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
from models.liver.model_liver import create_model as create_liver_model
from models.kidney.model_kidney import create_model as create_kidney_model
from models.body.model_body import create_model as create_body_model
if __name__ == "__main__":
results_path = "./models"
# create tissue models
create_kidney_model(results_path)
create_liver_model(results_path)
# create whole-body model
[_, _, sbml_path] = create_body_model(results_path)
print(sbml_path)
assert os.path.exists(sbml_path)
sbml_path_flat = "./models/codeine_body_flat.xml"
import libsbml
doc = libsbml.readSBMLFromFile(
os.path.abspath(sbml_path)) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
## FIXME: not working with relative paths
flattenSBMLFile(os.path.abspath(sbml_path),
output_path=os.path.abspath(sbml_path_flat))
# create model report
sbmlreport.create_report(sbml_path_flat, "./models/")
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
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 = 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
###########################################
# Create single models
###########################################
model_factory.create_fba(fba_file)
model_factory.create_ode_bounds(ode_bounds_file)
model_factory.create_ode_update(ode_update_file)
model_factory.create_ode_model(ode_model_file)
###########################################
# Create top level model
###########################################
comp_factory.create_top_level_model(top_level_file)
# flatten the combined model
comp.flattenSBMLFile(top_level_file, output_file=flattened_file)
###########################################
# Simulate the comp models
###########################################
def simulate_model(tend=50.0, step_size=0.1):
# Run simulation of the hybrid model
from simsettings import top_level_file, out_dir
import timeit
# Simulate
simulator = Simulator(top_level_file=top_level_file)
start_time = timeit.default_timer()
df = simulator.simulate(tstart=0.0, tend=tend, step_size=step_size)
elapsed = timeit.default_timer() - start_time
# rbc
creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_rbc_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
# liver
creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_liver_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
# exit()
# create comp model
[_, _, body_path] = creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_pkpd_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
from pylimax.models.glucose_pkpd.glucose_pkpd_model import mid, version
flat_body_path = os.path.join(target_dir,
"{}_{}_flat.xml".format(mid, version))
flattenSBMLFile(body_path, output_path=flat_body_path)
# create model report
sbmlreport.create_sbml_report(flat_body_path, out_dir=target_dir)