}
inv.update(test_inv)
reagent_plate = p.ref("re_reagent_plate",
id=inv['reagent_plate'],
cont_type="96-pcr",
storage="cold_20")
ecori_hindiii_well = reagent_plate.wells(["A1"])[0]
cutsmart_well = reagent_plate.wells(["B1"])[0]
pUC19_well = reagent_plate.wells(["H12"])[0]
# Initialize all existing inventory
all_inventory_wells = [ecori_hindiii_well, cutsmart_well, pUC19_well]
for well in all_inventory_wells:
init_inventory_well(well)
# Tubes and plates we use and then discard
water_tube = p.ref("water_tube", cont_type="micro-1.5", discard=True).well(0)
pcr_plate = p.ref("pcr_plate", cont_type="96-pcr", discard=True)
# The result of the experiment, a pUC19 cut by EcoRI and HindIII, goes in this tube for storage
puc19_cut_tube = p.ref(expid("puc19_cut", experiment_name),
cont_type="micro-1.5",
storage="cold_20").well(0)
# -------------------------------------------------------------
# Provisioning and diluting.
# Diluted EcoRI can be used more than once
#
p.provision(inv["water"], water_tube, ul(500))
#
inv = {
"src_bacteria_plate":
"ct18zdk7bp43ew", # inventory; Original source of bacteria
}
#highest flourescence reading well
BEST_WELL_ID = 'B7'
if "--test" in sys.argv:
test_inv = {
"src_bacteria_plate":
"ct18ybg4qb5kzr", # inventory; Original source of bacteria
}
inv.update(test_inv)
#Source of bacteria
source_bacteria_well = p.ref('src_bacteria_plate',
id=inv['src_bacteria_plate'],
cont_type="96-flat",
storage="cold_4").well(BEST_WELL_ID)
utils.init_inventory_well(source_bacteria_well)
amplify_and_store_bacteria(source_bacteria_well)
# ---------------------------------------------------------------
# Output protocol
#
jprotocol = json.dumps(p.as_dict(), indent=2)
print(jprotocol)
q5_buffer_well = pcr_reagent_plate.wells(["A2"])[0]
dNTP_well = pcr_reagent_plate.wells(["B1"])[0]
# New inventory resulting from this experiment
sfgfp_pcroe_out_tube = p.ref(expid("amplified",experiment_name), cont_type="micro-1.5", storage="cold_20").well(0)
# Temporary tubes for use, then discarded (you can't set storage if you are going to discard)
mastermix_well = p.ref("mastermix", cont_type="micro-1.5", discard=True).well(0)
water_well = p.ref("water", cont_type="micro-1.5", discard=True).well(0)
pcr_plate = p.ref("pcr_plate", cont_type="96-pcr", discard=True)
# Initialize all existing inventory
all_inventory_wells = [template_tube] + primer_wells
for well in all_inventory_wells:
init_inventory_well(well)
# -----------------------------------------------------
# Provision water once, for general use
#
p.provision(inv["water"], water_well, ul(500))
# -----------------------------------------------------
# Q5 PCR protocol
# www.neb.com/protocols/2013/12/13/pcr-using-q5-high-fidelity-dna-polymerase-m0491
#
# 25ul reaction (we will run it 4 times, totally 100uL of solution)
# ------------- 4rxn total
# Q5 reaction buffer 5 ul --> 20uL
# Q5 polymerase 0.25 ul --> 1uL
# 10mM dNTP 0.5 ul --> 2uL
if __name__ == '__main__':
# -----------------------------------------------------------------------
# Inventory
#
inv = {
"src_bacteria_plate" : "ct18zdk7bp43ew", # inventory; Original source of bacteria
}
#highest flourescence reading well
BEST_WELL_ID = 'B7'
if "--test" in sys.argv:
test_inv = {
"src_bacteria_plate" : "ct18ybg4qb5kzr", # inventory; Original source of bacteria
}
inv.update(test_inv)
#Source of bacteria
source_bacteria_well = p.ref('src_bacteria_plate', id=inv['src_bacteria_plate'], cont_type="96-flat", storage="cold_4").well(BEST_WELL_ID)
utils.init_inventory_well(source_bacteria_well)
amplify_and_store_bacteria(source_bacteria_well)
# ---------------------------------------------------------------
# Output protocol
#
jprotocol = json.dumps(p.as_dict(), indent=2)
print(jprotocol)
