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 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 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