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):
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 __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
#####################
# import standard modules
from collections import OrderedDict
import time
import numpy as np
# import Opentrons modules
from opentrons import labware, instruments, modules, robot, types
# magnetic module
magdeck = modules.load('magdeck', '9')
magdeck.disengage()
# Deep well plate
plate_name = 'fischerbrand_96_wellplate_2000ul'
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=(8.96, 8.96), # distances (mm) between each (column, row)
diameter=8.5, # diameter (mm) of each well on the plate
depth=41, # depth (mm) of each well on the plate
volume=2000)
# PCR plate
axy_plate = 'axygen_96_wellplate_400ul'
if axy_plate not in labware.list():
custom_2_plate = labware.create(
axy_plate, # name of you labware
grid=(12, 8), # specify amount of (columns, rows)
spacing=(9, 9), # distances (mm) between each (column, row)
destination_slot = '3'
destination_type = '48-well-plate-sarsted'
destination_DMSO_rows = ['A','B','C']
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)
'''
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)
for c in robot.commands():
if 'Picking up tip wells' in c:
tc += 8
elif 'Picking up tip well' in c:
tc += 1
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]
if destVector is not None:
plan[i]["dispense"]["location"] = (plan[i]["dispense"]["location"],
destVector)
_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],
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),
'source' : 'https://github.com/Zildj1an/SELEX'
}
# [0] Our design for the three modules
# X,Y,Z,A speeds for lateral,front and vertical motion for left and right
# B,C plunger speed for motor
#max_speed_per_axis = {'x': 600,'y': 400,'z': 125,'a': 125,'b': 40,'c': 40}
max_speed_per_axis = {'x': 600,'y': 400,'z': 125,'a': 125,'b': 40,'c': 40}
robot.head_speed(**max_speed_per_axis)
'''
database.delete_container('Falcon_Samples')
database.delete_container('Eppendorf_Samples')
'''
plate_falcon = 'Falcon_Samples'
if plate_falcon not in labware.list():
Falcon = labware.create(
plate_falcon,
grid = (3,2),
spacing = (35,43),
diameter = 10,
depth = 110,
volume = 800)
plate_eppendorf = 'Eppendorf_Samples'
if plate_eppendorf not in labware.list():
Eppendorf = labware.create(
plate_eppendorf,
grid = (8,4),
spacing = (15,20),
diameter = 10,
from opentrons import labware, instruments, modules, robot
metadata = {
'protocolName': 'NGS Library Prep Part 2',
'author': 'Alise <*****@*****.**>',
'source': 'Custom Protocol Request'
}
# custom labware creation
mag_plate_name = 'framestar-96-semi-skirted-PCR'
if mag_plate_name not in labware.list():
labware.create(mag_plate_name,
grid=(12, 8),
spacing=(9, 9),
diameter=5.5,
depth=20.2)
temp_plate_name = 'aluminum-block-framestar-96-semi-skited-PCR'
if temp_plate_name not in labware.list():
labware.create(temp_plate_name,
grid=(12, 8),
spacing=(9, 9),
diameter=5.5,
depth=20.2)
# labware setup
reagent_plate = labware.load('PCR-strip-tall', '1')
trough = labware.load('trough-12row', '2')
mag_module = modules.load('magdeck', '4')
mag_plate = labware.load(mag_plate_name, '4', share=True)
temp_module = modules.load('tempdeck', '7')
'''
from opentrons import labware, instruments, modules, robot
from opentrons.data_storage import database
from time import sleep
metadata = {
'protocolName': 'ELONA',
'description': 'Aptamer binding',
'source': 'https://github.com/Zildj1an/SELEX'
}
# [1] Labware
storage_name = 'Storage_Module'
if storage_name not in labware.list():
Storage = labware.create(storage_name,
grid=(10, 1),
spacing=(12.5, 0),
diameter=9,
depth=40,
volume=200000)
Storage = labware.load(storage_name, slot=5)
plate_samples = labware.load('96-flat', slot=2)
plate_buffers = labware.load('96-flat', slot=3)
trash_liquid = labware.load('corning_384_wellplate_112ul_flat', slot=4)
Eppendorf = labware.load('Eppendorf_Samples', slot=10)
tiprack_l = labware.load('opentrons-tiprack-300ul', slot=9)
tiprack_r = labware.load('opentrons-tiprack-10ul', slot=6)
URL_PCR = "http://ninjapcr.local/command"
URL_AUX = "http://thermaux.local/command"
# [1] Labware
# X,Y,Z,A speeds for lateral,front and vertical motion for left and right
# B,C plunger speed for motor
max_speed_per_axis = {'X': 600,'Y': 400,'Z': 125,'A': 125,'B': 40,'C': 40}
robot.head_speed(**max_speed_per_axis)
database.delete_container('Thermic_Module')
thermic_name = 'Thermic_Module' #TODO check
if thermic_name not in labware.list():
thermic = labware.create(
thermic_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 = 10, # Depth (mm) of each well on the plate
volume = 50)
plate_samples = labware.load('96-flat', slot ='11') # Samples TODO Eppendorf 1.5
tiprack = labware.load('tiprack-10ul', slot ='6') # Tipracks
magnetic = modules.load('magdeck', slot ='4') # Magnetic Deck
plate_magnet = labware.load('96-flat', slot ='4', share = True) # Magnetic Deck plate
thermocycler = NinjaPCR(slot='10', simulating = robot.is_simulating()) # Ninja-PCR
thermic_module = labware.load(thermic_name, slot ='1') # Auxiliar thermic module
trash = labware.load('trash-box', slot = '12', share = True) # Trash
destination_slot = '3'
destination_type = '48-well-plate-sarsted'
destination_drug_wells = [
'A1', 'A3', 'A5', 'A7', 'B2', 'B4', 'B6', 'B8', 'C1', 'C3', 'C5', 'C7',
'D2', 'D4', 'D6', 'D8', 'E1', 'E3', 'E5', 'E7', 'F2', 'F4', 'F6', 'F8'
]
destination_dmso_wells = [
'A2', 'A4', 'A6', 'A8', 'B1', 'B3', 'B5', 'B7', 'C2', 'C4', 'C6', 'C8',
'D1', 'D3', 'D5', 'D7', 'E2', 'E4', 'E6', 'E8', 'F1', 'F3', 'F5', 'F7'
]
agar_thickness = +3 # mm from the bottom of the well
############################# define custom 48wellplate
if source_type not in labware.list():
custom_plate = labware.create(
source_type, # 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)
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)
# Attach correct pipettors (P300 Multi on left mount)
# Set OT-2 to calibrate to the bottom of wells
# Calibrate OT-2
# Fill 12-row trough based on lines 57-59, prepare claseek kit end-conversion and adapter ligation mixes.
from opentrons import labware, instruments, modules, robot
#set robot gantry speed
robot.head_speed(x=50, y=50, z=60, a=60, b=40, c=40)
#To enable debug mode (all wait peroiods run for 1 min only) change debug value to 1
debug = 0
#import custom labware
enzrack = 'coolrack-96'
if enzrack not in labware.list():
enzrack = labware.create(enzrack,
grid=(12, 8),
spacing=(9, 9),
diameter=5,
depth=20,
volume=200)
#deepwell = 'deepwell-plate-96'
#if deepwell not in labware.list():
#deepwell = labware.create(
#deepwell,
#grid=(12, 8),
#spacing=(9, 9),
#diameter=5,
#depth=20,
'temp': 65,
'name': 'Heat',
'ramp': 0
}]
}
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'
metadata = {
'protocolName' : 'Separation of cells',
'description' : 'Separation of cells',
'source' : 'https://github.com/Zildj1an/SELEX'
}
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)
# FUNCTIONS ························································································
def robot_wait():
if not robot.is_simulating():
robot.comment("Waiting...")
robot._driver.turn_on_red_button_light()
#If false, ignores any labware that is already defined in robot
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])
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 plate holders (E2396-1641) with cuttable nonskirted cuttable PCR plates (E1403-0100) on top
plate_name = 'starlab-E1403-0100'
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=5.5, # diameter (mm) of each well on the plate
depth=21, # depth (mm) of each well on the plate
volume=350)
# Starlab fully skirted PCR plates (E1403-5200) (no holder needed)
plate_name = 'starlab-E1403-5200'
if plate_name not in labware.list():
labware.create(plate_name,
grid=(12, 8),
spacing=(8.9, 8.9),
diameter=5.6,
dispensing_volume = 10
# M9 trough
M9_source_slot = '7'
M9_source_type = 'trough-12row'
M9_source_well = 'A2'
M9_volume = 10
# destination plates
agar_thickness = +5 # mm from the bottom of the well
destination_slots = ['3']
destination_type = '96-well-plate-sqfb-whatman'
############################# 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
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
"""
#tubeRack9 = labware.load(
# 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', slot='11'
#)
#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']
for ds in destination_slots:
# create entry in dict
dst_cols = src_cols.copy() # array of column numbers to be shuffled
np.random.shuffle(dst_cols) # shuffle columns in destination. This acts in place!!
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
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'
engage()
# (44) Store 300ul at 4ºC
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),
dst_cols = src_cols.copy() # array of column numbers to be shuffled
np.random.shuffle(
dst_cols) # shuffle columns in destination. This acts in place!!
drugs_mapping[(ss, 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 '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
import logging
metadata = {
'protocolName': 'ELONA',
'description': 'Aptamer binding',
'author': 'Carlos Bilbao, Pablo Villalobos',
'source': 'https://github.com/Zildj1an/SELEX'
}
logging.basicConfig(filename='/root/elona')
log = logging.getLogger('elona')
# [1] Labware
storage_name = 'Storage_Module'
if storage_name not in labware.list():
Storage = labware.create(storage_name,
grid=(10, 1),
spacing=(12.5, 0),
diameter=9,
depth=40,
volume=200000)
ninja_name = "NinjaTempDeck"
if ninja_name not in labware.list():
labware.create(
ninja_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