def simulate_with_bioscrape_via_sbml(self,
timepoints,
filename=None,
initial_condition_dict=None,
return_dataframe=True,
stochastic=False,
safe=False,
return_model=False,
check_validity=True,
**kwargs):
"""Simulate CRN model with bioscrape via writing a SBML file temporarily.
[Bioscrape on GitHub](https://github.com/biocircuits/bioscrape).
Returns the data for all species as Pandas dataframe.
"""
result = None
m = None
try:
from bioscrape.simulator import py_simulate_model
from bioscrape.types import Model
if filename is None:
self.write_sbml_file(file_name="temp_sbml_file.xml",
stochastic_model=stochastic,
for_bioscrape=True,
check_validity=check_validity)
file_name = "temp_sbml_file.xml"
elif isinstance(filename, str):
file_name = filename
else:
raise ValueError(
f"filename must be None or a string. Recievied: {filename}"
)
if 'sbml_warnings' in kwargs:
sbml_warnings = kwargs.get('sbml_warnings')
else:
sbml_warnings = False
m = Model(sbml_filename=file_name, sbml_warnings=sbml_warnings)
# m.write_bioscrape_xml('temp_bs'+ file_name + '.xml') # Uncomment if you want a bioscrape XML written as well.
if initial_condition_dict is not None:
processed = process_initial_concentration_dict(
initial_condition_dict)
m.set_species(processed)
result = py_simulate_model(timepoints,
Model=m,
stochastic=stochastic,
safe=safe,
return_dataframe=return_dataframe)
except ModuleNotFoundError:
warnings.warn('bioscrape was not found, please install bioscrape')
if return_model:
return result, m
else:
return result
def simulate_with_bioscrape(self,
timepoints,
initial_condition_dict={},
stochastic=False,
return_dataframe=True,
safe=False,
via_sbml=True):
from bioscrape.simulator import py_simulate_model
m = self.create_bioscrape_model()
m.set_species(initial_condition_dict)
if not stochastic and safe:
safe = False
result = py_simulate_model(timepoints,
Model=m,
stochastic=stochastic,
return_dataframe=return_dataframe,
safe=safe)
return result
def simulate_with_bioscrape(self, timepoints, initial_condition_dict = {},
stochastic = False, return_dataframe = True,
safe = False, **kwargs):
'''
Simulate CRN model with bioscrape (https://github.com/biocircuits/bioscrape).
Returns the data for all species as Pandas dataframe.
'''
from bioscrape.simulator import py_simulate_model
m = self.create_bioscrape_model()
m.set_species(initial_condition_dict)
if not stochastic and safe:
safe = False
result = py_simulate_model(timepoints, Model = m,
stochastic = stochastic,
return_dataframe = return_dataframe,
safe = safe)
return result
CRN = CRNs[i]
CRN.write_sbml_file(file_name=fname)
print("Saved")
from bioscrape.types import Model
from bioscrape.simulator import py_simulate_model
from bioscrape.sbmlutil import *
M = Model(sbml_filename=fname)
A_list = [0, 1, 2, 5, 10]
for ind in range(len(A_list)):
x0[repr(A)] = A_list[ind]
M.set_species(x0)
R = py_simulate_model(timepoints, Model=M)
plt.plot(timepoints,
R["protein_X"],
label="A=" + str(A_list[ind]),
color='blue',
alpha=(ind + 1) / len(A_list))
txt = ""
for rxn in CRN.reactions:
txt += repr(rxn) + "\n"
plt.title(txt[:-1], fontsize=8)
plt.legend()
plt.show()
#CRN.simulate_with_bioscrape(timepoints, initial_condition_dict = x0)
from bioscrape.types import import_sbml, read_model_from_sbml, Model
from bioscrape.simulator import py_simulate_model
import numpy as np
import matplotlib.pyplot as plt
# Import SBML
M_sbml = import_sbml('models/sbml_test.xml')
# Load SBML using the old method that works with strings -
# M_sbml = read_model_from_sbml('models/sbml_test.xml')
# Write it to bioscrape
M_sbml.write_bioscrape_xml('models/sbml_test_bioscrape.xml')
timepoints = np.linspace(0, 100, 1000)
result = py_simulate_model(timepoints, Model=M_sbml)
plt.figure()
for s in M_sbml.get_species_list():
plt.plot(timepoints, result[s], label=s)
plt.legend()
plt.show()