def sample_turbs():
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
#shaker.stop() TODO: for asynchrony
for batch in batches:
tip_poss = new_tips()
aspirate(ham_int, [(turb_plate, i) for i in batch], [read_sample_vol]*8)
dispense(ham_int, [(reader_plate, i) for i in batch], [read_sample_vol]*8)
tip_eject(ham_int, tip_poss)
def new_tips():
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
while True:
try:
positions =[next(disp_tips_gen) for i in range(8)]
tip_pick_up(ham_int, positions)
return positions
except pyhamilton.TipPresentError:
tip_eject(ham_int)
except pyhamilton.NoTipError:
pass
def replace_mix_tips(ham_int, pump_int, reader_int):
change_96_tips(ham_int, mixing_tips)
put_96_tips(ham_int, DEFAULT_WASTE, immediately=True)
for col in range(num_reused_lagoons / 8):
while True:
try:
tip_pick_up(ham_int, next(replace_tips_gen))
break
except pyhamilton.NoTipError:
continue
tip_eject(
ham_int,
list(zip([mixing_tips] * 8, range(col * 8, (col + 1) * 8))))
def replace_media(replace_vols):
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
if sys_state.waffle_clean_thread:
sys_state.waffle_clean_thread.join()
pump_int.refill(30)
shaker.stop()
for batch in batches:
tip_poss = new_tips()
aspirate(ham_int, [(media_reservoir, i%8) for i in batch], [replace_vols[i] for i in batch])
dispense(ham_int, [(turb_plate, i) for i in batch], [replace_vols[i] for i in batch], liquidHeight=fly_disp_height, dispenseMode=9)
shaker.start(shake_speed)
tip_eject(ham_int, tip_poss) #TODO: only for tip reuse
tip_poss = new_tips() #TODO: only for tip reuse
shaker.stop()
aspirate(ham_int, [(turb_plate, i) for i in batch], [800]*8, liquidHeight=fixed_turb_height)
dispense(ham_int, [(bleach_site, i%8 + 88) for i in batch], [800]*8, liquidHeight=15) # +88 for far right side of bleach
tip_eject(ham_int, tip_poss)
shaker.start(shake_speed)
def service(replace_vols, plate, tips, media_reservoir):
ham_int, *_ = sys_state.instruments
if not remember.replace_vols:
return # no transfer volumes ready to act on
liq_move_param = {
'liquidClass': std_class,
'airTransportRetractDist': 0
}
for col_num, col_vols in enumerate(replace_vols):
array_idxs = [col_num * 8 + i for i in range(8)]
tip_poss = [(tips, j) for j in array_idxs]
tip_pick_up(ham_int, tip_poss)
media_poss = [(media_reservoir, j) for j in array_idxs]
aspirate(ham_int, media_poss, col_vols, **liq_move_param)
plate_poss = [(plate, j) for j in array_idxs]
dispense(ham_int,
plate_poss,
col_vols,
liquidHeight=disp_height,
mixCycles=2,
mixVolume=mix_vol,
dispenseMode=9,
**liq_move_param)
excess_vols = [max_transfer_vol for _ in media_poss]
aspirate(ham_int,
plate_poss,
excess_vols,
liquidHeight=fixed_turb_height,
**liq_move_param)
dispense(
ham_int,
[(waste_site, j % 8 + 88) for j in array_idxs],
excess_vols, # +88 for far right side of bleach
liquidHeight=15,
**liq_move_param)
wash_vols = [wash_vol for _ in media_poss]
bleach_poss = [(bleach_site, j) for j in array_idxs]
aspirate(ham_int, bleach_poss, wash_vols, **liq_move_param)
dispense(ham_int, bleach_poss, wash_vols, **liq_move_param)
water_poss = [(water_site, j) for j in array_idxs]
aspirate(ham_int, water_poss, wash_vols, **liq_move_param)
dispense(ham_int, water_poss, wash_vols, **liq_move_param)
tip_eject(ham_int, tip_poss)
remember.replace_vols = None # make sure these transfers are only executed once
def prepare_assays(phage_dilutions, culture_wells, plate_wells): # deal with up to 8 at the same time
ham_int, *_ = sys_state.instruments
num_phage_dilutions = len(phage_dilutions)
agar_positions = all_agar_positions[:num_phage_dilutions]
if prep_hard_agar:
logging.info('\n##### Filling assay plates with hard agar.')
if next(replace_agar_tips):
tip_eject(ham_int)
new_tips(num_phage_dilutions)
aspirate(ham_int, agar_positions, [hard_agar_vol*dipenses_per_prep_tip*1.3]*num_phage_dilutions, liquidClass=agar_class) # Aspirate 10% more to avoid bubbles
dispense(ham_int, plate_wells, [hard_agar_vol]*num_phage_dilutions, liquidHeight=6, liquidClass=agar_class)
return
logging.info('\n##### Moving culture into dilution wells.')
new_tips(num_phage_dilutions, 'culture')
aspirate(ham_int, culture_wells, [culture_vol]*num_phage_dilutions, liquidClass=std_class)
dispense(ham_int, phage_dilutions, [culture_vol]*num_phage_dilutions, liquidClass=std_class)
tip_eject(ham_int)
logging.info('\n##### Moving agar into dilution tubes.')
new_tips(num_phage_dilutions)
aspirate(ham_int, agar_positions, [soft_agar_vol + 50]*num_phage_dilutions, liquidClass=agar_class)
dispense(ham_int, phage_dilutions, [soft_agar_vol + 50]*num_phage_dilutions, liquidHeight=6, liquidClass=agar_class)
logging.info('\n##### Moving finished phage_dilutions into plate wells.')
aspirate(ham_int, phage_dilutions, [soft_agar_vol]*num_phage_dilutions, liquidClass=agar_class)
dispense(ham_int, plate_wells, [soft_agar_vol]*num_phage_dilutions, liquidHeight=6, liquidClass=agar_class)
tip_eject(ham_int)
def service_lagoons(ham_int, pump_int, reader_int):
logging.info(
'\n\n##### ------------------ Servicing lagoons ------------------'
)
logging.info('\n##### Filling reservoir and adding inducer.')
culture_fill_thread = run_async(
lambda: pump_int.refill(culture_supply_vol))
#while True:
# try:
# tip_pick_up(ham_int, [next(inducer_tip_pos_gen)])
# break
# except pyhamilton.NoTipError:
# continue
#liq_class_300uL = 'StandardVolumeFilter_Water_DispenseJet_Empty_with_transport_vol'
while True:
try:
tip_pick_up(ham_int, next(disp_lagoon_tips_gen))
break
except pyhamilton.NoTipError:
continue
tip_eject(ham_int, disp_tip_poss)
culture_fill_thread.join()
#aspirate(ham_int, [(inducer_site, 0)], [inducer_vol], liquidClass=liq_class_300uL)
#dispense(ham_int, [(culture_reservoir, 93)], [inducer_vol], liquidClass=liq_class_300uL)
#tip_eject(ham_int)
logging.info('\n##### Moving fresh culture into lagoons.')
change_96_tips(ham_int, culture_tips)
aspirate_96(ham_int,
culture_reservoir,
cycle_replace_vol,
mixCycles=6,
mixVolume=100,
liquidHeight=.5,
airTransportRetractDist=30)
waffle_clean_thread = run_async(lambda: (pump_int.empty(
culture_supply_vol), clean_reservoir(pump_int, shaker)))
dispense_96(ham_int,
lagoon_plate,
cycle_replace_vol,
liquidHeight=lagoon_fly_disp_height,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, culture_tips, immediately=True)
logging.info('\n##### Mixing lagoons.')
if sys_state.need_to_read_plate:
logging.info(
'\n##### Sampling liquid from lagoons to reader plates.')
while True:
try:
reader_plate = next(reader_plate_gen)
move_plate(ham_int, reader_plate, reader_plate_site)
break
except pyhamilton.LabwareError:
pass
change_96_tips(ham_int, mixing_tips)
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
reader_plate_site,
read_sample_vol,
liquidHeight=5,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
else:
change_96_tips(ham_int, mixing_tips)
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
lagoon_plate,
read_sample_vol,
liquidHeight=fixed_lagoon_height + 3,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
logging.info('\n##### Draining lagoons to constant height.')
excess_vol = max_transfer_vol * .8
aspirate_96(ham_int,
lagoon_plate,
excess_vol,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
bleach_site,
excess_vol,
liquidHeight=10,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, mixing_corral)
change_96_tips(ham_int, temp_layout)
if sys_state.need_to_read_plate:
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
reader_plate_site,
read_sample_vol,
liquidHeight=5,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
else:
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
lagoon_plate,
read_sample_vol,
liquidHeight=fixed_lagoon_height + 3,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
logging.info('\n##### Draining lagoons to constant height.')
aspirate_96(ham_int,
lagoon_plate,
excess_vol,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
bleach_site,
excess_vol,
liquidHeight=10,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, DEFAULT_WASTE, immediately=True)
def bleach():
change_96_tips(ham_int, mixing_corral)
bleach_mounted_tips(ham_int, destination=mixing_tips)
change_96_tips(ham_int, None)
if sys_state.need_to_read_plate:
plate_id = reader_plate_id(reader_plate)
protocols = ['17_8_12_lum', '17_8_12_abs']
data_types = ['lum', 'abs']
platedatas = read_plate(
ham_int,
reader_int,
reader_tray,
reader_plate_site,
protocols,
plate_id,
plate_destination=plate_trash,
async_task=bleach
) # throw out plate when done and asynchronously bleach
if simulation_on:
platedatas = [
PlateData(os.path.join('assets', 'dummy_platedata.csv'))
] * 2 # sim dummies
for platedata, data_type in zip(platedatas, data_types):
platedata.wait_for_file()
db_add_plate_data(platedata, data_type, reader_plate, lagoons,
[
*range(8 * 10),
*range(8 * 11, 8 * 11 + num_disp_lagoons)
])
reader_int.plate_in(block=False)
sys_state.need_to_read_plate = False
else:
bleach()
change_96_tips(ham_int, None)
waffle_clean_thread.join()
logging.info(
'\n##### --------------- Done servicing lagoons ---------------\n')
culture_fill_thread = run_async(
lambda: pump_int.refill(culture_supply_vol))
# dispense inducer in an x-pattern into the reservoir
logging.info('\n##### Filling reservoir and adding inducer.')
# use 8-channel to fetch a tip to put in the tip staging
# pick up tip with 8-channel
while True:
try:
tip_pick_up(ham_int, [next(inducer_tip_pos_gen)])
break
except pyhamilton.NoTipError:
continue
# put in tip staging
tip_eject(ham_int, [(tip_staging, 95)])
# pick up inducer tip with 96-head and wait for fill to finish
tip_pick_up_96(ham_int, tip_staging)
culture_fill_thread.join()
# add inducer
aspirate_96(ham_int, inducer_site, inducer_vol)
dispense_96(ham_int, culture_reservoir, inducer_vol)
tip_eject_96(ham_int)
## With 96-head, perform culture swap
# move the next batch of 48 tips to tip_staging using the 8-channel head
shaker.start(250) # start shaker to mix in inducer in meantime
for i in range(6):
tip_pick_up(