def create_distrib(tmp=False):
""" Create demo model.
:return:
"""
factory = Factory(modules=['sbmlutils.examples.models.distrib.distrib_ex1'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create(tmp=False):
"""Create model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(modules=["model"], output_dir=os.path.join(models_dir, "results"))
factory.create(tmp)
def create_distrib(tmp=False):
""" Create demo model.
:return:
"""
factory = Factory(
modules=['sbmlutils.examples.models.distrib.distrib_ex1'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create(tmp=False):
""" Create model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(modules=['model'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create(tmp=False):
""" Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(modules=['sbmlutils.examples.models.example1.model'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create_distrib(tmp=False):
"""Create demo model.
:return:
"""
factory = Factory(
modules=["sbmlutils.examples.models.distrib.distrib_ex1"],
output_dir=os.path.join(models_dir, "results"),
)
factory.create(tmp)
def create(tmp=False):
"""Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(
modules=["sbmlutils.examples.models.example1.model"],
output_dir=os.path.join(models_dir, "results"),
)
factory.create(tmp)
def create(tmp=False):
""" Create model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-' * 80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.assignment.model'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create(tmp=False):
"""Create demo model.
:return:
"""
models_dir = Path(__file__).parent
factory = Factory(
modules=["sbmlutils.examples.models.tiny_model.model"],
output_dir=models_dir / "results",
annotations=models_dir / "annotations.xlsx",
)
factory.create(tmp)
def create(tmp=False):
"""Create model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print("-" * 80)
print(models_dir)
print("-" * 80)
factory = Factory(
modules=["sbmlutils.examples.models.assignment.model"],
output_dir=os.path.join(models_dir, "results"),
)
factory.create(tmp)
def create(tmp=False):
""" Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-'*80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'],
target_dir=os.path.join(models_dir, 'results'),
annotations=os.path.join(models_dir, 'annotations.xlsx'))
factory.create(tmp)
def create(tmp=False):
""" Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-' * 80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'],
target_dir=os.path.join(models_dir, 'results'),
annotations=os.path.join(models_dir, 'annotations.xlsx'))
factory.create(tmp)
def create(tmp=False):
""" Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(modules=['sbmlutils.examples.models.fbc.fbc_ex1'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
factory = Factory(modules=['sbmlutils.examples.models.fbc.fbc_ex2'],
target_dir=os.path.join(models_dir, 'results'))
factory.create(tmp)
def create(tmp=False):
"""Create demo model.
:return:
"""
models_dir = Path(__file__).parent
output_dir = models_dir / "results"
factory = Factory(modules=["sbmlutils.examples.models.fbc.fbc_ex1"],
output_dir=output_dir)
factory.create(tmp)
factory = Factory(modules=["sbmlutils.examples.models.fbc.fbc_ex2"],
output_dir=output_dir)
factory.create(tmp)
def create(tmp=False):
""" Create demo model.
:return:
"""
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-' * 80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.demo.model'],
target_dir=os.path.join(models_dir, 'results'),
annotations=os.path.join(models_dir,
'demo_annotations.xlsx'))
factory.create(tmp)
# without annotations
factory_no_annotations = Factory(
modules=['sbmlutils.examples.models.demo.model'],
target_dir=os.path.join(models_dir, 'results'),
mid="{}_{}_{}".format(model.mid, model.version, "no_annotations"))
factory_no_annotations.create(tmp)
])
# ---------------------------------------------------------------------------------------------------------------------
# Assignments
# ---------------------------------------------------------------------------------------------------------------------
assignments = [
InitialAssignment('S1', '10.0 mM', UNIT_mM),
]
# ---------------------------------------------------------------------------------------------------------------------
# Rules
# ---------------------------------------------------------------------------------------------------------------------
rules = []
# ---------------------------------------------------------------------------------------------------------------------
# Reactions
# ---------------------------------------------------------------------------------------------------------------------
reactions = [
]
if __name__ == "__main__":
import os
from sbmlutils.modelcreator.creator import Factory
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(modules=['sbmlutils.examples.models.example1.model'],
target_dir=os.path.join(models_dir, 'results'))
factory.create()
from matplotlib import pylab as plt
from sbmlutils.modelcreator.creator import Factory
import cobra
from cobra.io import read_sbml_model
# -----------------------------------------------------------------------------
# create model
# -----------------------------------------------------------------------------
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-' * 80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'],
target_dir=os.path.join(models_dir, 'results'),
annotations=os.path.join(models_dir, 'annotations.xlsx'))
_, _, tiny_sbml = factory.create(tmp=False)
# -----------------------------------------------------------------------------
# run ode simulation
# -----------------------------------------------------------------------------
# tiny_sbml = os.path.join(os.path.dirname(os.path.abspath(__file__)),
# 'results',
# '{}_{}.xml'.format(model.mid, model.version))
r = roadrunner.RoadRunner(tiny_sbml)
r.timeCourseSelections = [
"time"
] + r.model.getBoundarySpeciesIds() + r.model.getFloatingSpeciesIds(
) + r.model.getReactionIds() + r.model.getGlobalParameterIds()
def create(tmp: bool = False) -> None:
factory = Factory(
modules=["sbmlutils.examples.models.boundary_condition_2.model"],
output_dir=Path(__file__).parent / "results",
)
factory.create(tmp)
# ---------------------------------------------------------------------------------------------------------------------
# Assignments
# ---------------------------------------------------------------------------------------------------------------------
assignments = [
InitialAssignment("S1", "10.0 mM", UNIT_mM),
]
# ---------------------------------------------------------------------------------------------------------------------
# Rules
# ---------------------------------------------------------------------------------------------------------------------
rules = []
# ---------------------------------------------------------------------------------------------------------------------
# Reactions
# ---------------------------------------------------------------------------------------------------------------------
reactions = []
if __name__ == "__main__":
import os
from sbmlutils.modelcreator.creator import Factory
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
factory = Factory(
modules=["sbmlutils.examples.models.example1.model"],
output_dir=os.path.join(models_dir, "results"),
)
factory.create()
#
# The list of tuples can be provided on object generation
#
# ```
# Species(sid='e__gal', compartment='ext', initialConcentration=3.0,
# substanceUnit=UNIT_KIND_MOLE, boundaryCondition=True,
# name='D-galactose', sboTerm=SBO_SIMPLE_CHEMICAL,
# annotations=[
# (BQB.IS, "bigg.metabolite/gal"), # galactose
# (BQB.IS, "chebi/CHEBI:28061"), # alpha-D-galactose
# (BQB.IS, "vmhmetabolite/gal"),
# ]
# ),
# ```
#
# For the full example see [model_with_annotations.py](./model_with_annotations.py)
# In[4]:
import os
from sbmlutils.modelcreator.creator import Factory
factory = Factory(modules=['model_with_annotations'], target_dir='./models')
[_, _, sbml_path] = factory.create()
# check the annotations on the species
import libsbml
doc = libsbml.readSBMLFromFile(sbml_path) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
s1 = model.getSpecies('e__gal') # type: libsbml.Species
print(s1.toSBML())
from matplotlib import pylab as plt
from sbmlutils.modelcreator.creator import Factory
import cobra
from cobra.io import read_sbml_model
# -----------------------------------------------------------------------------
# create model
# -----------------------------------------------------------------------------
models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
print('-'*80)
print(models_dir)
print('-' * 80)
factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'],
target_dir=os.path.join(models_dir, 'results'),
annotations=os.path.join(models_dir, 'annotations.xlsx'))
_, _, tiny_sbml = factory.create(tmp=False)
# -----------------------------------------------------------------------------
# run ode simulation
# -----------------------------------------------------------------------------
# tiny_sbml = os.path.join(os.path.dirname(os.path.abspath(__file__)),
# 'results',
# '{}_{}.xml'.format(model.mid, model.version))
r = roadrunner.RoadRunner(tiny_sbml)
r.timeCourseSelections = ["time"] + r.model.getBoundarySpeciesIds() + r.model.getFloatingSpeciesIds() + r.model.getReactionIds() + r.model.getGlobalParameterIds()
r.timeCourseSelections += ["[{}]".format(key) for key in r.model.getFloatingSpeciesIds()]
def create(tmp: bool = False) -> None:
factory = Factory(
modules=["sbmlutils.examples.models.initial_assignment.model"],
output_dir=Path(__file__).parent / "results",
)
factory.create(tmp)
from sbmlutils.examples.models.tiny_model import model as model_definition
from sbmlutils.fbc.cobra import read_cobra_model
from sbmlutils.modelcreator.creator import Factory
# -----------------------------------------------------------------------------
# create model
# -----------------------------------------------------------------------------
tiny_dir = Path(__file__).parent
print("-" * 80)
print(tiny_dir)
print("-" * 80)
factory = Factory(
modules=["sbmlutils.examples.models.tiny_model.model"],
output_dir=tiny_dir / "results",
annotations=tiny_dir / "annotations.xlsx",
)
_, _, tiny_sbml = factory.create(tmp=False)
# -----------------------------------------------------------------------------
# run ode simulation
# -----------------------------------------------------------------------------
# tiny_sbml = os.path.join(os.path.dirname(os.path.abspath(__file__)),
# 'results',
# '{}_{}.xml'.format(model.mid, model.version))
r = roadrunner.RoadRunner(str(tiny_sbml))
r.timeCourseSelections = (["time"] + r.model.getBoundarySpeciesIds() +
r.model.getFloatingSpeciesIds() +
r.model.getReactionIds() +