def create_module(sbml_model_file, model_name, model_output_dir):
"""Create Python module from SBML model
Arguments:
sbml_model_file: SBML file
model_name: Name of the model
model_output_dir: Directory for model code
Returns:
list of parameters,
dictionary with observables (id: formula)
"""
sbml_importer = amici.SbmlImporter(sbml_model_file)
sbml_model = sbml_importer.sbml
observables = petab.get_observables(sbml_model, remove=True)
sigmas = petab.get_sigmas(sbml_model, remove=True)
fixed_parameters = ['k0']
sbml_importer.sbml2amici(modelName=model_name,
output_dir=model_output_dir,
observables=observables,
constantParameters=fixed_parameters,
sigmas=sigmas)
return fixed_parameters, observables
def simulate_AMICI(sbml_name: str):
"""
Compiles, simulates and plots the SBML in AMICI.
:param yaml_name:
:return:
"""
model_name = os.path.splitext(sbml_name)[0]
model_output_dir = 'AMICI_models'
sbml_importer = amici.SbmlImporter(sbml_name)
sbml_importer.sbml2amici(model_name, model_output_dir)
# import model
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = importlib.import_module(model_name)
# create model + solver instance
amici_model = model_module.getModel()
solver = amici_model.getSolver()
# Define time points ans run simulation using default model parameters/solver options
amici_model.setTimepoints(np.linspace(0, 5, 101))
rdata = amici.runAmiciSimulation(amici_model, solver)
return amici_model, rdata
def load_model_objective(example_name):
# name of the model that will also be the name of the python module
model_name = 'model_' + example_name
# sbml file
sbml_file = os.path.join('doc', 'example', example_name,
model_name + '.xml')
# directory to which the generated model code is written
model_output_dir = os.path.join('doc', 'example', 'tmp', model_name)
# import sbml model, compile and generate amici module
sbml_importer = amici.SbmlImporter(sbml_file)
sbml_importer.sbml2amici(model_name, model_output_dir, verbose=False)
# load amici module (the usual starting point later for the analysis)
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = importlib.import_module(model_name)
model = model_module.getModel()
model.requireSensitivitiesForAllParameters()
model.setTimepoints(np.linspace(0, 10, 11))
model.setParameterScale(amici.ParameterScaling_log10)
model.setParameters([-0.3, -0.7])
solver = model.getSolver()
solver.setSensitivityMethod(amici.SensitivityMethod_forward)
solver.setSensitivityOrder(amici.SensitivityOrder_first)
# generate experimental data
rdata = amici.runAmiciSimulation(model, solver, None)
edata = amici.ExpData(rdata, 0.05, 0.0)
return (pypesto.AmiciObjective(model, solver, [edata], 2), model)
def sbml_example_presimulation_module():
"""SBML example_presimulation model module fixture"""
sbml_file = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
constant_parameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbml_importer.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir = 'test_model_presimulation'
module_name = 'test_model_presimulation'
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
verbose=False,
observables=observables,
constant_parameters=constant_parameters)
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)
yield model_module
shutil.rmtree(outdir, ignore_errors=True)
def setUp(self):
self.default_path = copy.copy(sys.path)
self.resetdir = os.getcwd()
if os.path.dirname(__file__) != '':
os.chdir(os.path.dirname(__file__))
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
constantParameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT'
)
outdir = 'test_model_presimulation'
sbmlImporter.sbml2amici('test_model_presimulation',
outdir,
verbose=False,
observables=observables,
constantParameters=constantParameters)
sys.path.insert(0, outdir)
import test_model_presimulation as modelModule
self.model = modelModule.getModel()
self.model.setTimepoints(np.linspace(0, 60, 61))
self.solver = self.model.getSolver()
rdata = amici.runAmiciSimulation(self.model, self.solver)
self.edata = [amici.ExpData(rdata, 0.01, 0)]
# test copy constructor
self.edata_copy = amici.ExpData(self.edata[0])
def test_presimulation(self):
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
constantParameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT')
outdir = 'test_model_presimulation'
sbmlImporter.sbml2amici('test_model_presimulation',
outdir,
verbose=False,
observables=observables,
constantParameters=constantParameters)
sys.path.insert(0, outdir)
import test_model_presimulation as modelModule
model = modelModule.getModel()
solver = model.getSolver()
model.setTimepoints(amici.DoubleVector(np.linspace(0, 60, 61)))
model.setReinitializeFixedParameterInitialStates(True)
rdata = amici.runAmiciSimulation(model, solver)
edata = amici.ExpData(rdata, 0.1, 0.0)
edata.fixedParameters = amici.DoubleVector([10, 2])
edata.fixedParametersPresimulation = amici.DoubleVector([10, 2])
edata.fixedParametersPreequilibration = amici.DoubleVector([3, 0])
self.assertIsInstance(amici.runAmiciSimulation(model, solver, edata),
dict)
def model_steadystate_module():
sbml_file = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
observables = amici.assignmentRules2observables(
sbml_importer.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
outdir = 'test_model_steadystate_scaled'
module_name = 'test_model_steadystate_scaled'
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
observables=observables,
constant_parameters=['k0'],
sigmas={'observable_x1withsigma': 'observable_x1withsigma_sigma'})
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)
yield model_module
shutil.rmtree(outdir, ignore_errors=True)
def model_units_module():
sbml_file = os.path.join(os.path.dirname(__file__), '..', 'examples',
'example_units', 'model_units.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
outdir = 'test_model_units'
module_name = 'test_model_units'
sbml_importer.sbml2amici(model_name=module_name, output_dir=outdir)
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)
yield model_module
shutil.rmtree(outdir, ignore_errors=True)
def model_test_likelihoods():
sbml_file = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
observables = amici.assignmentRules2observables(
sbml_importer.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
# assign different noise models
obs_keys = list(observables.keys())
# exponentiate observable formulas
obs1 = observables[obs_keys[1]]
obs3 = observables[obs_keys[3]]
obs1['formula'] = '10^(' + obs1['formula'] + ')'
obs3['formula'] = 'exp(' + obs3['formula'] + ')'
# customize noise distributions
noise_distributions = {
obs_keys[0]: 'normal',
obs_keys[1]: 'log-normal',
obs_keys[2]: 'laplace',
obs_keys[3]: 'log10-laplace',
}
module_name = 'test_likelihoods'
outdir = 'test_likelihoods'
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
observables=observables,
constant_parameters=['k0'],
sigmas={'observable_x1withsigma':
'observable_x1withsigma_sigma'},
noise_distributions=noise_distributions
)
yield amici.import_model_module(module_name=module_name,
module_path=outdir)
shutil.rmtree(outdir, ignore_errors=True)
def generate_models():
# SBML model we want to import
sbml_file = os.path.join(os.path.dirname(__file__), '..', 'examples',
'example_constant_species',
'model_constant_species.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
# Name of the model that will also be the name of the python module
model_name = model_output_dir = 'model_constant_species'
model_name_cl = model_output_dir_cl = 'model_constant_species_cl'
# Define constants, observables, sigmas
constant_parameters = ['synthesis_substrate', 'init_enzyme']
observables = {
'observable_product': {
'name': '',
'formula': 'product'
},
'observable_substrate': {
'name': '',
'formula': 'substrate'
},
}
sigmas = {'observable_product': 1.0, 'observable_substrate': 1.0}
# wrap models with and without conservations laws
sbml_importer.sbml2amici(model_name_cl,
model_output_dir_cl,
observables=observables,
constant_parameters=constant_parameters,
sigmas=sigmas)
sbml_importer.sbml2amici(model_name,
model_output_dir,
observables=observables,
constant_parameters=constant_parameters,
sigmas=sigmas,
compute_conservation_laws=False)
# load both models
model_without_cl_module = amici.import_model_module(
model_name, module_path=os.path.abspath(model_name))
model_with_cl_module = amici.import_model_module(
model_name_cl, module_path=os.path.abspath(model_name_cl))
# get the models and return
model_without_cl = model_without_cl_module.getModel()
model_with_cl = model_with_cl_module.getModel()
return model_with_cl, model_without_cl
def test_presimulation(self):
def assert_fun(x):
return self.assertTrue(x)
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
constantParameters = ['DRUG_0', 'KIN_0']
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir = 'test_model_presimulation'
sbmlImporter.sbml2amici('test_model_presimulation',
outdir,
verbose=False,
observables=observables,
constantParameters=constantParameters)
sys.path.insert(0, outdir)
import test_model_presimulation as modelModule
model = modelModule.getModel()
solver = model.getSolver()
solver.setNewtonMaxSteps(0)
model.setTimepoints(np.linspace(0, 60, 61))
model.setSteadyStateSensitivityMode(
amici.SteadyStateSensitivityMode_simulationFSA
)
solver.setSensitivityOrder(amici.SensitivityOrder_first)
model.setReinitializeFixedParameterInitialStates(True)
rdata = amici.runAmiciSimulation(model, solver)
edata = amici.ExpData(rdata, 0.1, 0.0)
edata.fixedParameters = [10, 2]
edata.fixedParametersPresimulation = [10, 2]
edata.fixedParametersPreequilibration = [3, 0]
self.assertIsInstance(
amici.runAmiciSimulation(model, solver, edata),
amici.ReturnDataView)
solver.setRelativeTolerance(1e-12)
solver.setAbsoluteTolerance(1e-12)
check_derivatives(model, solver, edata, assert_fun, epsilon=1e-4)
def compile_model(self):
"""
Compile the model. If the output folder exists already, it is first
deleted.
"""
# check prerequisites
if not petab.condition_table_is_parameter_free(
self.petab_problem.condition_df):
raise AssertionError(
"Parameter dependent conditions in the condition file "
"are not yet supported.")
# delete output directory
if os.path.exists(self.output_folder):
shutil.rmtree(self.output_folder)
# constant parameters
condition_columns = self.petab_problem.condition_df.columns.values
constant_parameter_ids = list(
set(condition_columns) - {'conditionId', 'conditionName'})
# observables
observables = self.petab_problem.get_observables()
# sigmas
sigmas = self.petab_problem.get_sigmas(remove=True)
# noise distributions
noise_distrs = _to_amici_noise_distributions(
self.petab_problem.get_noise_distributions())
# model to string
sbml_string = libsbml.SBMLWriter().writeSBMLToString(
self.petab_problem.sbml_document)
# init sbml importer
sbml_importer = amici.SbmlImporter(sbml_string, from_file=False)
# convert
sbml_importer.sbml2amici(modelName=self.model_name,
output_dir=self.output_folder,
observables=observables,
constantParameters=constant_parameter_ids,
sigmas=sigmas,
noise_distributions=noise_distrs)
def test_sympy_exp_monkeypatch():
"""
This model contains a removeable discontinuity at t=0 that requires
monkeypatching sympy.Pow._eval_derivative in order to be able to compute
non-nan sensitivities
"""
url = 'https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000529.2?' \
'filename=BIOMD0000000529_url.xml'
importer = amici.SbmlImporter(urlopen(url).read().decode('utf-8'),
from_file=False)
module_name = 'BIOMD0000000529'
outdir = 'BIOMD0000000529'
importer.sbml2amici(module_name, outdir)
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)
model = model_module.getModel()
model.setTimepoints(np.linspace(0, 8, 250))
model.requireSensitivitiesForAllParameters()
model.setAlwaysCheckFinite(True)
model.setParameterScale(
amici.parameterScalingFromIntVector([
amici.ParameterScaling.none
if re.match(r'n[0-9]+$', par_id) else amici.ParameterScaling.log10
for par_id in model.getParameterIds()
]))
solver = model.getSolver()
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
rdata = amici.runAmiciSimulation(model, solver)
# print sensitivity-related results
assert rdata['status'] == amici.AMICI_SUCCESS
check_derivatives(model,
solver,
None,
assert_fun,
atol=1e-2,
rtol=1e-2,
epsilon=1e-3)
def compile_model(path, test_id, model_dir):
"""Import the given test model to AMICI"""
sbml_file = find_model_file(path, test_id)
wrapper = amici.SbmlImporter(sbml_file)
if not os.path.exists(model_dir):
os.makedirs(model_dir)
model_name = 'SBMLTest' + test_id
wrapper.sbml2amici(model_name, output_dir=model_dir,
generate_sensitivity_code=False)
# settings
model_module = amici.import_model_module(model_name, model_dir)
model = model_module.getModel()
solver = model.getSolver()
return model, solver, wrapper
def model_test_likelihoods():
"""Test model for various likelihood functions."""
# load sbml model
sbml_file = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
# define observables
observables = {
'o1': {'formula': 'x1'},
'o2': {'formula': '10^x1'},
'o3': {'formula': '10^x1'},
'o4': {'formula': 'x1'},
'o5': {'formula': '10^x1'},
'o6': {'formula': '10^x1'},
'o7': {'formula': 'x1'}
}
# define different noise models
noise_distributions = {
'o1': 'normal', 'o2': 'log-normal', 'o3': 'log10-normal',
'o4': 'laplace', 'o5': 'log-laplace', 'o6': 'log10-laplace',
'o7': lambda str_symbol: f'Abs({str_symbol} - m{str_symbol}) '
f'/ sigma{str_symbol}',
}
module_name = 'test_likelihoods'
outdir = 'test_likelihoods'
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
observables=observables,
constant_parameters=['k0'],
noise_distributions=noise_distributions,
)
yield amici.import_model_module(module_name=module_name,
module_path=outdir)
shutil.rmtree(outdir, ignore_errors=True)
def compile_model(path, test_id):
"""Import the given test model to AMICI"""
sbml_file = find_model_file(path, test_id)
wrapper = amici.SbmlImporter(sbml_file)
model_dir = os.path.join(os.path.dirname(__file__), 'SBMLTestModels',
test_id)
if not os.path.exists(model_dir):
os.makedirs(model_dir)
model_name = 'SBMLTest' + test_id
wrapper.sbml2amici(model_name, output_dir=model_dir)
# settings
sys.path.insert(0, model_dir)
model_module = importlib.import_module(model_name)
model = model_module.getModel()
solver = model.getSolver()
return model, solver, wrapper
def model_special_likelihoods():
"""Test model for special likelihood functions."""
# load sbml model
sbml_file = os.path.join(os.path.dirname(__file__), '..', 'examples',
'example_steadystate',
'model_steadystate_scaled.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
# define observables
observables = {
'o1': {
'formula': '100*10^x1'
},
'o2': {
'formula': '100*10^x1'
},
}
# define different noise models
noise_distributions = {
'o1': 'binomial',
'o2': 'negative-binomial',
}
module_name = 'test_special_likelihoods'
outdir = 'test_special_likelihoods'
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
observables=observables,
constant_parameters=['k0'],
noise_distributions=noise_distributions,
)
yield amici.import_model_module(module_name=module_name,
module_path=outdir)
shutil.rmtree(outdir, ignore_errors=True)
def test_likelihoods_error():
"""Test whether wrong inputs lead to expected errors."""
sbml_file = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbml_importer = amici.SbmlImporter(sbml_file)
# define observables
observables = {'o1': {'formula': 'x1'}}
# define different noise models
noise_distributions = {'o1': 'nörmal'}
module_name = 'test_likelihoods'
outdir = 'test_likelihoods'
with pytest.raises(ValueError):
sbml_importer.sbml2amici(
model_name=module_name,
output_dir=outdir,
observables=observables,
constant_parameters=['k0'],
noise_distributions=noise_distributions,
)
def compile_model(self):
"""
Compile the model. If the output folder exists already, it is first
deleted.
"""
# check prerequisites
if not petab.condition_table_is_parameter_free(
self.petab_problem.condition_df):
raise AssertionError(
"Parameter dependent conditions in the condition file "
"are not yet supported.")
# delete output directory
if os.path.exists(self.output_folder):
shutil.rmtree(self.output_folder)
# init sbml importer
sbml_importer = amici.SbmlImporter(self.petab_problem.sbml_file)
# constant parameters
condition_columns = self.petab_problem.condition_df.columns.values
constant_parameter_ids = list(
set(condition_columns) - {'conditionId', 'conditionName'})
# observables
observables = petab.get_observables(sbml_importer.sbml)
# sigmas
sigmas = petab.get_sigmas(sbml_importer.sbml)
# convert
sbml_importer.sbml2amici(modelName=self.petab_problem.model_name,
output_dir=self.output_folder,
observables=observables,
constantParameters=constant_parameter_ids,
sigmas=sigmas)
def test_likelihoods(self):
"""
Test the custom noise distributions used to define cost functions.
"""
def assert_fun(x):
return self.assertTrue(x)
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
# assign different noise models
obs_keys = list(observables.keys())
# exponentiate observable formulas
obs1 = observables[obs_keys[1]]
obs3 = observables[obs_keys[3]]
obs1['formula'] = '10^(' + obs1['formula'] + ')'
obs3['formula'] = 'exp(' + obs3['formula'] + ')'
# customize noise distributions
noise_distributions = {
obs_keys[0]: 'normal',
obs_keys[1]: 'log-normal',
obs_keys[2]: 'laplace',
obs_keys[3]: 'log10-laplace',
}
outdir = 'test_likelihoods'
sbmlImporter.sbml2amici('test_likelihoods',
outdir,
observables=observables,
constantParameters=['k0'],
sigmas={'observable_x1withsigma':
'observable_x1withsigma_sigma'},
noise_distributions=noise_distributions
)
sys.path.insert(0, outdir)
import test_likelihoods as modelModule
model = modelModule.getModel()
model.setTimepoints(np.linspace(0, 60, 60))
solver = model.getSolver()
solver.setSensitivityOrder(amici.SensitivityOrder_first)
# run model once to create an edata
rdata = amici.runAmiciSimulation(model, solver)
edata = [amici.ExpData(rdata, 1, 0)]
# just make all observables positive since some are logarithmic
for ed in edata:
y = ed.getObservedData()
y = tuple([max(val, 1e-4) for val in y])
ed.setObservedData(y)
# and now run for real and also compute likelihood values
rdata = amici.runAmiciSimulations(model, solver, edata)[0]
# output for easy debugging
for key in ['llh', 'sllh']:
print(key, rdata[key])
# it would be good to compute the expected llh+sllh by hand,
# here, we only check if they make overall sense
self.assertTrue(np.isfinite(rdata['llh']))
self.assertTrue(np.all(np.isfinite(rdata['sllh'])))
self.assertTrue(np.any(rdata['sllh']))
# sbml_model.setName(model_name+'_Annot')
# sbml_model.setId(model_name+'_Annot')
# sbml_filewAnnot = model_name+'_Annot.xml'
# writer = libsbml.SBMLWriter()
# writer.writeSBML(sbml_doc, sbml_filewAnnot)
# sbml_file = sbml_filewAnnot # Comment-out to use the file name w/t annotations
model_name = sbml_file[0:-4]
model_output_dir = model_name
sbml_reader = libsbml.SBMLReader()
sbml_doc = sbml_reader.readSBML(sbml_file)
sbml_model = sbml_doc.getModel()
# Create an SbmlImporter instance for our SBML model
sbml_importer = amici.SbmlImporter(sbml_file)
constantParameters = [
params.getId() for params in sbml_model.getListOfParameters()
]
observables = {
'actp53': {
'formula': 'p53ac'
},
'phERK': {
'formula': 'ppERK'
},
'egfLR': {
'formula': 'EE1'
}
def test_steadystate_scaled(self):
'''
Test SBML import and simulation from AMICI python interface
'''
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml,
filter_function=lambda variable: variable.getId().startswith(
'observable_') and not variable.getId().endswith('_sigma'))
outdir = 'test_model_steadystate_scaled'
sbmlImporter.sbml2amici(
'test_model_steadystate_scaled',
outdir,
observables=observables,
constantParameters=['k0'],
sigmas={'observable_x1withsigma': 'observable_x1withsigma_sigma'})
sys.path.insert(0, outdir)
import test_model_steadystate_scaled as modelModule
model = modelModule.getModel()
model.setTimepoints(amici.DoubleVector(np.linspace(0, 60, 60)))
solver = model.getSolver()
rdata = amici.runAmiciSimulation(model, solver)
edata = [amici.ExpData(rdata, 0.01, 0)]
rdata = amici.runAmiciSimulations(model, solver, edata)
# check roundtripping of DataFrame conversion
df_edata = amici.getDataObservablesAsDataFrame(model, edata)
edata_reconstructed = amici.getEdataFromDataFrame(model, df_edata)
self.assertTrue(
np.isclose(
amici.edataToNumPyArrays(edata[0])['observedData'],
amici.edataToNumPyArrays(
edata_reconstructed[0])['observedData'],
).all())
self.assertTrue(
np.isclose(
amici.edataToNumPyArrays(edata[0])['observedDataStdDev'],
amici.edataToNumPyArrays(
edata_reconstructed[0])['observedDataStdDev'],
).all())
if edata[0].fixedParameters.size():
self.assertListEqual(
list(edata[0].fixedParameters),
list(edata_reconstructed[0].fixedParameters),
)
else:
self.assertListEqual(
list(model.getFixedParameters()),
list(edata_reconstructed[0].fixedParameters),
)
self.assertListEqual(
list(edata[0].fixedParametersPreequilibration),
list(edata_reconstructed[0].fixedParametersPreequilibration),
)
df_state = amici.getSimulationStatesAsDataFrame(model, edata, rdata)
self.assertTrue(
np.isclose(rdata[0]['x'],
df_state[list(model.getStateIds())].values).all())
df_obs = amici.getSimulationObservablesAsDataFrame(model, edata, rdata)
self.assertTrue(
np.isclose(rdata[0]['y'],
df_obs[list(model.getObservableIds())].values).all())
amici.getResidualsAsDataFrame(model, edata, rdata)
def import_model(sbml_model: Union[str, 'libsbml.Model'],
condition_table: Optional[Union[str, pd.DataFrame]] = None,
observable_table: Optional[Union[str, pd.DataFrame]] = None,
measurement_table: Optional[Union[str, pd.DataFrame]] = None,
model_name: Optional[str] = None,
model_output_dir: Optional[str] = None,
verbose: Optional[Union[bool, int]] = True,
allow_reinit_fixpar_initcond: bool = True,
**kwargs) -> None:
"""
Create AMICI model from PEtab problem
:param sbml_model:
PEtab SBML model or SBML file name.
:param condition_table:
PEtab condition table. If provided, parameters from there will be
turned into AMICI constant parameters (i.e. parameters w.r.t. which
no sensitivities will be computed).
:param observable_table:
PEtab observable table.
:param measurement_table:
PEtab measurement table.
:param model_name:
Name of the generated model. If model file name was provided,
this defaults to the file name without extension, otherwise
the SBML model ID will be used.
:param model_output_dir:
Directory to write the model code to. Will be created if doesn't
exist. Defaults to current directory.
:param verbose:
Print/log extra information.
:param allow_reinit_fixpar_initcond:
See :class:`amici.ode_export.ODEExporter`. Must be enabled if initial
states are to be reset after preequilibration.
:param kwargs:
Additional keyword arguments to be passed to
:meth:`amici.sbml_import.SbmlImporter.sbml2amici`.
"""
set_log_level(logger, verbose)
logger.info(f"Importing model ...")
# Get PEtab tables
observable_df = petab.get_observable_df(observable_table)
# to determine fixed parameters
condition_df = petab.get_condition_df(condition_table)
if observable_df is None:
raise NotImplementedError("PEtab import without observables table "
"is currently not supported.")
# Model name from SBML ID or filename
if model_name is None:
if isinstance(sbml_model, libsbml.Model):
model_name = sbml_model.getId()
else:
model_name = os.path.splitext(os.path.split(sbml_model)[-1])[0]
if model_output_dir is None:
model_output_dir = os.path.join(os.getcwd(), model_name)
logger.info(f"Model name is '{model_name}'. "
f"Writing model code to '{model_output_dir}'.")
# Load model
if isinstance(sbml_model, str):
# from file
sbml_reader = libsbml.SBMLReader()
sbml_doc = sbml_reader.readSBMLFromFile(sbml_model)
sbml_model = sbml_doc.getModel()
else:
# Create a copy, because it will be modified by SbmlImporter
sbml_doc = sbml_model.getSBMLDocument().clone()
sbml_model = sbml_doc.getModel()
show_model_info(sbml_model)
sbml_importer = amici.SbmlImporter(sbml_model)
sbml_model = sbml_importer.sbml
if observable_df is not None:
observables, noise_distrs, sigmas = \
get_observation_model(observable_df)
logger.info(f'Observables: {len(observables)}')
logger.info(f'Sigmas: {len(sigmas)}')
if not len(sigmas) == len(observables):
raise AssertionError(
f'Number of provided observables ({len(observables)}) and sigmas '
f'({len(sigmas)}) do not match.')
# TODO: adding extra output parameters is currently not supported,
# so we add any output parameters to the SBML model.
# this should be changed to something more elegant
# <BeginWorkAround>
formulas = chain((val['formula'] for val in observables.values()),
sigmas.values())
output_parameters = OrderedDict()
for formula in formulas:
# we want reproducible parameter ordering upon repeated import
free_syms = sorted(sp.sympify(formula).free_symbols,
key=lambda symbol: symbol.name)
for free_sym in free_syms:
sym = str(free_sym)
if sbml_model.getElementBySId(sym) is None:
output_parameters[sym] = None
logger.debug(f"Adding output parameters to model: {output_parameters}")
for par in output_parameters.keys():
petab.add_global_parameter(sbml_model, par)
# <EndWorkAround>
# TODO: to parameterize initial states or compartment sizes, we currently
# need initial assignments. if they occur in the condition table, we
# create a new parameter initial_${startOrCompartmentID}.
# feels dirty and should be changed (see also #924)
# <BeginWorkAround>
initial_states = [
col for col in condition_df if sbml_model.getSpecies(col) is not None
]
initial_sizes = [
col for col in condition_df
if sbml_model.getCompartment(col) is not None
]
fixed_parameters = []
if len(initial_states) or len(initial_sizes):
# add preequilibration indicator variable
# NOTE: would only be required if we actually have preequilibration
# adding it anyways. can be optimized-out later
if sbml_model.getParameter(PREEQ_INDICATOR_ID) is not None:
raise AssertionError("Model already has a parameter with ID "
f"{PREEQ_INDICATOR_ID}. Cannot handle "
"species and compartments in condition table "
"then.")
indicator = sbml_model.createParameter()
indicator.setId(PREEQ_INDICATOR_ID)
indicator.setName(PREEQ_INDICATOR_ID)
# Can only reset parameters after preequilibration if they are fixed.
fixed_parameters.append(PREEQ_INDICATOR_ID)
for assignee_id in initial_sizes + initial_states:
init_par_id_preeq = f"initial_{assignee_id}_preeq"
init_par_id_sim = f"initial_{assignee_id}_sim"
for init_par_id in [init_par_id_preeq, init_par_id_sim]:
if sbml_model.getElementBySId(init_par_id) is not None:
raise ValueError(
"Cannot create parameter for initial assignment "
f"for {assignee_id} because an entity named "
f"{init_par_id} exists already in the model.")
init_par = sbml_model.createParameter()
init_par.setId(init_par_id)
init_par.setName(init_par_id)
assignment = sbml_model.createInitialAssignment()
assignment.setSymbol(assignee_id)
formula = f'{PREEQ_INDICATOR_ID} * {init_par_id_preeq} '\
f'+ (1 - {PREEQ_INDICATOR_ID}) * {init_par_id_sim}'
math_ast = libsbml.parseL3Formula(formula)
assignment.setMath(math_ast)
# <EndWorkAround>
fixed_parameters.extend(
get_fixed_parameters(sbml_model=sbml_model, condition_df=condition_df))
logger.debug(f"Fixed parameters are {fixed_parameters}")
logger.info(f"Overall fixed parameters: {len(fixed_parameters)}")
logger.info(
"Variable parameters: " +
str(len(sbml_model.getListOfParameters()) - len(fixed_parameters)))
# Create Python module from SBML model
sbml_importer.sbml2amici(
model_name=model_name,
output_dir=model_output_dir,
observables=observables,
constant_parameters=fixed_parameters,
sigmas=sigmas,
allow_reinit_fixpar_initcond=allow_reinit_fixpar_initcond,
noise_distributions=noise_distrs,
verbose=verbose,
**kwargs)
def runTest(testId, logfile):
try:
current_test_path = os.path.join(test_path, testId)
# results
resultsFile = os.path.join(current_test_path, testId + '-results.csv')
results = np.genfromtxt(resultsFile, delimiter=',')
# model
sbmlFile = findModelFile(current_test_path, testId)
wrapper = amici.SbmlImporter(sbmlFile)
modelDir = os.path.join(os.path.dirname(__file__), 'SBMLTestModels',
testId)
if not os.path.exists(modelDir):
os.makedirs(modelDir)
wrapper.sbml2amici('SBMLTest' + testId, output_dir=modelDir)
# settings
settings = readSettingsFile(current_test_path, testId)
ts = np.linspace(
float(settings['start']),
float(settings['start']) + float(settings['duration']),
int(settings['steps']) + 1)
atol = float(settings['absolute'])
rtol = float(settings['relative'])
sys.path.insert(0, wrapper.modelPath)
mod = importlib.import_module(wrapper.modelName)
model = mod.getModel()
model.setTimepoints(ts)
solver = model.getSolver()
solver.setMaxSteps(int(1e6))
solver.setRelativeTolerance(rtol / 1000.0)
solver.setAbsoluteTolerance(atol / 1000.0)
rdata = amici.runAmiciSimulation(model, solver)
amountSpecies = settings['amount'].replace(' ',
'').replace('\n',
'').split(',')
simulated_x = rdata['x']
test_x = results[1:, [
1 + wrapper.speciesIndex[variable]
for variable in settings['variables'].replace(' ', '').
replace('\n', '').split(',')
if variable in wrapper.speciesIndex.keys()
]]
for species in amountSpecies:
if not species == '':
volume = wrapper.speciesCompartment[
wrapper.speciesIndex[species]].subs(
wrapper.compartmentSymbols, wrapper.compartmentVolume)
simulated_x[:, wrapper.speciesIndex[
species]] = simulated_x[:, wrapper.
speciesIndex[species]] * volume
adev = abs(simulated_x - test_x)
adev[np.isnan(adev)] = True
rdev = abs((simulated_x - test_x) / test_x)
rdev[np.isnan(rdev)] = True
if not np.all(np.logical_or(adev < atol, rdev < rtol)):
if (not np.all(adev < atol)):
raise Exception('Absolute tolerance violated')
if (not np.all(rdev < rtol)):
raise Exception('Relative tolerance violated')
except amici.SBMLException as err:
print("Did not run test " + testId + ": {0}".format(err))
except Exception as err:
str = "Failed test " + testId + ": {0}".format(err)
traceback.print_exc(10)
logfile.write(str + '\n')
return
def conversion_reaction_model():
# read in sbml file
model_name = 'conversion_reaction'
example_dir = os.path.join(os.path.dirname(__file__), '..', '..', 'doc',
'example')
sbml_file = os.path.join(example_dir, model_name,
f'model_{model_name}.xml')
model_output_dir = os.path.join(example_dir, 'tmp',
f'{model_name}_enhanced')
# try to import the exisiting model, if possible
try:
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = amici.import_model_module(model_name, model_output_dir)
model = model_module.getModel()
except ValueError:
# read in and adapt the sbml slightly
if os.path.abspath(model_output_dir) in sys.path:
sys.path.remove(os.path.abspath(model_output_dir))
sbml_importer = amici.SbmlImporter(sbml_file)
# add observables to sbml model
def create_observable(sbml_model, obs_id):
# create a parameter, which will get a rule assignmed as observable
parameter = sbml_model.createParameter()
parameter.setId(f'observable_{obs_id}')
parameter.setName(f'observable_{obs_id}')
parameter.constant = True
rule = sbml_importer.sbml.createAssignmentRule()
rule.setId(f'observable_{obs_id}')
rule.setName(f'observable_{obs_id}')
rule.setVariable(f'observable_{obs_id}')
rule.setFormula(obs_id)
# add initial assignments to sbml model
def create_intial_assignment(sbml_model, spec_id):
# create a parameter, which will get a rule assignmed as observable
parameter = sbml_model.createParameter()
parameter.setId(f'{spec_id}0')
parameter.setName(f'{spec_id}0')
parameter.constant = True
assignment = sbml_importer.sbml.createInitialAssignment()
assignment.setSymbol(f'{spec_id}')
math = ('<math xmlns="http://www.w3.org/1998/Math/MathML"><ci>'
f'{spec_id}0</ci></math>')
assignment.setMath(libsbml.readMathMLFromString(math))
for spec in ('A', 'B'):
create_observable(sbml_importer.sbml, spec)
create_intial_assignment(sbml_importer.sbml, spec)
# add constant parameters and observables to AMICI model
constant_parameters = ['A0', 'B0']
observables = amici.assignmentRules2observables(
sbml_importer.sbml, # the libsbml model object
filter_function=lambda variable: variable.getId().startswith(
'observable_'),
)
# generate the python module for the model.
sbml_importer.sbml2amici(
model_name,
model_output_dir,
verbose=False,
observables=observables,
constant_parameters=constant_parameters,
)
# Importing the module and loading the model
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = amici.import_model_module(model_name, model_output_dir)
model = model_module.getModel()
except RuntimeError as err:
print('pyPESTO unit test ran into an error importing the conversion '
'reaction enhanced model. This may happen due to an old version '
'of this model being present in your python path (e.g., '
'incorrect AMICI version comparing to the installed one). '
'Delete the conversion_reaction_enhanced model from your python '
'path and retry. Your python path is currently:')
print(sys.path)
print('Original error message:')
raise err
return model
def import_model(sbml_file: str,
condition_file: str,
measurement_file: str = None,
model_name: str = None,
model_output_dir: str = None,
verbose: bool = True,
allow_reinit_fixpar_initcond: bool = False,
**kwargs):
"""Import AMICI model"""
if model_name is None:
model_name = os.path.splitext(os.path.split(sbml_file)[-1])[0]
if model_output_dir is None:
model_output_dir = os.path.join(os.getcwd(), model_name)
if verbose:
print(f"{Fore.GREEN}Importing model '{sbml_file}' using fixed "
f"parameters file '{condition_file}'")
print(f"{Fore.GREEN}Model name is '{model_name}' Writing model code "
f"to '{model_output_dir}'")
sbml_importer = amici.SbmlImporter(sbml_file)
sbml_model = sbml_importer.sbml
show_model_info(sbml_model)
observables = petab.get_observables(sbml_importer.sbml, remove=True)
sigmas = petab.get_sigmas(sbml_importer.sbml, remove=True)
measurement_df = petab.get_measurement_df(measurement_file)
noise_distrs = petab_noise_distributions_to_amici(
petab.get_noise_distributions(measurement_df))
# Replace observables in assignment
import sympy as sp
for observable_id, formula in sigmas.items():
repl = sp.sympify(formula).subs(observable_id,
observables[observable_id]['formula'])
sigmas[observable_id] = str(repl)
if verbose:
print('Observables', len(observables))
print('Sigmas', len(sigmas))
if not len(sigmas) == len(observables):
raise AssertionError(
f'Number of provided observables ({len(observables)}) and sigmas '
f'({len(sigmas)}) do not match.')
fixed_parameters = get_fixed_parameters(condition_file, sbml_model)
if verbose:
print("Overall fixed parameters", len(fixed_parameters))
print("Non-constant global parameters",
len(sbml_model.getListOfParameters()) - len(fixed_parameters))
# Create Python module from SBML model
start = time.time()
sbml_importer.sbml2amici(
model_name,
output_dir=model_output_dir,
observables=observables,
constantParameters=fixed_parameters,
sigmas=sigmas,
allow_reinit_fixpar_initcond=allow_reinit_fixpar_initcond,
noise_distributions=noise_distrs,
**kwargs)
end = time.time()
if verbose:
print(f"{Fore.GREEN}Model imported successfully in "
f"{round(end - start, 2)}s")
def test_steadystate_scaled(self):
"""
Test SBML import and simulation from AMICI python interface
"""
def assert_fun(x):
return self.assertTrue(x)
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_steadystate',
'model_steadystate_scaled.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml,
filter_function=lambda variable:
variable.getId().startswith('observable_') and
not variable.getId().endswith('_sigma')
)
outdir = 'test_model_steadystate_scaled'
sbmlImporter.sbml2amici('test_model_steadystate_scaled',
outdir,
observables=observables,
constantParameters=['k0'],
sigmas={'observable_x1withsigma':
'observable_x1withsigma_sigma'})
sys.path.insert(0, outdir)
import test_model_steadystate_scaled as modelModule
model = modelModule.getModel()
model.setTimepoints(np.linspace(0, 60, 60))
solver = model.getSolver()
solver.setSensitivityOrder(amici.SensitivityOrder_first)
rdata = amici.runAmiciSimulation(model, solver)
edata = [amici.ExpData(rdata, 1, 0)]
rdata = amici.runAmiciSimulations(model, solver, edata)
# check roundtripping of DataFrame conversion
df_edata = amici.getDataObservablesAsDataFrame(model, edata)
edata_reconstructed = amici.getEdataFromDataFrame(model, df_edata)
self.assertTrue(
np.isclose(
amici.ExpDataView(edata[0])
['observedData'],
amici.ExpDataView(edata_reconstructed[0])
['observedData'],
).all()
)
self.assertTrue(
np.isclose(
amici.ExpDataView(edata[0])
['observedDataStdDev'],
amici.ExpDataView(edata_reconstructed[0])
['observedDataStdDev'],
).all()
)
if len(edata[0].fixedParameters):
self.assertListEqual(
list(edata[0].fixedParameters),
list(edata_reconstructed[0].fixedParameters),
)
else:
self.assertListEqual(
list(model.getFixedParameters()),
list(edata_reconstructed[0].fixedParameters),
)
self.assertListEqual(
list(edata[0].fixedParametersPreequilibration),
list(edata_reconstructed[0].fixedParametersPreequilibration),
)
df_state = amici.getSimulationStatesAsDataFrame(model, edata, rdata)
self.assertTrue(
np.isclose(
rdata[0]['x'],
df_state[list(model.getStateIds())].values
).all()
)
df_obs = amici.getSimulationObservablesAsDataFrame(model, edata, rdata)
self.assertTrue(
np.isclose(
rdata[0]['y'],
df_obs[list(model.getObservableIds())].values
).all()
)
amici.getResidualsAsDataFrame(model, edata, rdata)
solver.setRelativeTolerance(1e-12)
solver.setAbsoluteTolerance(1e-12)
check_derivatives(model, solver, edata[0], assert_fun, atol=1e-3,
rtol=1e-3, epsilon=1e-4)
def test_compare_to_sbml_import(self):
constant_parameters = ['DRUG_0', 'KIN_0']
# -------------- PYSB -----------------
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..',
'python', 'examples',
'example_presimulation'))
if 'createModelPresimulation' in sys.modules:
importlib.reload(sys.modules['createModelPresimulation'])
model_module = sys.modules['createModelPresimulation']
else:
model_module = importlib.import_module('createModelPresimulation')
model = copy.deepcopy(model_module.model)
model.name = 'test_model_presimulation_pysb'
amici.pysb2amici(model,
model.name,
verbose=False,
observables=['pPROT_obs'],
constant_parameters=constant_parameters)
sys.path.insert(0, model.name)
import test_model_presimulation_pysb as modelModulePYSB
model_pysb = modelModulePYSB.getModel()
edata = get_data(model_pysb)
rdata_pysb = get_results(model_pysb, edata)
# -------------- SBML -----------------
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir = 'test_model_presimulation_sbml'
sbmlImporter.sbml2amici('test_model_presimulation_sbml',
outdir,
verbose=False,
observables=observables,
constantParameters=constant_parameters)
sys.path.insert(0, outdir)
import test_model_presimulation_sbml as modelModuleSBML
model_sbml = modelModuleSBML.getModel()
rdata_sbml = get_results(model_sbml, edata)
for field in rdata_pysb:
if field not in ['ptr', 't_steadystate', 'numsteps',
'newton_numsteps', 'numrhsevals',
'numerrtestfails', 'order', 'J', 'xdot',
'wrms_steadystate', ]:
with self.subTest(field=field):
if rdata_pysb[field] is None:
self.assertIsNone(
rdata_sbml[field],
)
elif rdata_sbml[field] is None:
self.assertIsNone(
rdata_pysb[field],
)
else:
self.assertTrue(np.isclose(
rdata_sbml[field],
rdata_pysb[field],
atol=1e-6, rtol=1e-6
).all())
"""
Testing basic functionality of amici.
"""
import os
import amici
if __name__ == "__main__":
model_path = os.path.abspath(
'./examples/example_steadystate/model_steadystate_scaled.xml')
if not os.path.exists(model_path):
raise IOError(f"path does not exist: {model_path}")
# SBML import
sbml_importer = amici.SbmlImporter(model_path)
# Constants
# parameters that should be considered constants can be specified in a list of strings specifying the respective SbmlId of a parameter.
constantParameters = ['k0']
observables = {
'observable_x1': {
'name': '',
'formula': 'x1'
},
'observable_x2': {
'name': '',
'formula': 'x2'
},
'observable_x3': {
'name': '',
'formula': 'x3'
def plotObservables(iModel, iFile):
# call function 'getObservables()'
#getAllObservables(iModel,iFile)
# create folder for models with observables
if not os.path.exists('../sbml2amici/amici_models_with_observables'):
os.makedirs('../sbml2amici/amici_models_with_observables')
# loop over all models
#list_directory_sedml = os.listdir('./sedml_models')
#for iModel in list_directory_sedml:
# list_directory_sbml = os.listdir('./sedml_models' + iModel + '/sbml_models')
# for iFile in list_directory_sbml:
if os.path.exists(
'./BioModelsDatabase_models/' + iModel
): # no comparison for observables available, so no simulation needed
# important paths
model_output_dir = '../sbml2amici/amici_models_with_observables/' + iModel + '/' + iFile
model_path = './sedml_models/' + iModel + '/sbml_models_with_observables/' + iFile + '_with_observabels.xml' ##### needs automatisation
# sbml2amici import
sbml_importer = amici.SbmlImporter(model_path)
sbml_importer.sbml2amici(iModel, model_output_dir, verbose=False)
else:
# important paths
model_output_dir = '../sbml2amici/amici_models_with_observables/' + iModel + '/' + iFile
model_path = './sedml_models/' + iModel + '/sbml_models_with_observables/' + iFile + '_with_observabels.xml'
sedml_path = './sedml_models/' + iModel + '/' + iModel + '.sedml'
# get observables
sbml_doc = libsbml.readSBML(model_path)
model = sbml_doc.getModel()
observables = get_observables(model, False)
# sbml2amici import
sbml_importer = amici.SbmlImporter('./sedml_models/' + iModel +
'/sbml_models_with_observables/' +
iFile + '_with_observabels.xml')
sbml_importer.sbml2amici(iModel,
model_output_dir,
observables=observables,
verbose=False)
# load specific model
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = importlib.import_module(iModel)
model = model_module.getModel()
# set time points
sedml_file = libsedml.readSedML(sedml_path)
for iTask in range(0, sedml_file.getNumTasks()):
all_tasks = sedml_file.getTask(iTask)
tsk_Id = all_tasks.getId()
task_name = all_tasks.getName()
task_modRef = all_tasks.getModelReference()
task_simReference = all_tasks.getSimulationReference()
# time courses
try:
all_simulations = sedml_file.getSimulation(iTask)
sim_Id = all_simulations.getId()
except: # need 'except' clause if more models have same time period
if all_simulations == None:
all_simulations = sedml_file.getSimulation(0)
sim_Id = all_simulations.getId()
try:
while task_simReference != sim_Id:
iTask = iTask + 1
all_simulations = sedml_file.getSimulation(iTask)
sim_Id = all_simulations.getId()
except:
iTask = 0
while task_simReference != sim_Id:
all_simulations = sedml_file.getSimulation(iTask)
sim_Id = all_simulations.getId()
iTask = iTask + 1
sim_start_time = all_simulations.getOutputStartTime()
sim_end_time = all_simulations.getOutputEndTime()
sim_num_time_points = all_simulations.getNumberOfPoints()
model.setTimepoints(
np.linspace(sim_start_time, sim_end_time, sim_num_time_points))
# print observables
#print("Model observables: ", model.getObservableIds())
# get solver instance
#solver = model.getSolver()
# simulate model once
#sim_data = amici.runAmiciSimulation(model,solver)
# np.set_printoptions(threshold=8, edgeitems=2)
#for key, value in sim_data.items():
# print('%12s: ' % key, value)
# plot observable trajectories
#amici.plotting.plotObservableTrajectories(sim_data)
# amici.plotting.plotStateTrajectories(sim_data)
# show plot
#plt.show()
return model