SBML creator

sbmlutils provides helpers for the creation of SBML models from scratch.

Create FBA Model

This example demonstrates the creation of an SBML FBA model from scratch.



In [1]:

    
from sbmlutils import comp
from sbmlutils import fbc
from sbmlutils import sbmlio
from sbmlutils import factory
from sbmlutils.dfba import builder

from sbmlutils.units import *
from sbmlutils.annotation.sbo import *
from sbmlutils.factory import *

Unit definitions

Units for the model are defined in the following manner.



In [2]:

    
model_units = ModelUnits(time=UNIT_KIND_SECOND, 
                         extent=UNIT_KIND_ITEM, 
                         substance=UNIT_KIND_ITEM, 
                         length=UNIT_KIND_METRE,
                         area='m2', 
                         volume='m3')

units = [
    Unit('kg', [(UNIT_KIND_KILOGRAM, 1.0)]),
    Unit('m2', [(UNIT_KIND_METRE, 2.0)]),
    Unit('m3', [(UNIT_KIND_METRE, 3.0)]),
    Unit('mM', [(UNIT_KIND_MOLE, 1.0, 0),
                   (UNIT_KIND_METRE, -3.0)]),
    Unit('per_s', [(UNIT_KIND_SECOND, -1.0)]),
    Unit('item_per_s', [(UNIT_KIND_ITEM, 1.0),
                           (UNIT_KIND_SECOND, -1.0)]),
    Unit('item_per_m3', [(UNIT_KIND_ITEM, 1.0),
                            (UNIT_KIND_METRE, -3.0)]),
]

# constants for reuse
UNIT_TIME = UNIT_KIND_SECOND
UNIT_AMOUNT = UNIT_KIND_ITEM
UNIT_AREA = 'm2'
UNIT_VOLUME = 'm3'
UNIT_CONCENTRATION = 'item_per_m3'
UNIT_FLUX = 'item_per_s'

Model building

Creation of FBA model using multiple packages (comp, fbc).



In [5]:

    
# Create SBMLDocument with fba
doc = builder.template_doc_fba(model_id="toy")
model = doc.getModel()

factory.create_objects(model, units)
factory.set_model_units(model, model_units)

objects = [
    # compartments
    Compartment(sid='extern', value=1.0, unit=UNIT_VOLUME, constant=True, name='external compartment',
                   spatialDimensions=3),
    Compartment(sid='cell', value=1.0, unit=UNIT_VOLUME, constant=True, name='cell', spatialDimensions=3),
    Compartment(sid='membrane', value=1.0, unit=UNIT_AREA, constant=True, name='membrane', spatialDimensions=2),

    # exchange species
    Species(sid='A', name="A", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
               compartment="extern"),
    Species(sid='C', name="C", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
               compartment="extern"),

    # internal species
    Species(sid='B1', name="B1", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
               compartment="cell"),
    Species(sid='B2', name="B2", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
               compartment="cell"),

    # bounds
    Parameter(sid="ub_R1", value=1.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
    Parameter(sid="zero", value=0.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
    Parameter(sid="ub_default", value=builder.UPPER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True,
                 sboTerm=builder.FLUX_BOUND_SBO),
    
    # reactions
    Reaction(sid="R1", name="A import (R1)",
             equation="A <-> B1", compartment='membrane', lowerFluxBound="zero", upperFluxBound="ub_R1"),
    Reaction(sid="R2", name="B1 <-> B2 (R2)",
             equation="B1 <-> B2", compartment='cell',
             lowerFluxBound="zero", upperFluxBound="ub_default"),
    Reaction(sid="R3", name="B2 export (R3)", fast=False, reversible=True,
             equation="B2 <-> C", compartment='membrane',
             lowerFluxBound="zero", upperFluxBound="ub_default"
    ),
    
]
factory.create_objects(model, objects)

# exchange reactions
builder.create_exchange_reaction(model, species_id="A", flux_unit=UNIT_FLUX)
builder.create_exchange_reaction(model, species_id="C", flux_unit=UNIT_FLUX)

# objective function
model_fbc = model.getPlugin("fbc")
fbc.create_objective(model_fbc, oid="R3_maximize", otype="maximize",
                    fluxObjectives={"R3": 1.0}, active=True)

# write SBML file
import tempfile
sbml_file = tempfile.NamedTemporaryFile(suffix=".xml")
sbmlio.write_sbml(doc=doc, filepath=sbml_file.name)









    




--------------------------------------------------------------------------------
/tmp/tmpdfc9h_4w.xml
valid                    : TRUE
check time (s)           : 0.008
--------------------------------------------------------------------------------



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