Python Protocol.provision方法代码示例

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
def get_synthesized_oligo_tube_protocol(tube_name, sequence):
    """

    Synthesize and prepare an oligo tube
    25nm seems to be more than enough for most downstream work (25pmol seems to be all that is used for transcriptic's pcr)
    
    """
    global inv
    
    scale = '25nm'
    
    p = Protocol()

    dna_tube = p.ref(tube_name, 
                       cont_type="micro-1.5",
                       storage="cold_20", discard=False)
    
    dna_tube.well(0).properties = {'Molar Concentration':'100uM',
                                   'original moles':'25nm'}
    
    p.oligosynthesize([{"sequence": sequence,
                        "destination": dna_tube.well(0),
                        "scale": scale,
                        "purification": "standard"}]
                      )
    
    #spin
    p.spin(dna_tube, '2000:g', '30:second')
    
    
    #dilute to 100uM
    #safe min volume of 1.5uL is 20uL so we want a lot more than this so we don't lose too much
    #how do you go from scale and desired concentration to volume --> n = CV --> V = n/C --> V = 25nmol / 100uM = 25nmol / (100E3 nmol / 1L)
    #          = 2.5E-4 L = 250 uL
    
                      #convert 100uM to nM #convert to uL
    te_volume = 25 / (100 * pow(10, 3)) * pow(10, 6) 
    
    #add 250uL
    p.provision(inv["te"], dna_tube.well(0), ul(te_volume))

    #spin
    p.spin(dna_tube, '2000:g', '30:second')
    
    return json.dumps(p.as_dict(), indent=2)

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
import json
from autoprotocol.protocol import Protocol
from utils import ul

inv = {
    'gblock_dna':'ct18vs7cmjat2c',     # my inventory
    'te': 'rs17pwyc754v9t',           # catalog; TE
}

p = Protocol()

#existing inventory
dna_sample = p.ref("gblock_dna", id=inv['gblock_dna'], cont_type="micro-1.5", storage='cold_20')

#tubes are thawed before being placed into workcell

#Centrifuge the tube for 3-5 sec at a minimum of 3000 x g to pellet the material to the bottom of the tube.
p.spin(dna_sample, '3000:g', '5:second')

#Add 500uL TE (to reach 1 ng/uL)
p.provision(inv["te"], dna_sample.well(0), ul(500))

#Briefly vortex (here we have to use mix) and centrifuge

p.mix(dna_sample.well(0),'480:microliter',speed='480:microliter/second',repetitions=10)

p.spin(dna_sample, '3000:g', '3:second')

print(json.dumps(p.as_dict(), indent=2))

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
import json
from autoprotocol.protocol import Protocol

from utils import ul

"""
This protoocol will take a tube and fill it with water

"""


inv = {
     'water':'rs17gmh5wafm5p'    #autoclave milliq h2o
}

p = Protocol()

#create a container 

water_tube = p.ref("water_tube", cont_type="micro-1.5", storage="cold_4", discard=False).well(0)

p.provision(inv["water"], water_tube, ul(1500))


print(json.dumps(p.as_dict(), indent=2))

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
import json
from autoprotocol.protocol import Protocol

from utils import ul

"""
This protoocol will take a tube and fill it with water

"""


inv = {
     'te':'rs17pwyc754v9t'    #catalog: te
}

p = Protocol()

#create a container 

te_well = p.ref("te_tube", cont_type="micro-1.5", storage="cold_4", discard=False).well(0)

p.provision(inv["te"], te_well, ul(1500))


print(json.dumps(p.as_dict(), indent=2))

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
    inv.update(test_inv)

p = Protocol()

if 'use_existing_pcr_reagent_plate' not in options:
    #we use a PCR plate since it has less dead volume (we would be throwing out $30 if we use normal tubes)
    #pcr well has 3uL of dead volume and 5uL safe min (you can't pipette from less than this)
    pcr_reagent_plate = p.ref("pcr_reagent_plate", cont_type="96-pcr", storage="cold_20",  discard=False)
else:
    pcr_reagent_plate = p.ref("pcr_reagent_plate", id=inv['pcr_reagent_plate'], 
                              cont_type="96-pcr", storage="cold_20",  discard=False)

if 'include_Q5_set' in options:
    #We use 1uL per set of 4 experiments. To get 4 sets of experiments, we need 8uL
    q5_poly_well = pcr_reagent_plate.wells(["A1"])[0]
    p.provision(inv["Q5_Polymerase"], q5_poly_well, ul(14))
    q5_poly_well.name = 'Q5_Polymerase'

if 'include_Q5_set' in options:
    #We use 20uL per 4 experiments. 3 of dead volume + 20 uL * 4 sets of 4 experiments =  
    q5_buffer_well = pcr_reagent_plate.wells(["A2"])[0]
    p.provision(inv["Q5_Buffer"], q5_buffer_well, ul(83))
    q5_buffer_well.name = 'Q5_Buffer'

if 'include_Q5_set' in options:
    #we aren't using this but you get it for 20 cents because it comes with the Q5 kit
    q5_enhancer_well = pcr_reagent_plate.wells(["A3"])[0]
    p.provision(inv["Q5_Enhancer"], q5_enhancer_well, ul(83))
    q5_enhancer_well.name = 'Q5_Enhancer'

if 'include_dNTP_Mixture_10mM' in options:

# 需要导入模块: from autoprotocol.protocol import Protocol [as 别名]
# 或者: from autoprotocol.protocol.Protocol import provision [as 别名]
p = Protocol()

if 'use_existing_reagent_plate' not in options:
    dead_volume = ul(3)
    reagent_plate = p.ref(plate_name, cont_type="96-pcr", storage="cold_20")
else:
    dead_volume = ul(0)
    reagent_plate = p.ref(plate_name, id=inv['reagent_plate'], 
                              cont_type="96-pcr", storage="cold_20")

ecori_hindiii_well = reagent_plate.wells(["A1"])[0]
#provisioning less than 10uL is dangerous due to pipetting mistakes (can't mix after)
volume_per_experiment = ul(1)
re_volume = max(ul(10),number_of_experiments*volume_per_experiment+dead_volume/2)
p.provision(inv["EcoRI"], ecori_hindiii_well, re_volume)
p.provision(inv["hindiii"], ecori_hindiii_well, re_volume)
ecori_hindiii_well.name = 'EcoRI+hindiii'
ecori_hindiii_well.properties = {'Unit Concentration':'10 units/ul'} 

#there is an extra negative control for every 2 experiments so we use 3/2*experiments
cutsmart_well = reagent_plate.wells(["B1"])[0]
volume_per_experiment = ul(5)
p.provision(inv["CutSmart"], cutsmart_well, number_of_experiments*3/2*volume_per_experiment+dead_volume)
cutsmart_well.name = 'CutSmart 10x'

pUC19_well = reagent_plate.wells(["H12"])[0]
volume_per_experiment = ul(1)
pUC19_volume = max(ul(10),number_of_experiments*volume_per_experiment+dead_volume)
p.provision(inv["pUC19"], pUC19_well, pUC19_volume)
pUC19_well.name = 'pUC19'