def plasmidprep(protocol, params):
names = [item['name'] for item in params['samples']]
num_samples = len(params['samples'])
if len(names) != len(set(names)):
raise UserError("All plasmidprep names have to be unique.")
if num_samples > 96:
raise UserError("A maximum of 96 preps per run is allowed.")
if params['type'] == "Miniprep":
prep = protocol.miniprep
dest_plate = protocol.ref('miniprep_%s' % printdatetime(),
cont_type="96-pcr", storage="cold_20")
transfer_vol = "35:microliter"
duration = "16:hour"
elif params['type'] == 'Maxiprep':
prep = protocol.maxiprep
transfer_vol = "300:microliter"
dest_plate = protocol.ref('maxiprep_%s' % printdatetime(),
cont_type="96-deep", storage="cold_20")
duration = "16:hour"
dests = dest_plate.wells_from(0, num_samples, columnwise=True)
cols = int(math.ceil(float(num_samples)/8.0))
dispense_cols = [{"column": col, "volume": "1800:microliter"}
for col in range(0, cols)]
# Aliquot, grow, prep
growth_plate = protocol.ref("plasmid_prep_growth_plate_%s" % printdatetime(),
cont_type="96-deep", discard=True)
protocol.dispense(growth_plate, params['media'], dispense_cols)
src_samples = WellGroup([item['sample'] for item in params['samples']])
protocol.transfer(src_samples,
growth_plate.wells_from(0, num_samples, columnwise=True),
"10:microliter")
protocol.cover(params["growth_plate"], lid="low_evaporation")
protocol.cover(growth_plate, lid="standard")
protocol.incubate(growth_plate, "warm_37", duration, shaking=True, co2=0)
prep(growth_plate.wells_from(0, num_samples, columnwise=True),
dests)
if params['type'] == 'Maxiprep':
new_dests = []
for i in range(0, num_samples):
new_dests.append(protocol.ref('maxiprep_%d_%s' % (i+1, printdatetime()),
cont_type="micro-1.5",
storage="cold_20").well(0))
protocol.transfer(dests[i], new_dests[i], transfer_vol)
dests = new_dests
for name, well in zip(names, dests):
well.set_name("%s_%s" % (name, printdatetime(time=False)))
def assemble(protocol, params):
def provision_reagents(reagents, dest, num_rxts, mm_mult=1.3, num_rxts_plus=3.0):
for reagent in reagents.values():
protocol.provision(reagent['resource_id'], dest, "%s:microliter" % ((num_rxts + num_rxts_plus) * reagent['reagent_ratio'] * mm_mult))
def transfer_kwargs(pre_buffer, one_tip=False, one_source=False):
kwargs = {"one_tip": one_tip,
"one_source": one_source,
"pre_buffer": "%s:microliter" % pre_buffer,
"blowout_buffer": True}
return(kwargs)
# general parameters
ssDNA = params['ssDNA']
constructs = [construct['oligos'] for construct in params['constructs']]
num_constructs = len(constructs)
flattened = [val for oligo in constructs for val in oligo]
oligos = list({v: v for v in flattened}.values())
num_oligos = len(oligos)
mm_mult = 1.3
num_rxts_plus = 3
# provision water
water = protocol.ref( 'water', cont_type='96-deep', discard=True )
protocol.dispense_full_plate( water, 'water', '1000:microliter' )
# water = [provision_to_tube(protocol, "water%s" % (i + 1), "micro-2.0", "rs17gmh5wafm5p", 1900)
# for i in range(int(math.ceil(num_constructs/float(9.0))))
# ]
#
# for w in water:
# w.set_volume('1800:microliter')
# provision atp for entire protocol
atp_reagents = {'atp': {"resource_id": 'rs16pccshb6cb4',
'reagent_ratio': 0.1},
'water': {"resource_id": 'rs17gmh5wafm5p', 'reagent_ratio': 0.9}}
atp_rxts = (num_oligos + num_constructs)
atp = protocol.ref("atp_10mM", cont_type='micro-1.5', discard=True).well(0)
provision_reagents(atp_reagents, atp, atp_rxts, mm_mult, num_rxts_plus=6)
# provision kinase mix
kinase_mix = []
for i in range(int(math.ceil(num_oligos/60.0))):
kinase_mix.append(protocol.ref("kinase_mix-%s" % (i + 1), None, "micro-1.5", discard=True).well(0))
reagents = {'pnkbuffer': {"resource_id": 'rs16pc9rd5sg5d', "reagent_ratio": 3},
'water': {"resource_id": 'rs17gmh5wafm5p', "reagent_ratio": 18},
'pnk': {"resource_id": 'rs16pc9rd5hsf6', "reagent_ratio": 1}}
provision_reagents(reagents, kinase_mix, num_oligos, mm_mult, num_rxts_plus)
protocol.transfer(atp, kinase_mix, "%s:microliter" % ((num_oligos + num_rxts_plus) * 1 * mm_mult), new_group=True)
# kinase oligos
kinase_oligo_plate = protocol.ref("kinase_oligo_plate_%s" % printdatetime(time=False), None, "96-pcr",
discard=True)
wells_to_kinase = kinase_oligo_plate.wells_from("A1", num_oligos)
protocol.transfer(kinase_mix,
wells_to_kinase,
"23:microliter",
**transfer_kwargs(15, True, True))
for i, oligo in enumerate(oligos):
protocol.transfer(oligo,
wells_to_kinase[i],
"7:microliter",
mix_after=False,
new_group=det_new_group(i),
aspirate_source=aspirate_source(depth=depth("ll_following",
lld="pressure",
distance="0.0:meter")),
**transfer_kwargs(10))
protocol.seal(kinase_oligo_plate)
protocol.thermocycle(kinase_oligo_plate,
[{"cycles": 1, "steps": [
{"temperature": "37:celsius",
"duration": "60:minute"},
]}
], volume="30:microliter")
# dilute oligos
protocol.unseal(kinase_oligo_plate)
diluted_oligo_plate = protocol.ref("dilute_oligo_plate", None, "96-flat", discard=True)
diluted_oligo_wells = diluted_oligo_plate.wells_from(0, num_constructs)
protocol.transfer(water.all_wells(),
diluted_oligo_wells,
"200:microliter",
disposal_vol="0:microliter",
**transfer_kwargs(40, True, True))
for i, m in enumerate(constructs):
for kin_oligo in m:
index = list(oligos).index(kin_oligo)
protocol.transfer(kinase_oligo_plate.well(index), diluted_oligo_plate.well(i),
"2:microliter",
mix_after=False,
mix_vol="5:microliter")
diluted_oligo_plate.well(i).set_name(params['constructs'][i]['mutant_name'])
protocol.cover(diluted_oligo_plate)
protocol.spin(diluted_oligo_plate, "250:g", "2:minute")
# make ssDNA_mastermix
mm_mult_ssDNA = 1.5
mix_plate = protocol.ref("mix_plate", None, "96-pcr", discard=True)
ssDNA_mix = mix_plate.well(0)
protocol.transfer(ssDNA,
ssDNA_mix,
"%s:microliter" % ((num_constructs + num_rxts_plus) * 2.0 * mm_mult_ssDNA),
**transfer_kwargs((num_constructs + 1) * 1))
protocol.provision('rs17sh5rzz79ct', ssDNA_mix, "%s:microliter" % ((num_constructs + num_rxts_plus) * 0.2 * mm_mult_ssDNA))
# anneal oligos
protocol.uncover(diluted_oligo_plate)
annealing_plate = protocol.ref("annealing_oligo_plate", None, "384-pcr", storage="cold_20")
anneal_wells = annealing_plate.wells_from(0, num_constructs)
protocol.transfer(ssDNA_mix,
anneal_wells.wells,
"2.2:microliter",
dispense_speed="50:microliter/second",
**transfer_kwargs(7, True, True))
for dil_oligo, reaction in zip(diluted_oligo_wells.wells, anneal_wells.wells):
protocol.transfer(dil_oligo,
reaction,
"2:microliter",
aspirate_source=aspirate_source(depth("ll_bottom", distance=".001:meter")),
mix_after=True,
mix_vol="2:microliter",
flowrate="50:microliter/second",
repetitions=2,
new_group=det_new_group(i),
**transfer_kwargs(5))
reaction.set_name(dil_oligo.name)
protocol.seal(annealing_plate)
protocol.spin(annealing_plate, "250:g", "2:minute")
protocol.thermocycle(annealing_plate, [{
"cycles": 1,
"steps": thermocycle_ramp("95:celsius", "25:celsius", "60:minute", "4:minute")
}],
volume="5:microliter",
dataref=None,
dyes=None)
# polymerize
protocol.unseal(annealing_plate)
polymerize_MM = mix_plate.well(12)
reagents = {"buffer": {"resource_id": 'rs17sh5rzz79ct', "reagent_ratio": 0.6},
"t4ligase": {"resource_id": 'rs16pc8krr6ag7', "reagent_ratio": 0.4},
"t7polymerase": {"resource_id": 'rs16pca2urcz74', "reagent_ratio": 0.4},
"dntp": {"resource_id": 'rs16pcb542c5rd', "reagent_ratio": 0.4}
}
provision_reagents(reagents, polymerize_MM, num_constructs, mm_mult, num_rxts_plus)
protocol.transfer(atp, polymerize_MM, "%s:microliter" % ((num_constructs + num_rxts_plus) * 0.4 * mm_mult), new_group=True)
for reaction in anneal_wells.wells:
protocol.transfer(polymerize_MM,
reaction,
"2.2:microliter",
mix_after=False,
**transfer_kwargs(10))
if 'mutant_objs' in params.keys():
mut = next(m for m in params['mutant_objs'] if m.name == reaction.name)
mut.anneal_well = reaction
protocol.seal(annealing_plate)
protocol.incubate(annealing_plate, "ambient", "1.5:hour")
# pass plate back for unsealing
return annealing_plate
def kunkel_full(protocol, params):
growth_media = params["construct_setup"]['growth_media']
num_colonies = params["construct_setup"]['num_colonies']
ssDNA = params["construct_setup"]['ssDNA']
mutant_constructs = []
# make mutant objects for accessibility
construct_collect = {}
for csv_row in params["construct_setup"]['mutant_upload']:
if csv_row["mutant_label"] not in construct_collect.keys():
construct_collect[csv_row["mutant_label"]] = []
construct_collect[csv_row["mutant_label"]].append(
{
"sequence": csv_row["sequence"],
"purification": csv_row["purification"],
"scale": csv_row["scale"],
"oligo_label": csv_row["oligo_label"]
})
else:
construct_collect[csv_row["mutant_label"]].append(
{
"sequence": csv_row["sequence"],
"purification": csv_row["purification"],
"scale": csv_row["scale"],
"oligo_label": csv_row["oligo_label"]
}
)
oligo_collect = {}
for row in params["construct_setup"]["mutant_upload"]:
if (row["sequence"] not in oligo_collect.keys() and row["oligo_label"] in protocol.refs.keys()):
raise RuntimeError("You cannot specify two different "
"oligos to be synthesized with the "
"same name %s" % row['oligo_label'])
elif row["sequence"] not in oligo_collect.keys():
oligo_collect[row["sequence"]] = {
"sequence": row["sequence"],
"purification": row["purification"],
"scale": row["scale"],
"destination": protocol.ref(row["oligo_label"], None, "micro-2.0", storage="cold_4").well(0)
}
for mut in construct_collect.keys():
mut_oligos = [o for o in construct_collect[mut]]
mutant = Mutant(mut)
for oligo in mut_oligos:
mutant.add_oligos(oligo_collect[oligo["sequence"]]["destination"])
mutant_constructs.append(mutant)
oligos_to_synthesize = []
for o in oligo_collect.keys():
scale_default(len(oligo_collect[o]["sequence"]), oligo_collect[o]["scale"], oligo_collect[o]["destination"].container.name)
oligos_to_synthesize.append(oligo_collect[o])
protocol.oligosynthesize(oligos_to_synthesize)
assemble_params = {
'ssDNA': ssDNA,
'constructs': [{
'mutant_name': mu.name,
'oligos': mu.oligos} for mu in mutant_constructs],
'mutant_objs': mutant_constructs
}
annealing_plate = assemble(protocol, assemble_params)
protocol.unseal(annealing_plate)
transform_params = {
'num_colonies': num_colonies,
'growth_media': growth_media,
'constructs': [mu.anneal_well for mu in mutant_constructs],
'mutant_objs': mutant_constructs
}
growth_plate = transform(protocol, transform_params)
seq_primers = []
for seq_primer in params["sequencing"]:
if seq_primer["seq_choice"] != "No sequencing.":
# make temp container with name of stock primer
primer = protocol.ref(seq_primer["seq_choice"], None, "micro-1.5",
discard=True).well(0)
primer.set_name(seq_primer["seq_choice"])
primer_vol = "1:microliter"
seq_primers.append(primer)
sequence_params = {
'seq_set': [{
'growth_wells': WellGroup([w for w in mu.growth_wells]),
'seq_primers': seq_primers} for mu in mutant_constructs]
}
if seq_primers:
protocol.uncover(growth_plate)
sequence(protocol, sequence_params)
protocol.cover(growth_plate, lid="low_evaporation")
if params["other_processing"]["other_processing"] != "No processing.":
protocol.uncover(growth_plate)
if params["other_processing"]["other_processing"] == "Miniprep":
mini_samples = []
for mu in mutant_constructs:
for w in mu.growth_wells:
mini_samples.append({"sample": w, "name": w.name})
miniprep_params = {
"type": "Miniprep",
"media": growth_media,
'samples': mini_samples,
"growth_plate": growth_plate
}
plasmidprep(protocol, miniprep_params)
if params["other_processing"]["other_processing"] == "Return Colonies":
return_plate = protocol.ref("return_plate_%s" % printdatetime(time=False), cont_type='96-pcr', storage='cold_4')
for mut in mutant_constructs:
for g_well in mut.growth_wells:
protocol.transfer(g_well, return_plate.well(g_well.index), "30:microliter")
return_plate.well(g_well.index).set_name(g_well.name)
protocol.seal(return_plate)
protocol.cover(growth_plate, lid="low_evaporation")
if params["other_processing"]["other_processing"] == "Return Colonies Glycerol":
return_plate = protocol.ref("return_plate_glycerol_%s" % printdatetime(time=False), cont_type='96-pcr', storage='cold_4')
for mut in mutant_constructs:
for g_well in mut.growth_wells:
protocol.transfer(g_well, return_plate.well(g_well.index), "30:microliter")
return_plate.well(g_well.index).set_name(g_well.name)
for mut in mutant_constructs:
for g_well in mut.growth_wells:
protocol.provision("rs17rrhqpsxyh2", return_plate.well(g_well.index), "30:microliter")
protocol.seal(return_plate)
protocol.cover(growth_plate, lid="low_evaporation")
def assemble(protocol, params):
def provision_reagents(reagents,
dest,
num_rxts,
mm_mult=1.3,
num_rxts_plus=3.0):
for reagent in reagents.values():
protocol.provision(
reagent['resource_id'], dest,
"%s:microliter" % ((num_rxts + num_rxts_plus) *
reagent['reagent_ratio'] * mm_mult))
def transfer_kwargs(pre_buffer, one_tip=False, one_source=False):
kwargs = {
"one_tip": one_tip,
"one_source": one_source,
"pre_buffer": "%s:microliter" % pre_buffer,
"blowout_buffer": True
}
return (kwargs)
# general parameters
ssDNA = params['ssDNA']
constructs = [construct['oligos'] for construct in params['constructs']]
num_constructs = len(constructs)
flattened = [val for oligo in constructs for val in oligo]
oligos = list({v: v for v in flattened}.values())
num_oligos = len(oligos)
mm_mult = 1.3
num_rxts_plus = 3
# provision water
water = protocol.ref('water', cont_type='96-deep', discard=True)
protocol.dispense_full_plate(water, 'water', '1000:microliter')
# water = [provision_to_tube(protocol, "water%s" % (i + 1), "micro-2.0", "rs17gmh5wafm5p", 1900)
# for i in range(int(math.ceil(num_constructs/float(9.0))))
# ]
#
# for w in water:
# w.set_volume('1800:microliter')
# provision atp for entire protocol
atp_reagents = {
'atp': {
"resource_id": 'rs16pccshb6cb4',
'reagent_ratio': 0.1
},
'water': {
"resource_id": 'rs17gmh5wafm5p',
'reagent_ratio': 0.9
}
}
atp_rxts = (num_oligos + num_constructs)
atp = protocol.ref("atp_10mM", cont_type='micro-1.5', discard=True).well(0)
provision_reagents(atp_reagents, atp, atp_rxts, mm_mult, num_rxts_plus=6)
# provision kinase mix
kinase_mix = []
for i in range(int(math.ceil(num_oligos / 60.0))):
kinase_mix.append(
protocol.ref("kinase_mix-%s" % (i + 1),
None,
"micro-1.5",
discard=True).well(0))
reagents = {
'pnkbuffer': {
"resource_id": 'rs16pc9rd5sg5d',
"reagent_ratio": 3
},
'water': {
"resource_id": 'rs17gmh5wafm5p',
"reagent_ratio": 18
},
'pnk': {
"resource_id": 'rs16pc9rd5hsf6',
"reagent_ratio": 1
}
}
provision_reagents(reagents, kinase_mix, num_oligos, mm_mult,
num_rxts_plus)
protocol.transfer(atp,
kinase_mix,
"%s:microliter" %
((num_oligos + num_rxts_plus) * 1 * mm_mult),
new_group=True)
# kinase oligos
kinase_oligo_plate = protocol.ref("kinase_oligo_plate_%s" %
printdatetime(time=False),
None,
"96-pcr",
discard=True)
wells_to_kinase = kinase_oligo_plate.wells_from("A1", num_oligos)
protocol.transfer(kinase_mix, wells_to_kinase, "23:microliter",
**transfer_kwargs(15, True, True))
for i, oligo in enumerate(oligos):
protocol.transfer(
oligo,
wells_to_kinase[i],
"7:microliter",
mix_after=False,
new_group=det_new_group(i),
aspirate_source=aspirate_source(depth=depth(
"ll_following", lld="pressure", distance="0.0:meter")),
**transfer_kwargs(10))
protocol.seal(kinase_oligo_plate)
protocol.thermocycle(
kinase_oligo_plate,
[{
"cycles": 1,
"steps": [
{
"temperature": "37:celsius",
"duration": "60:minute"
},
]
}],
volume="30:microliter")
# dilute oligos
protocol.unseal(kinase_oligo_plate)
diluted_oligo_plate = protocol.ref("dilute_oligo_plate",
None,
"96-flat",
discard=True)
diluted_oligo_wells = diluted_oligo_plate.wells_from(0, num_constructs)
protocol.transfer(water.all_wells(),
diluted_oligo_wells,
"200:microliter",
disposal_vol="0:microliter",
**transfer_kwargs(40, True, True))
for i, m in enumerate(constructs):
for kin_oligo in m:
index = list(oligos).index(kin_oligo)
protocol.transfer(kinase_oligo_plate.well(index),
diluted_oligo_plate.well(i),
"2:microliter",
mix_after=False,
mix_vol="5:microliter")
diluted_oligo_plate.well(i).set_name(
params['constructs'][i]['mutant_name'])
protocol.cover(diluted_oligo_plate)
protocol.spin(diluted_oligo_plate, "250:g", "2:minute")
# make ssDNA_mastermix
mm_mult_ssDNA = 1.5
mix_plate = protocol.ref("mix_plate", None, "96-pcr", discard=True)
ssDNA_mix = mix_plate.well(0)
protocol.transfer(
ssDNA, ssDNA_mix, "%s:microliter" %
((num_constructs + num_rxts_plus) * 2.0 * mm_mult_ssDNA),
**transfer_kwargs((num_constructs + 1) * 1))
protocol.provision(
'rs17sh5rzz79ct', ssDNA_mix, "%s:microliter" %
((num_constructs + num_rxts_plus) * 0.2 * mm_mult_ssDNA))
# anneal oligos
protocol.uncover(diluted_oligo_plate)
annealing_plate = protocol.ref("annealing_oligo_plate",
None,
"384-pcr",
storage="cold_20")
anneal_wells = annealing_plate.wells_from(0, num_constructs)
protocol.transfer(ssDNA_mix,
anneal_wells.wells,
"2.2:microliter",
dispense_speed="50:microliter/second",
**transfer_kwargs(7, True, True))
for dil_oligo, reaction in zip(diluted_oligo_wells.wells,
anneal_wells.wells):
protocol.transfer(dil_oligo,
reaction,
"2:microliter",
aspirate_source=aspirate_source(
depth("ll_bottom", distance=".001:meter")),
mix_after=True,
mix_vol="2:microliter",
flowrate="50:microliter/second",
repetitions=2,
new_group=det_new_group(i),
**transfer_kwargs(5))
reaction.set_name(dil_oligo.name)
protocol.seal(annealing_plate)
protocol.spin(annealing_plate, "250:g", "2:minute")
protocol.thermocycle(annealing_plate, [{
"cycles":
1,
"steps":
thermocycle_ramp("95:celsius", "25:celsius", "60:minute", "4:minute")
}],
volume="5:microliter",
dataref=None,
dyes=None)
# polymerize
protocol.unseal(annealing_plate)
polymerize_MM = mix_plate.well(12)
reagents = {
"buffer": {
"resource_id": 'rs17sh5rzz79ct',
"reagent_ratio": 0.6
},
"t4ligase": {
"resource_id": 'rs16pc8krr6ag7',
"reagent_ratio": 0.4
},
"t7polymerase": {
"resource_id": 'rs16pca2urcz74',
"reagent_ratio": 0.4
},
"dntp": {
"resource_id": 'rs16pcb542c5rd',
"reagent_ratio": 0.4
}
}
provision_reagents(reagents, polymerize_MM, num_constructs, mm_mult,
num_rxts_plus)
protocol.transfer(atp,
polymerize_MM,
"%s:microliter" %
((num_constructs + num_rxts_plus) * 0.4 * mm_mult),
new_group=True)
for reaction in anneal_wells.wells:
protocol.transfer(polymerize_MM,
reaction,
"2.2:microliter",
mix_after=False,
**transfer_kwargs(10))
if 'mutant_objs' in params.keys():
mut = next(m for m in params['mutant_objs']
if m.name == reaction.name)
mut.anneal_well = reaction
protocol.seal(annealing_plate)
protocol.incubate(annealing_plate, "ambient", "1.5:hour")
# pass plate back for unsealing
return annealing_plate