def get_protocol(self):
p = stepwise.Protocol()
s = ul()
if self.names:
p += pl(
f"Purify {','.join(self.names)} by ethanol precipitation [1,2]:",
s)
else:
p += pl("Perform an ethanol precipitation [1,2]:", s)
s += f"""\
Add {self.cation_name} to {self.cation_conc}."""
s += f"""\
Add {self.carrier_name} to {self.carrier_conc}."""
s += f"""\
Add {plural(self.solvent_volume):# volume/s}
{self.solvent_name} and mix well."""
s += f"""\
If necessary, divide the sample between microfuge tubes
such that none holds more than 400 µL."""
if self.incubation and (t := self.incubation_time):
incubation_time = "overnight" if t == 'overnight' else f"for {t}"
s += f"""\
def get_protocol(self):
transfer = self.volume * (f := self.inv_factor) / (1 - f)
initial_volume = self.volume + transfer
conc_high_str = format_quantity(self.conc_high, self.conc_unit, 'g')
material_str = f'{conc_high_str} {self.material}'.lstrip()
conc_table = [[i, format_quantity(conc, self.conc_unit, 'e')]
for i, conc in enumerate(self.concentrations, 1)]
num_tubes = self.steps if self.include_zero else self.steps - 1
each_tube = 'each tube *except the last*' if self.include_zero else 'each tube'
protocol = stepwise.Protocol()
protocol += pl(
"Perform a serial dilution [1]:",
ul(
f"Put {initial_volume:.2f} μL {material_str} in a tube.",
f"Put {self.volume:.2f} μL {self.diluent} in {plural(num_tubes):# adjacent tube/s}.",
f"Transfer {transfer:.2f} μL between {each_tube} to make {self.steps} {self.factor:.2g}-fold dilutions.",
),
)
protocol.footnotes[1] = pl(
"The final concentrations will be:",
pre(stepwise.tabulate(conc_table, align='>>')),
br='\n',
)
return protocol
def get_protocol(self):
phrases = []
n = plural(self.product_tags)
if self.show_product_tags:
phrases.append(f"Concentrate the following {n:sample/s}")
elif self.product_tags:
phrases.append(f"Concentrate the {n:sample/s}")
else:
phrases.append("Concentrate the sample(s)")
if self.volume and self.conc:
err = UsageError(volume=self.volume, conc=self.conc)
err.brief = "cannot specify volume and concentration"
err.info += "volume: {volume}"
err.info += "conc: {conc}"
raise err
elif self.volume:
phrases.append(f"to {self.volume}")
elif self.conc:
phrases.append(f"to {self.conc}")
else:
pass
if self.show_product_tags:
phrases.append(
f"by lyophilization: {', '.join(map(str, self.product_tags))}")
else:
phrases.append("by lyophilization.")
return stepwise.Protocol(steps=[' '.join(phrases)], )
def get_gel_electrophoresis_steps(self):
p = stepwise.Protocol()
n = plural(self.samples)
gel = Gel(self.gel_preset)
mix = gel.sample_mix
k = mix.volume / mix['sample'].volume
for sample in self.samples:
sample.stock_conc
sample.sample_volume_per_lane_uL = min(
sample.volume_uL,
sample.volume_uL / ceil(sample.mass_ug / '20 µg'),
mix['sample'].volume.value or inf,
)
sample.load_volume_per_lane_uL = k * sample.sample_volume_per_lane_uL
sample.num_lanes = int(ceil(sample.volume_uL / sample.sample_volume_per_lane_uL))
conc_vol_groups = group_by_identity(
self.samples,
key=lambda x: (x.stock_conc, x.volume_uL),
)
for (conc, volume_uL), group in conc_vol_groups:
prep_gel = Gel(self.gel_preset)
prep_gel.num_samples = len(group)
mix = prep_gel.sample_mix
mix.hold_ratios.volume = k * volume_uL, 'µL'
mix['sample'].name = ','.join(str(x.name) for x in group)
mix['sample'].stock_conc = conc
p += prep_gel.prep_step
if x := self.gel_percent:
gel.gel_percent = x
def get_protocol(self):
p = stepwise.Protocol()
## Clean your bench
p += stepwise.load('rnasezap')
## In vitro transcription
rxn = self.reaction
n = plural(rxn.num_reactions)
f = self.footnotes.get('reaction', [])
p += paragraph_list(
f"Setup {n:# in vitro transcription reaction/s}{p.add_footnotes(*f)}:",
rxn,
unordered_list(*self.instructions),
)
f = self.footnotes.get('incubation', [])
if self.short and affected_by_short(self.incubation_times_min):
f += [
f"Reaction time is different than usual because the template is short (<{self.template_length_threshold} bp)."
]
p += f"Incubate at {self.incubation_temp_C}°C for {format_min(pick_by_short(self.incubation_times_min, self.short))}{p.add_footnotes(*f)}."
## DNase treatment
if self.dnase:
f = self.footnotes.get('dnase', [])
p += paragraph_list(
f"Setup {n:# DNase reaction/s}{p.add_footnotes(*f)}:",
self.dnase_reaction,
)
p += f"Incubate at {self.dnase_incubation_temp_C}°C for {format_min(self.dnase_incubation_time_min)}."
return p
def get_gel_extraction_steps(self):
p = stepwise.Protocol()
names = self._cluster_names_by_molecule()
desired = oxford_comma(x) if (x := self.desired_bands) else 'desired'
n = plural(max(len(self.desired_bands), len(self.samples)))
f = "Based on Fitzy's DNA PAGE purification protocol, [Nilson2013], and [Petrov2013]."
p += pl(f"Cut the {desired} {n:band/s} out of the gel{p.add_footnotes(f)}.", ul(
"Place the gel over a TLC plate.",
"Use a UV light to visualize the RNA (dark spot).",
"Consider visualizing remaining gel to ensure that all desired RNA was excised.",
))
p += pl(f"Crush the gel {n:slice/s}.", ul(
"Poke a hole in the bottom of a 0.65 mL tube with a 27 g needle.",
"Place gel slice inside the 0.65 mL tube.",
"Place the 0.65 mL tube inside a 1.5 mL tube.",
"Spin at max speed for 5 min.",
))
eb = elution_buffer()
eb.hold_ratios.volume = 500 * len(self.samples), 'µL'
p += pl(
"Resuspend gel in 400 µL PAGE elution buffer:",
eb,
)
if names['RNA']:
p += f"Incubate {join_if(names['RNA'], names['DNA'])}at 4°C overnight with end-over-end mixing."
if names['DNA']:
p += f"Incubate {join_if(names['DNA'], names['RNA'])}at 55°C overnight with 800 rpm mixing."
return p
def get_stub_protocol(self):
tags = [x.tag for x in self.stocks]
in_diluent = f' in {self.diluent}' if self.diluent else ''
p = stepwise.Protocol()
p += f"Dilute {oxford_comma(tags)} to {self.target_conc}{in_diluent}."
return p
def get_protocol(self):
protocol = stepwise.Protocol()
pcr, primer_mix = self.reaction
thermocycler = self.thermocycler_protocol
footnotes = []
# Primer mix (if applicable):
example_uM = min(x.stock_uM for x in flatten(self.primer_pairs))
footnotes.append(pl(
f"For resuspending lyophilized primers:",
f"{example_uM} µM = {1e3 / example_uM:g} µL/nmol",
br='\n',
))
if primer_mix:
protocol += pl(
f"Prepare 10x primer mix{protocol.add_footnotes(*footnotes)}:",
primer_mix,
)
footnotes = []
# PCR reaction setup:
if self.footnote:
# Before the footnote on resuspending the primers, if it hasn't
# been added to the protocol already.
footnotes.insert(0, self.footnote)
if x := pcr['template DNA'].stock_conc:
footnotes.append(pl(
f"For diluting template DNA to {x}:",
f"Dilute 1 µL twice into {sqrt(1000/x.value):.1g}*sqrt([DNA]) µL",
br='\n',
))
def __init__(self, product):
args = product.maker_args
self.products = [product]
self.dependencies = args.get('deps', [])
if isinstance(self.dependencies, str):
self.dependencies = self.dependencies.split(',')
if 'protocol' in args:
self.protocol = stepwise.Protocol(steps=args['protocol'])
# Maker attributes:
if 'conc' in args:
self.product_conc = stepwise.Quantity.from_string(args['conc'])
if 'volume' in args:
self.product_volume = stepwise.Quantity.from_string(args['volume'])
# Synthesis attributes:
if 'seq' in args:
self.product_seqs = [args['seq']]
if 'molecule' in args:
self.product_molecule = args['molecule']
if 'circular' in args:
self.is_product_circular = freezerbox.parse_bool(args['circular'])
def get_protocol(self):
# Maybe this should be the getter function for the assembly param...
p = stepwise.Protocol()
rxn = self.reaction
n = rxn.num_reactions
n_frags = self.num_fragments
f = 'https://tinyurl.com/yaa5mqz5'
p += pl(
f"Setup {plural(n):# Golden Gate assembl/y/ies}{p.add_footnotes(f)}:",
rxn,
)
if n_frags <= 2:
p += pl(
"Run the following thermocycler protocol:",
ul("37°C for 5 min", ),
"Or, to maximize the number of transformants:",
ul(
"37°C for 60 min",
"60°C for 5 min",
),
)
elif n_frags <= 4:
p += pl(
"Run the following thermocycler protocol:",
ul(
"37°C for 60 min",
"60°C for 5 min",
),
)
elif n_frags <= 10:
p += pl(
"Run the following thermocycler protocol:",
ul(
"Repeat 30 times:",
ul(
"37°C for 1 min",
"16°C for 1 min",
),
"60°C for 5 min",
),
)
else:
p += pl(
"Run the following thermocycler protocol:",
ul(
"Repeat 30 times:",
ul(
"37°C for 5 min",
"16°C for 5 min",
),
"60°C for 5 min",
),
)
return p
def get_protocol(self):
anneal = AnnealMrnaLinker(self.mrnas, self.linkers)
anneal.num_reactions = self.num_reactions
anneal.linker_ratio = 0.6 # See expt #1
# Scale the reactions such that we'll end up with enough mRNA:
anneal_rxn = anneal.reaction
mrna_pmol = (
self.expected_dead_volume_uL * self.target_conc_uM /
self.expected_yield
)
mrna_conc_uM = anneal_rxn['mRNA'].stock_conc.value
anneal.mrna_volume_uL = max(
mrna_pmol / mrna_conc_uM,
self.mrna_volume_uL,
)
ligate = LigateMrnaLinker(anneal)
wash = WashBarendt()
wash.mwco_kDa = self.mwco_kDa
p = stepwise.Protocol()
p += anneal.protocol
p += ligate.protocol
if self.label:
p += f"Label the product: {self.label}"
if self.wash:
p += wash.protocol
if self.aliquot:
p += stepwise.load('aliquot "4 µL" "1 µM"')
return p
def get_protocol(self):
self._bind_samples()
p = stepwise.Protocol()
p += self.gel_electrophoresis_steps
p += self.gel_extraction_steps
p += self.product_recovery_steps
return p
def get_protocol(self):
p = stepwise.Protocol()
p += pl(
f"Setup {plural(self.num_reactions):# ligation reaction/s}:",
self.reaction,
)
p += "Incubate at room temperature for 1h."
return p
def test_to_stdout(capsysbinary):
unpickleable_protocol = stepwise.Protocol(steps=[lambda: None])
io = stepwise.ProtocolIO(unpickleable_protocol)
io.to_stdout()
cap = capsysbinary.readouterr()
io_out = pickle.loads(cap.out)
assert io_out.protocol == ''
assert io_out.errors == 1
assert "AttributeError: Can't pickle local object" in cap.err.decode()
def __init__(self, products):
from more_itertools import flatten
steps = list(
flatten(x.maker_args.get('protocol', []) for x in products))
deps = list(flatten(x.maker_args.get('deps', []) for x in products))
self.products = products
self.protocol = stepwise.Protocol(steps=steps)
self.dependencies = deps
def get_protocol(self):
p = stepwise.Protocol()
if self.sample_mix:
p += self.prep_step
p += self.run_step
if self.stain:
p += stepwise.load(self.stain)
return p
def get_protocol(self):
optics = [self.parse_optics(x) for x in self.optics]
lasers = [f"{plural(optics):laser/s}:"
] + [f"{x['laser']} nm" for x in optics]
filters = [f"{plural(optics):filter/s}:"
] + [x['filter'] for x in optics]
p = stepwise.Protocol()
p += pl(
"Image with a laser scanner:",
table([lasers, filters], align='<>>'),
)
return p
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
p += pl(
f"Setup {plural(self.num_reactions):# {self.title} reaction/s}{p.add_footnotes(self.setup_footnote)}:",
rxn,
ul(*self.setup_instructions),
)
if self.incubation_time != '0':
p += f"Incubate at {self.incubation_temp_C:g}°C for {self.incubation_time}{p.add_footnotes(self.incubation_footnote)}."
return p
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
n = rxn.num_reactions
f = "https://tinyurl.com/ychbvkra"
p += pl(
f"Setup {plural(n):# Gibson assembl/y/ies}{p.add_footnotes(f)}:",
rxn,
)
incubation_time = '15 min' if self.num_fragments <= 3 else '1h'
p += f"Incubate at 50°C for {incubation_time}."
return p
def get_protocol(self):
p = stepwise.Protocol()
pl = stepwise.paragraph_list()
ul = stepwise.unordered_list()
def break_if_too_long(pl, ul, n=4):
if len(ul) > n:
ul = stepwise.unordered_list()
pl += ul
return ul
footnotes = []
if self.protocol_link:
footnotes.append(self.protocol_link)
if self.column_capacity_ug:
footnotes.append(f"Column capacity: {self.column_capacity_ug} µg")
if self.product_tags and self.show_product_tags:
product_tags = oxford_comma(self.product_tags) + ' '
else:
product_tags = ''
p += pl
pl += f"Purify {product_tags}using {self.protocol_name}{p.add_footnotes(*footnotes)}:"
pl += ul
if self.spin_speed_g:
ul += f"Perform all spin steps at {self.spin_speed_g}g."
## Dilute
if x := self.target_sample_volume_uL:
v = self.sample_volume_uL
if not isinstance(x, dict):
target = f'{x} µL'
skip = v and v == x
self.sample_volume_uL = x
elif 'min' in x and 'max' in x:
target = f"between {x['min']}–{x['max']} µL"
skip = v and x['min'] <= v <= x['max']
elif 'min' in x:
target = f"at least {x['min']} µL"
skip = v and x['min'] <= v
elif 'max' in x:
target = f"at most {x['max']} µL"
skip = v and v <= x['max']
if not skip:
ul += f"Ensure that the sample is {target}."
def get_protocol(self):
p = stepwise.Protocol()
p += pl(
"Remove unligated linker by ultrafiltration:",
s := ul(
"Bring reaction to 500 µL with 8M urea.",
f"Load onto a {self.mwco_kDa} kDa MWCO spin-filter [1].",
"Spin 14000g, 15 min.",
"Wash with 500 µL 8M urea.",
"Wash with 500 µL nuclease-free water.",
"Wash with water again.",
"Wash with water again, but spin for 30 min.",
"Invert the filter into a clean tube and spin 1000g, 2 min to collect ligated product in a volume of ≈15 µL.",
),
)
def get_protocol(self):
Q = Quantity.from_string
if self.conc:
aliquot_info = f'{Q(self.volume)}, {Q(self.conc)}'
else:
aliquot_info = f'{Q(self.volume)}'
if self.product_tags and self.show_product_tags:
product_tags = f" of: {', '.join(self.product_tags)}"
else:
product_tags = "."
return stepwise.Protocol(
steps=[f"Make {aliquot_info} aliquots{product_tags}"], )
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
p += pl(
f"Setup {plural(rxn.num_reactions):# ligation reaction/s}{p.add_footnotes('https://tinyurl.com/y7gxfv5m')}:",
rxn,
)
p += pl(
"Incubate at the following temperatures:",
ul(
"25°C for 15 min",
"65°C for 10 min",
),
)
return p
def get_protocol(self):
protocol = stepwise.Protocol()
n = self.num_reactions
protocol += f"""\
Setup {plural(n):# annealing reaction/s}:
{self.reaction}
"""
protocol += f"""\
Perform the {plural(n):annealing reaction/s}:
- Incubate at 95°C for 2 min.
- Cool at room temperature.
"""
return protocol
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
rxn_name = 'ligation' if self.use_ligase else 'negative control'
n = rxn.num_reactions
p += stepwise.pl(
f"Setup {plural(n):# {rxn_name} reaction/s}:",
rxn,
)
if self.incubate:
p += pl(
f"Incubate the {plural(n):ligation reaction/s} as follows:",
s := ul(
f"{self.incubate_temp} for {self.incubate_time}."
),
)
if self.quench:
def get_product_recovery_steps(self):
p = stepwise.Protocol()
names = self._cluster_names_by_molecule()
# Filter material:
# - Corning has a good guide on which material to select:
# https://www.corning.com/catalog/cls/documents/selection-guides/t_filterselectionguide.pdf
#
# - I want 0.22 µm, because that's the standard size for filter
# sterilizing biological buffers (that's not my application here, but
# I can see myself wanting to do that).
#
# - I want cellulose acetate filters. Nylon and cellulose nitrate have
# high DNA binding, which will cause me to lose material. The
# downside to cellulose acetate is that it has a wetting agent that
# will end up in the sample. However, this will be removed by the
# Zymo column in the subsequent step.
#
# - Product number: 8161 (non sterile)
#
# Centrifugation speed:
# - Fitzy's DNA PAGE purification protocol calls for 4 min at 7000 rpm
# - The Corning guide (see above) includes an agarose gel purification
# protocol, which calls for 13,000g for 5-20 min. But this protocol
# has no incubation step, so I gather that the spin is supposed to
# pull the solvent out of the gel. I probably don't need to go so
# fast, but why not go as fast as the columns can tolerate?
f = "Nylon and cellulose nitrate have high DNA-binding: https://tinyurl.com/3pkyc8dr"
p += pl(
"Remove gel debris by spin filtration:",
ul(
f"Load samples onto a 0.22 µm cellose-acetate Spin-X column{p.add_footnotes(f)}.",
"Spin at 13,000g for 5 min."
),
)
if self.cleanup:
if names['RNA']:
p += cleanup(self.rna_cleanup_preset, names['RNA'], names['DNA'])
if names['DNA']:
p += cleanup(self.dna_cleanup_preset, names['DNA'], names['RNA'])
return p
def get_run_step(self):
p = stepwise.Protocol()
additive = f" with {x}" if (x := self.gel_additive) else ""
percent = x.replace('-', '–') if isinstance(x := self.gel_percent,
str) else x
p += pl(
f"Run a gel{p.add_footnotes(self.protocol_link)}:",
dl(
("gel", f"{percent}% {self.gel_type}{additive}"),
("buffer", f"{self.gel_buffer}"),
("ladder", self.ladder_name
and f"{self.ladder_volume_uL:g} µL {self.ladder_name}"),
("samples", self.load_volume_uL
and f"{self.load_volume_uL:.3g} µL/lane"),
("prerun", self.prerun_time_min and
f"{self.prerun_volts:g}V for {self.prerun_time_min:g} min"),
("run", f"{self.run_volts:g}V for {self.run_time_min:g} min"),
))
return p
def get_protocol(self):
protocol = stepwise.Protocol()
targets = iter_targets(
self.db, self.tags,
include_deps=self.include_deps,
)
for key, group in group_by_synthesis(targets):
for maker in iter_makers(self.db, key, group):
protocol += maker.protocol
if getattr(maker, 'label_products', True):
protocol += label_products(maker.products)
parents = [x.parent for x in group]
for key, subgroup in group_by_cleanup(parents):
for maker in iter_makers(self.db, key, subgroup):
protocol += maker.protocol
return protocol
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
p += f"""\
Setup {plural(self.num_reactions):# NEBExpress reaction/s} [1]:
{rxn}
- Thaw all components on ice.
- Mix the S30 extract and protein synthesis buffer
by gently vortexing.
"""
p += f"""\
Incubate at {self.incubation_temp_C}°C for {self.incubation_time} [4].
"""
p.footnotes[1] = """\
During the experimental setup, it is recommended
to add the linear DNA template in the last step to
allow GamS to bind and inhibit RecBCD exonuclease
before RecBCD has a chance to act on the DNA.
"""
p.footnotes[2] = """\
Aliquot to avoid multiple freeze/thaw cycles.
"""
p.footnotes[3] = """\
Optimal concentration must be determined
empirically for each template.
"""
p.footnotes[4] = """\
Additional incubation time (maximum 10 hours) at
37°C may increase yield.
"""
return p
def get_protocol(self):
p = stepwise.Protocol()
rxn = self.reaction
n = rxn.num_reactions
p += pl(
f"Setup {plural(n):# annealing reaction/s} [1]:",
rxn,
)
p.footnotes[1] = """\
Using 0.6x linker reduces the amount of unligated
linker, see expt #1."""
p += pl(
f"Perform the {plural(n):annealing reaction/s}:",
ul(
"Incubate at 95°C for 2 min.",
"Cool at room temperature.",
),
)
return p