers.create(
# "Starlab_96_Square_2mL", # name of you container
# grid=(8, 12), # 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=60) # depth (mm) of each well on the plate
containers.create(
"StarLab_96_tall", # name of you container
grid=(8, 12), # specify amount of (columns, rows)
spacing=(18, 18), # distances (mm) between each (column, row)
diameter=11, # diameter (mm) of each well on the plate
depth=46) # depth (mm) of each well on the plate
# ~~~~~~~~~~~ SET UP ~~~~~~~~~~
# max_speed_per_axis = { # Head Speed
# 'x': 2000, 'y': 1000, 'z':500, 'a':500, 'b':500, 'c':200}
# robot.head_speed(
# combined_speed=max(max_speed_per_axis.values()), **max_speed_per_axis)
tiprack = containers.load('tiprack-200ul', 'A2', 'tiprack')
waste = containers.load('96-deep-well', 'D2', 'waste') #waste in deep well to see cells in case speed has an impact in disruptions
wash_basin = containers.load('point', 'B2', 'wash basin')
cellwell = containers.load('96-PCR-flat', 'C1', 'cells') #microwell plate with cells in it #place hot plate beneath, 37 degrees.
output_low = containers.load('96-PCR-flat', 'B1', 'output low')
output_high = containers.load('96-PCR-flat', 'A1', 'output high')
containers.create(
'troughrow',
grid=(8,4),
spacing=(10,30),
diameter=6,
depth=35)
glucose_medium = containers.load('troughrow', 'D1', 'glucose medium')
LOW_GLUCOSE_MEDIUM_ROWS = '1' #'2', '3']
#1st & 2nd rows of trough (from front to back) require 15mL low glucose medium
#3rd row requires 16mL low glucose medium
HIGH_GLUCOSE_MEDIUM_LOCATION = '4'
#4th row requires 16mL low glucose medium
p200_multi_low_speed = instruments.Pipette( # Lowest pipette speed, use for washing
axis='a',
name='pip200low',
from opentrons import containers, instruments
'''
Create a new container
'''
containers.create(
'Epptubes', # name of you container
grid=(3, 4), # specify amount of (columns, rows)
spacing=(13, 13), # distances (mm) between each (column, row)
diameter=8, # diameter (mm) of each well on the plate
depth=40) # depth (mm) of each well on the plate)
# source of diluent
tuberack = containers.load('Epptubes', 'D3')
#plate_96 = containers.load('96-PCR-flat', 'B1')
pcr_strip_d1 = containers.load('PCR-strip-tall', 'B1')
#pcr_strip_d2 = containers.load('PCR-strip-tall', 'B1')
#Qpcr_strip = containers.load('opentrons-aluminum-block-PCR-strips-200ul', 'C1')
tiprack = containers.load('tiprack-200ul', 'A1')
trash = containers.load('trash-box', 'C2')
#diluent_source = trough['A1']
# HACK: need to explicitly load each container like this
# instead of using a for loop, so that deck map can be parsed out
# for protocol library
# plate dilution will happen in
# plate_slots = ['A1', 'B1', 'A2', 'B2', 'A3', 'B3']
# plates = [c o n t a i n e r s.load(
from opentrons import robot, containers, instruments
containers.create(
'jMX_big_vial_holder', # name of you container
grid=(3, 4), # specify amount of (columns, rows)
spacing=(23, 23), # distances (mm) between each (column, row)
diameter=1.3, # diameter (mm) of each well on the plate
depth=68.0) # depth (mm) of each well on the plate
containers.create(
'Para_dox_96_short', # name of you container
grid=(8, 12), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
diameter=7, # diameter (mm) of each well on the plate
depth=30) # depth (mm) of each well on the plate
print(containers.list())
print(containers)
# imports
from opentrons import containers, instruments, robot
# containers
containers.create('tiprack-100ul',
grid=(8, 12),
spacing=(12, 12),
diameter=3.5,
depth=60)
trash = containers.load('point', 'E2')
plate = containers.load('96-PCR-tall', 'B1')
samples = containers.load('96-flat', 'C1')
mastermix = containers.load('tube-rack-2ml', 'A2')
t10 = containers.load('tiprack-10ul', 'A1')
t100 = containers.load('tiprack-20ul', 'A3')
# pipettes
p100 = instruments.Pipette(axis='b',
max_volume=100,
tip_racks=[t10],
trash_container=trash)
p50 = instruments.Pipette(axis='a',
max_volume=50,
tip_racks=[t10],
trash_container=trash,
channels=8)
def print_history():
def getEquipment():
equipment = {}
############## DECK LAYOUT BEGINS HERE
#CONTAINER DEFINITIONS:
TransposeTipBox = True
containers.create("24corning",
grid=(4, 6),
spacing=(19.304, 19.304),
diameter=16.26,
depth=18) #24-well plate
#DECK:
equipment['trash'] = containers.load('point', "C1", "trash")
equipment['p200rack'] = containers.load('tiprack-200ul', 'E2',
'tiprack200')
if TransposeTipBox:
equipment['p1000rack'] = create_container_instance("TR1000-Transposed",
slot="A1",
grid=(8, 12),
spacing=(9.02,
-9.02),
diameter=5,
depth=85,
Transposed=True)
else:
equipment['p1000rack'] = create_container_instance("TR1000-Normal",
slot="A1",
grid=(8, 12),
spacing=(9.02,
9.02),
diameter=5,
depth=85)
equipment['CulturePlate'] = containers.load('24corning', 'B2',
'CulturePlate24')
equipment['CulturePlate96'] = containers.load('96-flat', 'B2')
equipment['CulturePlate2'] = containers.load('24corning', 'C2',
'CulturePlate242')
equipment['AliquotPlate'] = containers.load('96-flat', 'C2',
'AliquotPlate')
equipment['TubBlood'] = create_container_instance("TubBlood",
slot="D1",
grid=(8, 1),
spacing=(9.02, 9.02),
diameter=0,
depth=55)
equipment['TubMedia'] = create_container_instance("TubMedia",
slot="D1",
grid=(8, 1),
spacing=(9.02, 9.02),
diameter=0,
depth=55)
equipment['TubSybr'] = create_container_instance("TubSybr",
slot="D1",
grid=(8, 1),
spacing=(9.02, 9.02),
diameter=0,
depth=55)
#PIPETTE(S)
equipment['p1000'] = instruments.Pipette(
name="P1000",
axis="b",
min_volume=20,
max_volume=1000,
tip_racks=[equipment['p1000rack']],
trash_container=equipment['trash'])
equipment['p200x8'] = instruments.Pipette(
name="p200x8",
axis="a",
min_volume=20,
max_volume=300,
trash_container=equipment['trash'],
channels=8)
return (equipment)
from opentrons import robot, containers, instruments
robot.head_speed(x=18000, y=18000, z=5000, a=700, b=700)
containers.create(
'96_rack_pp',
grid=(8,12),
spacing=(18,18),
diameter=13,
depth=48
)
containers.create(
'96_rack_glass',
grid=(8,12),
spacing=(18,18),
diameter=13,
depth=48
)
rack_number=4
rack_stock_reactants=[]
r_positions=['A1','A2','B1','C1']
r_types=['halide','boronic acid','base','catalyst']
for i in range(0,rack_number):
rack_stock_reactants.append(containers.load("FluidX_24_5ml", r_positions[i], r_types[i]))
tiprack_1000 = containers.load("tiprack-1000ul-H", "D3")
source_trough4row = containers.load("trough-12row", "C2")
reaction_racks = [containers.load("96_rack_glass", "D1"),containers.load("96_rack_pp", "D2")]
trash = containers.load("point", "B3")
from opentrons import robot, containers, instruments
from utilities import *
# create the custom containers: 24 and 6 well plates
# this will create a file ./containers/_contaiers_create.json
# which will be used to load the custom containers
# It should not be necessary to run this script as the
# JSON file is part of the repo so this is mainly here
# for reference to show how it was created.
# When using this, check the created file for order of
# well, which should be given in the same order that
# they are to be used, i.e. A1, B1, C1 .. , A2, B2, C2...
containers.create("24corning",
grid=(4, 6),
spacing=(19.304, 19.304),
diameter=16.26,
depth=18) #24-well plate
containers.create("6corning",
grid=(2, 3),
spacing=(39.12, 39.12),
diameter=34.80,
depth=11.27) #6-well plate
if hasattr(instr, 'update_calibrator'):
instr.update_calibrator()
custom_container.properties['type'] = name
custom_container.get_name = lambda: label
# add to robot deck
robot.deck[slot].add(custom_container, label)
return custom_container
#define trough type for water
containers.create('trough-15ml',
grid=(1, 1),
spacing=(20, 20),
diameter=30,
depth=30)
#Setup directions to human in comments.
tiprack200 = containers.load('tiprack-200ul', 'A3') # p200 tip rack in slot A3
Tip_rack_8 = containers.load('tiprack-200ul',
'E1') # p200 tip rack for 8-channel in slot E1
TrashA = containers.load('trash-box', 'C1') # trash for 8-channel in slot C1
TrashB = containers.load('trash-box', 'A2') # trash for single in slot A2
Water = containers.load('trough-15ml', 'E2', 'water-trough')
SamplesLeft = create_container_instance(
'double-tube-rack-40-half', # aluminum tube rack for 1.7 ml microcentrifuge tubes; has 8x5 arrangement, fits in two slots
grid=(4, 5), # 4 columns and 5 rows
spacing=(19.5, 19.5), # 20 mm apart
diameter=10, # each tube 10 mm in diameter
def create(self, *args, **kwargs):
return cnt.create(*args, **kwargs)
from opentrons import robot, containers, instruments
#import pandas as pd
#all_info=pd.read_csv('new_protocol_steps.csv')
containers.create('FluidX_24_5ml',
grid=(4, 6),
spacing=(18, 18),
diameter=13,
depth=48)
robot.head_speed(x=18000, y=18000, z=5000, a=700, b=700)
rack_number = 4
rack_stock_reactants = []
r_positions = ['A1', 'A2', 'B1', 'B2']
r_types = ['halide', 'boronic acid', 'base', 'catalyst']
tiprack_1000 = containers.load("tiprack-1000ul-H", "D3")
source_trough4row = containers.load("trough-12row", "C2")
for i in range(0, rack_number):
rack_stock_reactants.append(
containers.load("FluidX_24_5ml", r_positions[i], r_types[i]))
trash = containers.load("point", "B3")
# Pipettes SetUp
p1000 = instruments.Pipette(
name='eppendorf1000',
axis='b',
trash_container=trash,
tip_racks=tiprack_1000,
max_volume=1000,
min_volume=30,
from opentrons import containers, instruments
containers.create(
'septum-plate', # name of you container
grid=(8, 7), # specify amount of (columns, rows)
spacing=(9, 18), # distances (mm) between each (column, row)
diameter=2.46, # diameter (mm) of each well on the plate
depth=10)
"""
Column A
"""
tiprack = containers.load('tiprack-200ul', 'A1')
tuberack = containers.load('tube-rack-2ml', 'A2')
"""
Column B
"""
septum1 = containers.load('septum-plate', 'B3')
"""
Column C
"""
septum2 = containers.load('septum-plate', 'C3')
trash = containers.load('trash-box', 'C2')
trough = containers.load('trough-12row', 'C1')
"""
Column D
"""
septum3 = containers.load('septum-plate', 'D1')
septum4 = containers.load('septum-plate', 'D2')
septum5 = containers.load('septum-plate', 'D3')
"""
Column E
