def newSolo(self, plateList):
new_solo = SoloSoft(
filename=self.filename_prefix + str(len(self.solosofts)) + ".hso",
plateList=plateList,
pipeline=[],
)
self.solosofts.append(new_solo)
def test_filename(self):
soloSoft = SoloSoft.SoloSoft("example_filename.hso")
assert soloSoft.filename == "example_filename.hso"
soloSoft.setFile("new_filename.hso")
assert soloSoft.filename == "new_filename.hso"
with pytest.raises(TypeError):
soloSoft.setFile(1)
soloSoft.filename = "once_more.hso"
assert soloSoft.filename == "once_more.hso"
def test_plates(self):
soloSoft = SoloSoft.SoloSoft(plateList=self.example_platelist)
assert soloSoft.plateList == self.example_platelist
soloSoft.setPlates([])
assert soloSoft.plateList == []
soloSoft.setPlates(self.example_platelist)
assert soloSoft.plateList == self.example_platelist
soloSoft.plateList = []
assert soloSoft.plateList == []
soloSoft.plateList = self.example_platelist
assert soloSoft.plateList == self.example_platelist
with pytest.raises(TypeError):
soloSoft.setPlates(3)
def test_pipeline(self):
soloSoft = SoloSoft.SoloSoft(pipeline=self.example_pipeline)
assert soloSoft.pipeline == self.example_pipeline
soloSoft.setPipeline([])
assert soloSoft.pipeline == []
soloSoft.setPipeline(self.example_pipeline)
assert soloSoft.pipeline == self.example_pipeline
soloSoft.pipeline = []
assert soloSoft.pipeline == []
soloSoft.pipeline = self.example_pipeline
assert soloSoft.pipeline == self.example_pipeline
with pytest.raises(TypeError):
soloSoft.setPipeline(3)
def test_empty(self):
soloSoft = SoloSoft.SoloSoft()
assert soloSoft.filename == None
assert soloSoft.pipeline == []
assert soloSoft.plateList == [
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
]
from liquidhandling import SoftLinx, SoloSoft
from liquidhandling import *
soloSoft = SoloSoft(
filename="cherry_picking_test.hso",
plateList=[
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Plate.96.Corning-3635.ClearUVAssay",
],
)
soloSoft.getTip()
soloSoft.aspirate(
position="Position8",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(1, 50),
aspirate_shift=[0, 0, 2],
)
for i in range(3):
soloSoft.dispense(
position="Position8",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(2, 10),
dispense_shift=[0, 0, 2],
)
#Reservoir.12col.Agilent-201256-100.BATSgroup
# * Program Variables ------------------
initial_well_volume = 1000
asp_volume = 10
asp_z_shift = .5
# * ---------------------------------------
soloSoft = SoloSoft(
filename="min_volume_z_shift_test.hso",
plateList=[
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
],
)
# soloSoft.getTip("Position7")
# for i in range(int(initial_well_volume/(asp_volume*8))+2):
# soloSoft.aspirate(
# position="Position8",
# aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().setColumn(1, asp_volume),
# aspirate_shift=[0,0,asp_z_shift],
# )
# soloSoft.dispense(
# position="Position8",
import sys
import os
from liquidhandling import SoloSoft
from liquidhandling import GenericPlate96Well
# Initialize Pipeline
soloSoft = SoloSoft.SoloSoft(
filename="stress_test.hso",
plateList=[
"TipBox-200uL Corning 4864",
"TipBox-50uL EV-50-R-S",
"TipBox-50uL EV-50-R-S",
"Empty",
"Empty",
"Agilent 12 Channel Reservoir (#201256-100) ",
"Omni",
"Falcon 353916- round 96",
],
)
# Main sequence of steps that we need to repeat across multiple rows
def sub_pipeline(i, interim_get_tips=False, interim_pause=False):
soloSoft.getTip(position="Position2")
soloSoft.aspirate(
position="Position8",
aspirate_shift=[0, 0, 0.2],
syringe_speed=50,
mix_at_start=True,
mix_cycles=5,
mix_volume=30,
serial_source_mixing_volume_s2 = 100
serial_source_num_mixes_s2 = 10
serial_destination_mixing_volume_s2 = 100
# Step 3 variables
antibiotic_transfer_volume_s3 = 90
antibiotic_mix_volume_s3 = 90
destination_mix_volume_s3 = 100
soloSoft = SoloSoft(
filename="steps_1_2_3.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
"""
STEP 1: INNOCULATE GROWTH PLATE FROM SOURCE BACTERIA PLATE -----------------------------------------------------------------
"""
# * Fill 6 columns of empty 96 well plate (corning 3383 or Falcon - ref 353916) with fresh lb media (12 channel in Position 3, column 1)
soloSoft.getTip()
j = 1
for i in range(1, 7):
soloSoft.aspirate(
position="Position3",
desired_volume_serial_dilution = 150
default_df = 1 / 10
# Step 3 variables
antibiotic_transfer_volume_s3 = 90
antibiotic_mix_volume_s3 = 90
destination_mix_volume_s3 = 120
# * Initialize and set deck layout (both 200uL and 50uL tips included)
soloSoft = SoloSoft(
filename="generate_protocol.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"12 Channel Reservoir",
"Corning 3383",
"96 Deep Protein",
"Corning 3383",
"Corning 3383",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
],
)
"""
STEP 1: INNOCULATE GROWTH PLATE FROM SOURCE BACTERIA PLATE -----------------------------------------------------------------
"""
# * Fill 6 columns of empty 96 well plate (corning 3383 or Falcon - ref 353916) with fresh lb media (12 channel in Position 3, column 1)
soloSoft.getTip()
j = 1
for i in range(1, 7):
soloSoft.aspirate(
position="Position3",
glucose_blowoff = 0
glucose_z_shift = 1
muconate_transfer_volume = 10
muconate_blowoff = 0
step3_mix_volume = 50
step3_num_mixes = 3
# * Initialize solosoft and deck layout
soloSoft = SoloSoft(
filename="day1_step1_TransferCells.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Empty",
],
)
# * STEP 1: Transfer Cells ------------------------------------------------------------
soloSoft.getTip(
) # 200uL tips -> all transfers are same cells, OK to keep same tips for all of step 1
for i in range(1, 3):
for j in range(1, 7):
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup(
serial_antibiotic_transfer_volume_s2 = 15
serial_source_mixing_volume_s2 = (
100 # mix volume in antibiotic stock solution well in 12 channel reservoir
)
serial_source_num_mixes_s2 = (
10 # num mixes in antibiotic stock solutuion well prior to first transfer
)
serial_destination_mixing_volume_s2 = 100
soloSoft = SoloSoft(
filename="antibiotic_serial_dilution.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
# * Fill colums 2-6 of generic 96 well plate with lb media - NOTE: could do this at the same time as media dispensing in step 1 to save tips
soloSoft.getTip()
for i in range(2, 7):
# no need for volume management, drawing from 12 channel at Position 3, 1st row (lb media)
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
dilution_mix_volume = 60
num_mixes = 5
default_z_shift = 2
spot_z_shift = 5
spot_volume = 3.5
# * -------------------------------------
soloSoft = SoloSoft(
filename="dilute_then_spot.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Empty",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"AgarPlate.40mL.OmniTray-242811.ColonyPicker",
],
)
# *Dispense diluent into full plate
# for now, fill each half of the plate with a different media well and have becca check/refill it between runs.
soloSoft.getTip()
for i in range(1, 13):
if i == 7:
media_aspirate_column += (
1 # switch to new media row for the second half of the plate
)
import sys
import os
from liquidhandling import SoftLinx
from liquidhandling import SoloSoft
soloSoft = SoloSoft("example.hso")
soloSoft.moveArm("Position1")
soloSoft.savePipeline()
softLinx = SoftLinx("ExampleProtocol", "example_protocol.slvp")
softLinx.setPlates({"SoftLinx.PlateCrane.Stack1": "PlateOne 96 V-Bottom"})
softLinx.plateCraneMovePlate(["SoftLinx.PlateCrane.Stack1"],
["SoftLinx.Solo.Position6"])
softLinx.plateCraneMoveCrane("SoftLinx.PlateCrane.Safe")
softLinx.soloSoftRun(
"C:\\Users\\svcaibio\\Dev\\liquidhandling\\example\\softlinx\\example.hso")
softLinx.soloSoftResetTipCount(position=6)
softLinx.conditional(
conditionalStatement="[SoftLinx.PlateCrane].Speed > 0",
branchTrue=[
softLinx.plateCraneMoveCrane("SoftLinx.PlateCrane.Safe", inplace=False)
],
branchFalse=[
softLinx.plateCraneMovePlate(["SoftLinx.PlateCrane.Home"],
inplace=False)
],
)
softLinx.saveProtocol()
"""
This is just an example file to test the creation of a manifest file
"""
import time
import datetime
from liquidhandling import SoloSoft, SoftLinx
# remember to import all the plates that you need
manifest_list = []
# generate a Solosoft protocol
# initialise soloSoft with an empty deck and no given file name
soloSoft = SoloSoft(filename="protocol_wManifest.hso")
soloSoft.moveArm(destination="Position1") # add items to the soloSoft pipeline
soloSoft.moveArm(destination="TipDisposal")
soloSoft.savePipeline()
softLinx = SoftLinx("Protocol with Manifest", "protocol_wManifest.slvp")
softLinx.setPlates({
"SoftLinx.PlateCrane.Stack1":
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage"
})
# add each step and add to manifest list if necessary
softLinx.soloSoftRun("C:\\labautomation\\instructions\\protocol_wManifest.hso")
manifest_list.append("protocol_wManifest.hso")
softLinx.plateCraneMovePlate(["SoftLinx.PlateCrane.Stack1"],
import json
import jsonref
import os
from json import dump
import errno
from jsonschema import validate
from liquidhandling import SoloSoft
from liquidhandling import GenericPlate96Well
soloSoft = SoloSoft.SoloSoft(
filename="agilent_rese.hso",
plateList=[
"TipBox-Corning 200uL",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Z_Agilent_Reservoir_1row",
"Corning 3383",
"Corning 3635",
],
)
soloSoft.loop(6)
soloSoft.getTip()
# Add 6 aspirate/dispense cycles
for i in range(1, 7):
soloSoft.aspirate(
position="Position6",
aspirate_shift=[0, 0, 2],
aspirate_volumes=GenericPlate96Well().setColumn(6, 180),
from liquidhandling import *
# Program Variables
transfer_volume = 20
blowoff_volume = 0
clearance_from_bottom = 3
deep_block_mix_volume = 100
num_mixes = 5
soloSoft = SoloSoft(
filename="putida_OD600_step3_TransferBacteria.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Agilent-5043-9310.RoundBottomStorage",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Empty",
],
)
for i in range(1, 13): # i = 1,2,..., 12
soloSoft.getTip(
) # need to get new tips every time -> assumes wells in bacterial suspension not all the same
soloSoft.aspirate(
position="Position5",
aspirate_volumes=DeepBlock_96VWR_75870_792_sterile().setColumn(
i, transfer_volume),
aspirate_shift=[0, 0, clearance_from_bottom],
aspirate_mix_volume = 20
aspirate_num_mixes = 3
aspirate_syringe_speed = 25
default_z_shift = 0.5
default_blowoff = 0
aspirate_column = 12
dispense_column = 11
# * Initialize solosoft and deck layout
soloSoft = SoloSoft(
filename="lysis_test.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Empty",
],
)
soloSoft.getTip()
for i in range(12):
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().setColumn(
aspirate_column, aspirate_volume
),
# * Program Variables
lysis_12_channel_column = 12
lysis_transfer_volume = 22.2
lysis_syringe_speed = 25
lysis_blowoff = 0
reservoir_z_shift = 0.5 # tested with lysis buffer, working
dispense_z_shift = 2
# * Initialize solosoft and deck layout
soloSoft = SoloSoft(
filename="day2_step1_AddLysisBuffer.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Empty",
],
)
# * STEP 1: Add Lysis Buffer from 12 channel reservoir to cell plate
for i in range(1, 13):
soloSoft.getTip(
) # 200uL ok to aspirate 22.2 uL, NEED NEW TIP FOR EACH TRANSFER
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(lysis_12_channel_column, lysis_transfer_volume),
current_reservoir_volume = reservoir_volume = 7000
reservoir_aspirate_volume = 180
source_mixing_volume = 100
destination_mixing_volume = 200
source_volume = 20
source_num_mixes = 5
destination_num_mixes = 5
soloSoft = SoloSoft.SoloSoft(
filename="hudson_exercise_0001.hso",
plateList=[
"TipBox-Corning 200uL",
"Empty",
"Empty",
"Empty",
"Empty",
"12 Channel Reservoir",
"96 Deep Protein",
"Corning 3383",
],
)
# volumeManager = VolumeManager(ZAgilentReservoir_1row(), 7, 1, 1) #TODO Update placeholder values - https://www.agilent.com/store/en_US/LCat-SubCat1ECS_112089/Reservoirs
soloSoft.getTip()
# * Fill each row of Plate 8 w/ "aspirate_volume" worth of water from reservoir
# TODO Build into api: w/ starting point in the reservoir and range in destination plate
j = 1
for i in range(1, 13):
import sys
import os
from liquidhandling import SoloSoft
soloSoft = SoloSoft(
filename="example.hso",
plateList=[
"TipBox-Corning 200uL",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Corning 3383",
"Corning 3383",
],
)
soloSoft.getTip()
soloSoft.loop(1)
soloSoft.aspirate()
soloSoft.dispense()
soloSoft.endLoop()
soloSoft.moveArm()
# print(soloSoft.pipeline)
soloSoft.savePipeline(CRLF=True)
# * Program Variables
blowoff_volume = 20
num_mixes = 5
# Step 3 variables
antibiotic_transfer_volume_s3 = 90
antibiotic_mix_volume_s3 = 90
destination_mix_volume_s3 = 120
soloSoft = SoloSoft(
filename="antibiotic_into_culture_plate.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
# no need to get tips (just ended at smallest serial dilution) -> work backwards in growth plate
soloSoft.getTip()
for i in range(6, 0, -1):
soloSoft.aspirate(
position="Position6",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, antibiotic_transfer_volume_s3),
mix_at_start=True,
def generate_steps_1_2_3(treatment, predicted_IC50=None):
return_val = "PASS"
# * Program variables
blowoff_volume = 10
num_mixes = 3
current_media_reservoir_volume = media_reservoir_volume = 7000
reservoir_z_shift = 0.5 # z shift for deep blocks (Deck Positions 3 and 5)
lambda6_path = "/lambda_stor/data/hudson/instructions/"
# Step 1 variables
culture_plate_column_num = 7 # Changed to column 7 for test on 06/15/21
media_transfer_volume_s1 = 60
culture_transfer_volume_s1 = 30
# dilution_media_volume = 198
half_dilution_media_volume = 99
dilution_culture_volume = 22
culture_plate_mix_volume_s1 = (
30 # best to mix with same volume transferred, ok for min volume
)
growth_plate_mix_volume_s1 = 40
# Step 2 variables
media_transfer_volume_s2 = (
108 # two times = 216 uL (will add 24 uL antibiotic for 1:10 dilution)
)
first_column_transfer_volume_s2 = (
120 # two times = 240uL (to equal volume in 1:10 dilution wells)
)
serial_antibiotic_transfer_volume_s2 = 24
serial_source_mixing_volume_s2 = 80
serial_source_num_mixes_s2 = 8
serial_destination_mixing_volume_s2 = 100
# Step 3 variables
antibiotic_transfer_volume_s3 = 90
antibiotic_mix_volume_s3 = 90
destination_mix_volume_s3 = 100
# * Get location of treatment
try:
treatment_plate_loc, treatment_column = find_treatment_loc(treatment)
except Error as e:
print(f"Unale to locate treatment {treatment}")
raise # need to know locaton of treatment, rest of protocol useless if not specified
# * TODO: handle predicted IC50
# * Create folder to store all instruction files
project = "Campaign1"
project_desc = "col" + str(culture_plate_column_num)
version_num = "v1"
timestamp = str(time.time()).split(".")[0]
directory_name = f"{project}-{project_desc}-{version_num}-{timestamp}"
directory_path = os.path.join(
os.path.realpath(os.path.dirname(lambda6_path)), directory_name)
print(f"Protocol directory created: {directory_path}")
# * create new directory to hold new instructions
try:
os.makedirs(directory_path, exist_ok=True)
except OSError as e:
print(e)
print(
f"failed to create new directory for instructions: {directory_path}"
)
"""
STEP 1: INNOCULATE GROWTH PLATE FROM SOURCE BACTERIA PLATE -----------------------------------------------------------------
"""
# * Initialize soloSoft (step 1)
step1_hso_filename = os.path.join(directory_path, "step_1.hso")
soloSoft = SoloSoft(
filename=step1_hso_filename,
plateList=[
"TipBox.180uL.Axygen-EVF-180-R-S.bluebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
# * Fill all columns of empty 96 well plate (corning 3383 or Falcon - ref 353916) with fresh lb media (12 channel in Position 3, column 1)
soloSoft.getTip()
j = 1
for i in range(1, 7): # first half plate = media from column 1
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(1, media_transfer_volume_s1),
aspirate_shift=[0, 0, reservoir_z_shift],
)
soloSoft.dispense(
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, media_transfer_volume_s1),
dispense_shift=[0, 0, 2],
)
for i in range(7, 13): # second half plate = media from column 2
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(2, media_transfer_volume_s1),
aspirate_shift=[0, 0, reservoir_z_shift],
)
soloSoft.dispense(
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, media_transfer_volume_s1),
dispense_shift=[0, 0, 2],
)
# * Fill first two columns of culture 10 fold dilution plate with fresh lb media (do in two steps due to 180uL filter tips)
for i in range(2): # first column
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(1, half_dilution_media_volume),
aspirate_shift=[0, 0, reservoir_z_shift],
)
soloSoft.dispense(
position="Position7",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
1, half_dilution_media_volume),
dispense_shift=[0, 0, 2],
)
for i in range(2): # second column
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(2, half_dilution_media_volume),
aspirate_shift=[0, 0, reservoir_z_shift],
)
soloSoft.dispense(
position="Position7",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
2, half_dilution_media_volume),
dispense_shift=[0, 0, 2],
)
# * Make culture 10 fold dilution (one column for each half of plate)
for i in range(1, 3):
soloSoft.aspirate(
position="Position5",
aspirate_volumes=DeepBlock_96VWR_75870_792_sterile().setColumn(
culture_plate_column_num, dilution_culture_volume),
aspirate_shift=[0, 0, 2],
mix_at_start=True,
mix_cycles=num_mixes,
mix_volume=culture_plate_mix_volume_s1,
dispense_height=2,
# pre_aspirate=blowoff_volume,
syringe_speed=25,
)
soloSoft.dispense(
position="Position7",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, dilution_culture_volume),
dispense_shift=[0, 0, 2],
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=culture_plate_mix_volume_s1,
aspirate_height=2,
syringe_speed=25,
# blowoff=blowoff_volume,
)
# * Add bacteria from 10 fold diluted culture plate (Position 7, column 1 and 2) to growth plate with fresh media (both halves)
for i in range(1, 7): # first half growth plate
soloSoft.aspirate( # already mixed the cells, no need to do it before every transfer
position="Position7",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
1, culture_transfer_volume_s1),
aspirate_shift=[
0,
0,
2,
], # prevents 50 uL tips from going too deep in 96 deep well plate
syringe_speed=25,
)
soloSoft.dispense( # do need to mix at end of transfer
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, culture_transfer_volume_s1),
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=growth_plate_mix_volume_s1,
aspirate_height=2,
dispense_shift=[0, 0, 2],
syringe_speed=25,
)
for i in range(7, 13): # second half growth plate
soloSoft.aspirate( # already mixed the cells, no need to do it before every transfer
position="Position7",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
2, culture_transfer_volume_s1),
aspirate_shift=[
0,
0,
2,
], # prevents 50 uL tips from going too deep in 96 deep well plate
syringe_speed=25,
)
soloSoft.dispense( # do need to mix at end of transfer
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, culture_transfer_volume_s1),
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=growth_plate_mix_volume_s1,
aspirate_height=2,
dispense_shift=[0, 0, 2],
syringe_speed=25,
)
soloSoft.shuckTip()
soloSoft.savePipeline()
"""
STEP 2: PERFORM SERIAL DILUTIONS ON TREATMENT -------------------------------------------------------------------------------
"""
# * Initialize soloSoft (step 2)
step2_hso_filename = os.path.join(directory_path, "step_2.hso")
soloSoft = SoloSoft(
filename=step2_hso_filename,
plateList=[
"TipBox.180uL.Axygen-EVF-180-R-S.bluebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
# * Fill colums 2-6 of generic 96 well plate with lb media (will use for both halves of plate)
soloSoft.getTip()
for i in range(2, 7):
# draws from both lb media wells to prevent running out of media -> TODO: volume management
soloSoft.aspirate( # first lb media well
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(1, media_transfer_volume_s2),
aspirate_shift=[0, 0, reservoir_z_shift],
# pre_aspirate=blowoff_volume,
)
soloSoft.dispense(
position="Position6",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, media_transfer_volume_s2),
dispense_shift=[0, 0, 2],
# blowoff=blowoff_volume,
)
soloSoft.aspirate( # second lb media well
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(2, media_transfer_volume_s2),
aspirate_shift=[0, 0, reservoir_z_shift],
# pre_aspirate=blowoff_volume,
)
soloSoft.dispense(
position="Position6",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, media_transfer_volume_s2),
dispense_shift=[0, 0, 2],
# blowoff=blowoff_volume,
)
# * Transfer undiluted treatment stock solution (12 channel in Position 3, 2rd row) into empty first row of serial dilution plate
for i in range(2):
soloSoft.aspirate(
position=treatment_plate_loc,
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().
setColumn(treatment_column, first_column_transfer_volume_s2),
pre_aspirate=blowoff_volume,
mix_at_start=True,
mix_cycles=serial_source_num_mixes_s2,
mix_volume=serial_source_mixing_volume_s2,
aspirate_shift=[0, 0, reservoir_z_shift],
dispense_height=reservoir_z_shift,
)
soloSoft.dispense(
position="Position6",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
1, first_column_transfer_volume_s2),
dispense_shift=[0, 0, 2],
blowoff=blowoff_volume,
# mix_at_finish=True,
# mix_cycles=num_mixes,
# mix_volume=serial_destination_mixing_volume_s2,
aspirate_height=2,
)
# * Serial dilution within Generic 96 well plate (Corning or Falcon) - mix 5 times before and after transfer
for i in range(1, 6):
if i == 4: # switch tips half way through to reduce error
soloSoft.getTip()
soloSoft.aspirate(
position="Position6",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, serial_antibiotic_transfer_volume_s2),
aspirate_shift=[0, 0, 2],
pre_aspirate=blowoff_volume,
mix_at_start=True,
mix_cycles=num_mixes,
mix_volume=serial_destination_mixing_volume_s2,
dispense_height=2,
)
soloSoft.dispense(
position="Position6",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i + 1, serial_antibiotic_transfer_volume_s2),
dispense_shift=[0, 0, 2],
blowoff=blowoff_volume,
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=serial_destination_mixing_volume_s2,
aspirate_height=2,
)
# no need to throw away excess volume from last column of serial dilution
soloSoft.shuckTip()
soloSoft.savePipeline()
"""
STEP 3: ADD ANTIBIOTIC TO CULTURE PLATES -------------------------------------------------------------------------------------
"""
# * Initialize soloSoft (step 3)
step3_hso_filename = os.path.join(directory_path, "step_3.hso")
soloSoft = SoloSoft(
filename=step3_hso_filename,
plateList=[
"TipBox.180uL.Axygen-EVF-180-R-S.bluebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
soloSoft.getTip()
for i in range(6, 0, -1): # first half of plate
if i == 3: # switch tips half way through to reduce error
soloSoft.getTip()
soloSoft.aspirate(
position="Position6",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, antibiotic_transfer_volume_s3),
mix_at_start=True,
mix_cycles=num_mixes,
mix_volume=antibiotic_mix_volume_s3,
dispense_height=2,
aspirate_shift=[0, 0, 2],
)
soloSoft.dispense(
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, antibiotic_transfer_volume_s3),
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=destination_mix_volume_s3,
aspirate_height=2,
dispense_shift=[0, 0, 2],
)
soloSoft.getTip()
for i in range(6, 0, -1): # second half of plate
if i == 3: # switch tips half way through to reduce error
soloSoft.getTip()
soloSoft.aspirate(
position="Position6",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, antibiotic_transfer_volume_s3),
mix_at_start=True,
mix_cycles=num_mixes,
mix_volume=antibiotic_mix_volume_s3,
dispense_height=2,
aspirate_shift=[0, 0, 2],
)
soloSoft.dispense(
position="Position4",
dispense_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i + 6, antibiotic_transfer_volume_s3),
mix_at_finish=True,
mix_cycles=num_mixes,
mix_volume=destination_mix_volume_s3,
aspirate_height=2,
dispense_shift=[0, 0, 2],
)
soloSoft.shuckTip()
soloSoft.savePipeline()
"""
ADD ALL STEPS TO SOFTLINX PROTOCOL AND SEND TO HUDSON01 -----------------------------------------------------------------------
"""
# initialize softLinx
softLinx = SoftLinx("Steps_1_2_3",
os.path.join(directory_path, "steps_1_2_3.slvp"))
# define starting plate layout
softLinx.setPlates(
{"SoftLinx.PlateCrane.Stack5": "Plate.96.Corning-3635.ClearUVAssay"})
# restock growth assay plate before run
softLinx.plateCraneMovePlate(["SoftLinx.PlateCrane.Stack5"],
["SoftLinx.Solo.Position4"])
softLinx.plateCraneMoveCrane("SoftLinx.PlateCrane.Safe")
# run all three liquid handling steps (with paths to .hso files on hudson01)
softLinx.soloSoftResetTipCount(
1) # SoloSoft will reset to full tip box before run
softLinx.soloSoftRun("C:\\labautomation\\instructions\\" + directory_name +
"\\" + os.path.basename(step1_hso_filename))
softLinx.soloSoftRun("C:\\labautomation\\instructions\\" + directory_name +
"\\" + os.path.basename(step2_hso_filename))
softLinx.soloSoftRun("C:\\labautomation\\instructions\\" + directory_name +
"\\" + os.path.basename(step3_hso_filename))
# move growth plate to Hidex
softLinx.plateCraneMovePlate(
["SoftLinx.Solo.Position4"],
["SoftLinx.Hidex.Nest"]) # no need to open hidex
softLinx.hidexClose()
softLinx.plateCraneMoveCrane("SoftLinx.PlateCrane.Safe")
softLinx.hidexRun("Campaign1")
# save protocol to write instructions to .slvp file, create .txt manifest, and .ahk remote start file
softLinx.saveProtocol()
"""
SEND NEW INSTRUCTIONS TO WORK CELL (HUDSON01) ------------------------------------------------------------------
"""
try:
# TODO: change to full path on lambda6
child_message_sender = child_pid = Popen(
[
"python",
"../../zeromq/lambda6_send_instructions.py",
"-d",
directory_path,
],
start_new_session=True,
).pid
print("New instruction directory passed to lambda6_send_message.py")
except Error as e:
print(e)
print("Could not send new instructions to hudson01")
return return_val
current_softLinx.plateCraneMovePlate(
[full_tip_storage],
[empty_tip_location],
hasLid=True,
)
#softLinx.saveProtocol()
# ---------------------------------------------------------------------------------------------------
#* Use all tips in a tip box
softLinx.soloSoftResetTipCount(6) # automatically reset the tip count (for testing)
soloSoft = SoloSoft(
filename="use_all_tips.hso",
plateList=[
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Empty",
])
for i in range(1,13):
soloSoft.getTip("Position6")
soloSoft.shuckTip()
soloSoft.savePipeline()
#* Test conditional recognition of empty tip box
# softLinx.conditional(
# conditionalStatement="[SoftLinx.PlateCrane].Speed > 0",
# branchTrue=[
import sys
from liquidhandling import SoloSoft
from liquidhandling import *
# Program Variables
transfer_volume = 150
blowoff_volume = 0
clearance_from_bottom = 1
soloSoft = SoloSoft(
filename="putida_OD600_step4_ClearUVToPlateOneVBottom.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Agilent-5043-9310.RoundBottomStorage",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Empty",
],
)
for i in range(1, 13): # i = 1,2,..., 12
soloSoft.getTip() # need to get new tips every time
soloSoft.aspirate(
position="Position6",
aspirate_volumes=Plate_96_Corning_3635_ClearUVAssay().setColumn(
i, transfer_volume
),
import os
import sys
from liquidhandling import SoloSoft
from liquidhandling import *
# Program Variables
transfer_volume = 180
blowoff_volume = 0
soloSoft = SoloSoft(
filename="putida_OD600_DispenseBuffer.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"Reservoir.12col.Agilent-201256-100.BATSgroup",
"Plate.96.Agilent-5043-9310.RoundBottomStorage",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.PlateOne-1833-9600.ConicalBottomStorage",
"Empty",
],
)
soloSoft.getTip()
for i in range(7, 9): # columns in 12 channel reservoir
for j in range(1, 7): # <- columns in round bottom storage
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().setColumn(
i, transfer_volume
from liquidhandling import SoftLinx, SoloSoft
from liquidhandling import *
# * Program Variables
trans_volume = 10
default_z_shift = 0.5
# * Initialize Solo
soloSoft = SoloSoft(
filename="plate_test_384.hso",
plateList=[
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"Empty",
"TipBox.50uL.Axygen-EV-50-R-S.tealbox",
"Plate.384.Corning-3540.BlackwClearBottomAssay",
],
)
soloSoft.getTip("Position7")
# * aspirate/dispense column 1, rows A C E G I K M O (odd rows) -> start A1
soloSoft.aspirate(
position="Position8",
aspirate_volumes=Plate_384_Corning_3540_BlackwClearBottomAssay().setColumn(
1, trans_volume
),
aspirate_shift=[0, 0, default_z_shift],
# Step 1 variables
culture_plate_column_num = 2
media_transfer_volume_s1 = 60
culture_transfer_volume_s1 = 30
dilution_media_volume = 198
dilution_culture_volume = 22
culture_plate_mix_volume_s1 = 50
growth_plate_mix_volume_s1 = 40
soloSoft = SoloSoft(
filename="innoculate_growth_plate.hso",
plateList=[
"TipBox.200uL.Corning-4864.orangebox",
"Empty",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"DeepBlock.96.VWR-75870-792.sterile",
"Plate.96.Corning-3635.ClearUVAssay",
"Plate.96.Corning-3635.ClearUVAssay",
"Empty",
],
)
# * Fill 6 columns of empty 96 well plate (corning 3383 or Falcon - ref 353916) with fresh lb media (12 channel in Position 3, column 1)
soloSoft.getTip()
j = 1
for i in range(1, 7):
soloSoft.aspirate(
position="Position3",
aspirate_volumes=Reservoir_12col_Agilent_201256_100_BATSgroup().setColumn(
1, media_transfer_volume_s1
