def test_toy_wholecell_simulation(self):
toyfactory.create_model(self.test_dir)
sbml_path = os.path.join(versioned_directory(self.test_dir, settings.VERSION),
settings.TOP_LOCATION)
print(sbml_path)
toysimulate.simulate_toy(sbml_path, self.test_dir, dts=[1.0], figures=False)
def test_diauxic_simulation(self):
dgfactory.create_model(self.test_dir)
sbml_path = os.path.join(versioned_directory(self.test_dir, dgsettings.VERSION),
dgsettings.TOP_LOCATION)
print(sbml_path)
dgsimulate.simulate_diauxic_growth(sbml_path, self.test_dir, dts=[0.01],
figures=False)
def test_toy_atp_simulation(self):
atpfactory.create_model(self.test_dir)
sbml_path = os.path.join(
versioned_directory(self.test_dir, atpsettings.VERSION),
atpsettings.TOP_LOCATION)
print(sbml_path)
atpsimulate.simulate_toy_atp(sbml_path,
self.test_dir,
dts=[1.0],
figures=False)
def test_validate_toy(self):
""" Validate the toy model. """
sbml_path = os.path.join(utils.versioned_directory(toysettings.OUT_DIR, toyfactory.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
# df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
validator.validate_dfba(sbml_path)
assert False
def test_validate_toy(self):
""" Validate the toy model. """
sbml_path = os.path.join(
utils.versioned_directory(toysettings.OUT_DIR, toyfactory.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
# df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
validator.validate_dfba(sbml_path)
assert False
def create_model(output_dir):
""" Create all submodels and comp model.
:param output_dir: results directory
:rtype:
:return directory in which model files exist.
"""
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'annotations.xlsx')
annotations = annotation.ModelAnnotator.annotations_from_file(f_annotations)
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION, directory, annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba, annotations=annotations)
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['atp', 'adp', 'glc', 'pyr'])
reaction_ids = ", ".join(['EX_atp', 'EX_adp', 'EX_glc', 'EX_pyr', 'RATP'])
create_sedml(settings.SEDML_LOCATION, settings.TOP_LOCATION, directory=directory,
dt=0.1, tend=15, species_ids=species_ids, reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all submodels and comp model.
:param output_dir: results directory
:rtype:
:return directory in which model files exist.
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)),
settings.ANNOTATIONS_LOCATION)
annotations = annotator.ModelAnnotator.read_annotations(f_annotations)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION, directory, annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba, annotations=annotations)
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['A', 'C', 'D'])
reaction_ids = ", ".join(['R4', 'EX_A', 'EX_C'])
create_sedml(settings.SEDML_LOCATION, settings.TOP_LOCATION, directory=directory,
dt=0.1, tend=50, species_ids=species_ids, reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all models.
:return:
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)), settings.ANNOTATIONS_LOCATION)
annotations = annotation.ModelAnnotator.annotations_from_file(f_annotations)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION, directory, annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
emds = {
"diauxic_fba": settings.FBA_LOCATION,
"diauxic_bounds": settings.BOUNDS_LOCATION,
"diauxic_update": settings.UPDATE_LOCATION,
}
top_model(settings.TOP_LOCATION, directory, emds, doc_fba=doc_fba, annotations=annotations)
# flatten top model
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['Ac', 'Glcxt', 'O2', 'X'])
reaction_ids = ", ".join(['vO2_transfer', 'EX_Ac', 'EX_Glcxt', 'EX_O2', 'EX_X'])
create_sedml(settings.SEDML_LOCATION, settings.TOP_LOCATION, directory=directory,
dt=0.01, tend=15, species_ids=species_ids, reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
print("FBA")
doc_fba = fba_model(settings.FBA_LOCATION, directory)
print("BOUNDS")
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
print("UPDATE")
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
print("TOP")
top_model(settings.TOP_LOCATION,
directory,
emds,
doc_fba=doc_fba,
validate=True)
# flatten top model
print("FLATTENING")
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
# create report
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
return directory
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
print("FBA")
doc_fba = fba_model(settings.FBA_LOCATION, directory)
print("BOUNDS")
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
print("UPDATE")
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
print("TOP")
top_model(settings.TOP_LOCATION, directory, emds, doc_fba=doc_fba, validate=False)
# flatten top model
print("FLATTENING")
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
# create report
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
return directory
if figures:
analysis.plot_reactions(os.path.join(out_dir, "fig_reactions_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.plot_species(os.path.join(out_dir, "fig_species_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.save_csv(os.path.join(out_dir, "data_simulation_generic_dt{}.csv".format(dt)))
# custom model plots
if figures:
print_species(dfs=dfs, filepath=os.path.join(out_dir, "fig_species.png"), **plot_kwargs)
print_fluxes(dfs=dfs, filepath=os.path.join(out_dir, "fig_fluxes.png"), **plot_kwargs)
return dfs
if __name__ == "__main__":
directory = versioned_directory(settings.OUT_DIR, settings.VERSION)
sbml_path = os.path.join(directory, settings.TOP_LOCATION)
# logging.basicConfig(level=logging.DEBUG)
from sbmlutils.dfba.model import DFBAModel
dfba_model = DFBAModel(sbml_path=sbml_path)
# simulate_toy(sbml_path, out_dir=directory, dts=[5.0], tend=10)
simulate_toy(sbml_path, out_dir=directory, ode_integrator="gillespie")
# create COMBINE archive
from tellurium.utils import omex
creators = [
from sbmlutils import dfba
from sbmlutils.dfba import utils
# ## Simulate DFBA model
# To run an existing DFBA model call use `simulate_dfba`.
# In[3]:
# get the absolute path to the top model
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
sbml_path = os.path.join(utils.versioned_directory(toysettings.OUT_DIR, toysettings.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
from sbmlutils.dfba.simulator import simulate_dfba
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
df
# ## Toy example
# In[4]:
from sbmlutils.dfba.toy_wholecell import settings as toysettings
def test_toy_atp_simulation(self):
atpfactory.create_model(self.test_dir)
sbml_path = os.path.join(versioned_directory(self.test_dir, atpsettings.VERSION),
atpsettings.TOP_LOCATION)
print(sbml_path)
atpsimulate.simulate_toy_atp(sbml_path, self.test_dir, dts=[1.0], figures=False)
def create_model(output_dir):
""" Create all models.
:return:
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)),
settings.ANNOTATIONS_LOCATION)
annotations = annotator.ModelAnnotator.annotations_from_file(f_annotations)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION,
directory,
annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION,
directory,
doc_fba=doc_fba,
annotations=annotations)
update_model(settings.UPDATE_LOCATION,
directory,
doc_fba=doc_fba,
annotations=annotations)
emds = {
"diauxic_fba": settings.FBA_LOCATION,
"diauxic_bounds": settings.BOUNDS_LOCATION,
"diauxic_update": settings.UPDATE_LOCATION,
}
top_model(settings.TOP_LOCATION,
directory,
emds,
doc_fba=doc_fba,
annotations=annotations)
# flatten top model
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['Ac', 'Glcxt', 'O2', 'X'])
reaction_ids = ", ".join(
['vO2_transfer', 'EX_Ac', 'EX_Glcxt', 'EX_O2', 'EX_X'])
create_sedml(settings.SEDML_LOCATION,
settings.TOP_LOCATION,
directory=directory,
dt=0.01,
tend=15,
species_ids=species_ids,
reaction_ids=reaction_ids)
return directory
import sbmlutils
from sbmlutils import dfba
from sbmlutils.dfba import utils
# ## Simulate DFBA model
# To run an existing DFBA model call use `simulate_dfba`.
# In[3]:
# get the absolute path to the top model
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
sbml_path = os.path.join(
utils.versioned_directory(toysettings.OUT_DIR, toysettings.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
from sbmlutils.dfba.simulator import simulate_dfba
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
df
# ## Toy example
# In[4]:
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
**plot_kwargs)
analysis.save_csv(
os.path.join(out_dir,
"data_simulation_generic_dt{}.csv".format(dt)))
# custom model plots
if figures:
print_species(dfs=dfs,
filepath=os.path.join(out_dir, "fig_species.png"),
**plot_kwargs)
# print_fluxes(dfs=dfs, filepath=os.path.join(out_dir, "fig_fluxes.png"), **plot_kwargs)
return dfs
if __name__ == "__main__":
directory = versioned_directory(settings.OUT_DIR, settings.VERSION)
sbml_path = os.path.join(directory, settings.TOP_LOCATION)
import logging
# logging.basicConfig(level=logging.DEBUG)
from sbmlutils.dfba.model import DFBAModel
dfba_model = DFBAModel(sbml_path=sbml_path)
# simulate_toy(sbml_path, out_dir=directory, dts=[5.0], tend=10)
simulate_toy_atp(sbml_path, out_dir=directory)
# create COMBINE archive
from tellurium.utils import omex
creators = [
omex.Creator(givenName="Matthias",
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
# create sbml
import time
t_start = time.time()
doc_fba = fba_model(settings.FBA_LOCATION, directory)
t_fba = time.time()
print('{:<10}: {:3.2f}'.format('fba', t_fba-t_start))
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
t_bounds = time.time()
print('{:<10}: {:3.2f}'.format('bounds', t_bounds-t_fba))
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
t_update = time.time()
print('{:<10}: {:3.2f}'.format('update', t_update-t_bounds))
emds = {
"ecoli_fba": settings.FBA_LOCATION,
"ecoli_bounds": settings.BOUNDS_LOCATION,
"ecoli_update": settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba=doc_fba)
t_top = time.time()
print('{:<10}: {:3.2f}'.format('top', t_top-t_update))
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
t_flat = time.time()
print('{:<10}: {:3.2f}'.format('flat', t_flat-t_top))
# create reports
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_sbml_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
sids = ['ac_e', 'acald_e', 'akg_e', 'co2_e', 'etoh_e', 'for_e', 'fru_e', 'fum_e', 'glc__D_e',
'gln__L_e', 'glu__L_e', 'h_e', 'h2o_e', 'lac__D_e', 'mal__L_e', 'nh4_e', 'o2_e', 'pi_e',
'pyr_e', 'succ_e', 'X']
species_ids = ", ".join(sids)
reaction_ids = ", ".join(['EX_{}'.format(sid) for sid in sids])
create_sedml(settings.SEDML_LOCATION, settings.TOP_LOCATION, directory=directory,
dt=0.01, tend=3.5, species_ids=species_ids, reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
# create sbml
import time
t_start = time.time()
doc_fba = fba_model(settings.FBA_LOCATION, directory)
t_fba = time.time()
print('{:<10}: {:3.2f}'.format('fba', t_fba - t_start))
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
t_bounds = time.time()
print('{:<10}: {:3.2f}'.format('bounds', t_bounds - t_fba))
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
t_update = time.time()
print('{:<10}: {:3.2f}'.format('update', t_update - t_bounds))
emds = {
"ecoli_fba": settings.FBA_LOCATION,
"ecoli_bounds": settings.BOUNDS_LOCATION,
"ecoli_update": settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba=doc_fba)
t_top = time.time()
print('{:<10}: {:3.2f}'.format('top', t_top - t_update))
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
t_flat = time.time()
print('{:<10}: {:3.2f}'.format('flat', t_flat - t_top))
# create reports
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
sids = [
'ac_e', 'acald_e', 'akg_e', 'co2_e', 'etoh_e', 'for_e', 'fru_e',
'fum_e', 'glc__D_e', 'gln__L_e', 'glu__L_e', 'h_e', 'h2o_e',
'lac__D_e', 'mal__L_e', 'nh4_e', 'o2_e', 'pi_e', 'pyr_e', 'succ_e', 'X'
]
species_ids = ", ".join(sids)
reaction_ids = ", ".join(['EX_{}'.format(sid) for sid in sids])
create_sedml(settings.SEDML_LOCATION,
settings.TOP_LOCATION,
directory=directory,
dt=0.01,
tend=3.5,
species_ids=species_ids,
reaction_ids=reaction_ids)
return directory
