def top_model(sbml_file, directory, emds, doc_fba=None, validate=True):
""" Create the top model. """
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model, notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "blood"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT,
create_port=False)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
# write SBML file
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=validate)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba=None, validate=True):
""" Create the top model. """
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model, notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "blood"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_CONCENTRATION,
create_port=False)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, unit_amount=UNIT_CONCENTRATION)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
# write SBML file
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=validate)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba, annotations=None):
""" Create top comp model.
Creates full comp model by combining fba, update and bounds
model with additional kinetics in the top model.
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators,
units=units,
main_units=main_units)
# dt
builder.create_dfba_dt(model,
step_size=DT_SIM,
time_unit=UNIT_TIME,
create_port=False)
# compartment
compartment_id = "cell"
builder.create_dfba_compartment(model,
compartment_id=compartment_id,
unit_volume=UNIT_VOLUME,
create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model,
model_fba,
compartment_id=compartment_id,
hasOnlySubstanceUnits=False,
unit_amount=UNIT_AMOUNT,
create_port=False)
# dummy species
builder.create_dummy_species(model,
compartment_id=compartment_id,
hasOnlySubstanceUnits=False,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX,
create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model,
model_fba,
compartment_id=compartment_id)
objects = [
# kinetic parameters
mc.Parameter(sid="Vmax_RATP", value=1, unit=UNIT_FLUX, constant=True),
mc.Parameter(sid='k_RATP',
value=0.1,
unit=UNIT_CONCENTRATION,
constant=True),
# balancing rules
mc.AssignmentRule(sid="atp_tot",
value="atp + adp",
unit=UNIT_CONCENTRATION),
mc.AssignmentRule(sid="c3_tot",
value="2 dimensionless * glc + pyr",
unit="mM")
]
mc.create_objects(model, objects)
ratp = mc.create_reaction(model,
rid="RATP",
name="atp -> adp",
fast=False,
reversible=False,
reactants={"atp": 1},
products={"adp": 1},
compartment=compartment_id,
formula='Vmax_RATP * atp/(k_RATP + atp)')
# initial concentrations for fba exchange species
initial_c = {'atp': 2.0, 'adp': 1.0, 'glc': 5.0, 'pyr': 0.0}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# write SBML file
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
# change back the working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba, annotations=None):
""" Create top comp model.
Creates full comp model by combining fba, update and bounds
model with additional kinetics in the top model.
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "extern"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, hasOnlySubstanceUnits=True,
unit_amount=UNIT_AMOUNT, create_port=False)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, hasOnlySubstanceUnits=True,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
# initial concentrations for fba exchange species
initial_c = {
'A': 10.0,
'C': 0.0,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# kinetic model
mc.create_objects(model, [
# kinetic species
mc.Species(sid='D', initialConcentration=0, substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True, compartment="extern"),
# kinetic
mc.Parameter(sid="k_R4", value=0.1, constant=True, unit="per_s", sboTerm="SBO:0000009"),
# bounds parameter
mc.Parameter(sid='ub_R1', value=1.0, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000625"),
])
# kinetic reaction (MMK)
mc.create_reaction(model, rid="R4", name="R4: C -> D", fast=False, reversible=False,
reactants={"C": 1}, products={"D": 1}, formula="k_R4*C", compartment="extern")
# kinetic flux bounds
comp.replace_elements(model, 'ub_R1', ref_type=comp.SBASE_REF_TYPE_PORT,
replaced_elements={'bounds': ['ub_R1_port'],
'fba': ['ub_R1_port']})
# write SBML file
if annotations:
annotation.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
# change back the working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba, annotations=None):
""" Create top comp model.
Creates full comp model by combining fba, update and bounds
model with additional kinetics in the top model.
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators,
units=units,
main_units=main_units)
# dt
builder.create_dfba_dt(model,
step_size=DT_SIM,
time_unit=UNIT_TIME,
create_port=False)
# compartment
compartment_id = "extern"
builder.create_dfba_compartment(model,
compartment_id=compartment_id,
unit_volume=UNIT_VOLUME,
create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model,
model_fba,
compartment_id=compartment_id,
hasOnlySubstanceUnits=True,
unit_amount=UNIT_AMOUNT,
create_port=False)
# dummy species
builder.create_dummy_species(model,
compartment_id=compartment_id,
hasOnlySubstanceUnits=True,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX,
create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model,
model_fba,
compartment_id=compartment_id)
# initial concentrations for fba exchange species
initial_c = {
'A': 10.0,
'C': 0.0,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# kinetic model
mc.create_objects(
model,
[
# kinetic species
mc.Species(sid='D',
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True,
compartment="extern"),
# kinetic
mc.Parameter(sid="k_R4",
value=0.1,
constant=True,
unit="per_s",
sboTerm="SBO:0000009"),
# bounds parameter
mc.Parameter(sid='ub_R1',
value=1.0,
unit=UNIT_FLUX,
constant=False,
sboTerm="SBO:0000625"),
])
# kinetic reaction (MMK)
mc.create_reaction(model,
rid="R4",
name="R4: C -> D",
fast=False,
reversible=False,
reactants={"C": 1},
products={"D": 1},
formula="k_R4*C",
compartment="extern")
# kinetic flux bounds
comp.replace_elements(model,
'ub_R1',
ref_type=comp.SBASE_REF_TYPE_PORT,
replaced_elements={
'bounds': ['ub_R1_port'],
'fba': ['ub_R1_port']
})
# write SBML file
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbml.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
# change back the working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba=None):
""" Create the top model. """
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
model_id = "ecoli"
doc = builder.template_doc_top(model_id, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators,
units=units,
main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "bioreactor"
builder.create_dfba_compartment(model,
compartment_id=compartment_id,
unit_volume=UNIT_VOLUME,
create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model,
model_fba,
compartment_id=compartment_id,
unit_amount=UNIT_AMOUNT,
create_port=False)
# minimal medium with single carbon source
initial_c = {
'ac_e': 1.0,
'acald_e': 1.0,
'akg_e': 1.0,
'co2_e': 1.0,
'etoh_e': 1.0,
'for_e': 1.0,
'fru_e': 1.0,
'fum_e': 1.0,
'glc__D_e': 20.0,
'gln__L_e': 10.0,
'glu__L_e': 1.0,
'h_e': 1.0,
'h2o_e': 20.0,
'lac__D_e': 1.0,
'mal__L_e': 1.0,
'nh4_e': 1.0,
'o2_e': 1.0,
'pi_e': 1.0,
'pyr_e': 1.0,
'succ_e': 1.0,
'X': 0.001,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# dummy species
builder.create_dummy_species(model,
compartment_id=compartment_id,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX,
create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model,
model_fba,
compartment_id=compartment_id)
# write SBML file
sbml.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba=None, annotations=None):
"""
Create diauxic comp model.
Test script for working with the comp extension in SBML.
One model composition combines all the kinetic models,
in addition the higher level comp model is created which combines everything (i.e. the FBA & ODE models).
For the simulation of the full combined model the tools have to figure out the subparts which are
simulated with which simulation environment.
Creates the full comp model as combination of FBA and comp models.
The submodels must already exist in the given directory
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model, notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "bioreactor"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT,
create_port=False)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
# initial kinetic concentrations
initial_c = {
'Glcxt': 10.8,
'Ac': 0.4,
'O2': 0.21,
'X': 0.001,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
objects = [
# biomass conversion factor
# mc.Parameter(sid="Y", name="biomass [g_per_l]", value=1.0, unit="g_per_l"),
# oxygen exchange parameters
mc.Parameter(sid="O2_ref", name="O2 reference", value=0.21, unit=UNIT_CONCENTRATION),
mc.Parameter(sid="kLa", name="O2 mass transfer", value=7.5, unit='per_h'),
]
mc.create_objects(model, objects)
# oxygen transfer reaction
mc.create_reaction(model, rid="vO2_transfer", name="oxygen transfer", reversible=True,
reactants={}, products={"O2": 1}, formula="kLa * (O2_ref-O2) * bioreactor",
compartment="bioreactor")
# write SBML file
if annotations:
annotation.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba=None):
""" Create the top model. """
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
model_id = "ecoli"
doc = builder.template_doc_top(model_id, emds)
model = doc.getModel()
utils.set_model_info(model, notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "bioreactor"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=False)
# minimal medium with single carbon source
initial_c = {
'ac_e': 1.0,
'acald_e': 1.0,
'akg_e': 1.0,
'co2_e': 1.0,
'etoh_e': 1.0,
'for_e': 1.0,
'fru_e': 1.0,
'fum_e': 1.0,
'glc__D_e': 20.0,
'gln__L_e': 10.0,
'glu__L_e': 1.0,
'h_e': 1.0,
'h2o_e': 20.0,
'lac__D_e': 1.0,
'mal__L_e': 1.0,
'nh4_e': 1.0,
'o2_e': 1.0,
'pi_e': 1.0,
'pyr_e': 1.0,
'succ_e': 1.0,
'X': 0.001,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
# write SBML file
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba=None, annotations=None):
"""
Create diauxic comp model.
Test script for working with the comp extension in SBML.
One model composition combines all the kinetic models,
in addition the higher level comp model is created which combines everything (i.e. the FBA & ODE models).
For the simulation of the full combined model the tools have to figure out the subparts which are
simulated with which simulation environment.
Creates the full comp model as combination of FBA and comp models.
The submodels must already exist in the given directory
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
# Necessary to change into directory with submodel files
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators,
units=units,
main_units=main_units)
# dt
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "bioreactor"
builder.create_dfba_compartment(model,
compartment_id=compartment_id,
unit_volume=UNIT_VOLUME,
create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model,
model_fba,
compartment_id=compartment_id,
unit_amount=UNIT_AMOUNT,
create_port=False)
# dummy species
builder.create_dummy_species(model,
compartment_id=compartment_id,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX,
create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model,
model_fba=model_fba,
unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model,
model_fba,
compartment_id=compartment_id)
# initial kinetic concentrations
initial_c = {
'Glcxt': 10.8,
'Ac': 0.4,
'O2': 0.21,
'X': 0.001,
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
objects = [
# biomass conversion factor
# Parameter(sid="Y", name="biomass [g_per_l]", value=1.0, unit="g_per_l"),
# oxygen exchange parameters
Parameter(sid="O2_ref",
name="O2 reference",
value=0.21,
unit=UNIT_CONCENTRATION),
Parameter(sid="kLa", name="O2 mass transfer", value=7.5, unit='per_h'),
]
factory.create_objects(model, objects)
# oxygen transfer reaction
create_reaction(model,
rid="vO2_transfer",
name="oxygen transfer",
reversible=True,
reactants={},
products={"O2": 1},
formula="kLa * (O2_ref-O2) * bioreactor",
compartment="bioreactor")
# write SBML file
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
# change back into working dir
os.chdir(working_dir)
def top_model(sbml_file, directory, emds, doc_fba, annotations=None):
""" Create top comp model.
Creates full comp model by combining fba, update and bounds
model with additional kinetics in the top model.
"""
top_notes = notes.format("""
<h2>TOP model</h2>
<p>Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.</p>
""")
working_dir = os.getcwd()
os.chdir(directory)
doc = builder.template_doc_top(settings.MODEL_ID, emds)
model = doc.getModel()
utils.set_model_info(model,
notes=top_notes,
creators=creators, units=units, main_units=main_units)
# dt
builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=False)
# compartment
compartment_id = "cell"
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=False)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, hasOnlySubstanceUnits=False,
unit_amount=UNIT_AMOUNT, create_port=False)
# dummy species
builder.create_dummy_species(model, compartment_id=compartment_id, hasOnlySubstanceUnits=False,
unit_amount=UNIT_AMOUNT)
# exchange flux bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=False)
# dummy reactions & flux assignments
builder.create_dummy_reactions(model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# replacedBy (fba reactions)
builder.create_top_replacedBy(model, model_fba=model_fba)
# replaced
builder.create_top_replacements(model, model_fba, compartment_id=compartment_id)
objects = [
# kinetic parameters
mc.Parameter(sid="Vmax_RATP", value=1, unit=UNIT_FLUX, constant=True),
mc.Parameter(sid='k_RATP', value=0.1, unit=UNIT_CONCENTRATION, constant=True),
# balancing rules
mc.AssignmentRule(sid="atp_tot", value="atp + adp", unit=UNIT_CONCENTRATION),
mc.AssignmentRule(sid="c3_tot", value="2 dimensionless * glc + pyr", unit="mM")
]
mc.create_objects(model, objects)
ratp = mc.create_reaction(model, rid="RATP", name="atp -> adp", fast=False, reversible=False,
reactants={"atp": 1}, products={"adp": 1}, compartment=compartment_id,
formula='Vmax_RATP * atp/(k_RATP + atp)')
# initial concentrations for fba exchange species
initial_c = {
'atp': 2.0,
'adp': 1.0,
'glc': 5.0,
'pyr': 0.0
}
for sid, value in initial_c.items():
species = model.getSpecies(sid)
species.setInitialConcentration(value)
# write SBML file
if annotations:
annotation.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
# change back the working dir
os.chdir(working_dir)