def compareModels(sbmlModel, antModel):
'''
This code needs to be rewritten.
'''
import roadrunner, pylab, antimony
sbmlModel = "00001-sbml-l2v4.xml"
antModel = sbmlModel.replace(sbmlModel[-3:], "ant")
# Make a round trip to and from Antimony
antimony.loadSBMLFile(sbmlModel)
antimony.writeAntimonyFile(antModel, antimony.getModuleNames()[1])
antimony.loadAntimonyFile(antModel)
antimony.writeSBMLFile("test.xml", antimony.getModuleNames()[1])
rr1 = roadrunner.RoadRunner(sbmlModel)
rr2 = roadrunner.RoadRunner("test.xml")
result1 = rr1.simulate(0, 10, 101)
result2 = rr2.simulate(0, 10, 101)
result = result1 - result2
pylab.plot(result[:, 0], result[:, 1:])
pylab.show()
def convertSBML2Antimony(filename):
if filename[-3:] == "xml":
model_name = filename.replace(filename[-3:], "ant")
antimony.loadSBMLFile(filename)
antimony.writeAntimonyFile(model_name, antimony.getMainModuleName())
elif filename[-3:] == "ant":
model_name = filename.replace(filename[-3:], "xml")
antimony.loadAntimonyFile(filename)
antimony.writeSBMLFile(model_name, antimony.getMainModuleName())
else:
print("Error, input file not SBML '*.xml' or Antimony '*.ant' ")
var species S3;
var species S4;
S3 = 0.5;
PP_S = 0.0;
S4 := 2*S3;
// Rule for S1
K1 = 0.5;
// Additional events for triggering re-integration
E1: at(time>=2): S3=5;
end
"""
model = antimony.loadString(model_txt)
sbml_file = "event_time.xml"
antimony.writeSBMLFile("event_time.xml", "event_time")
# load model in roadrunner and define the selection
r = roadrunner.RoadRunner(sbml_file)
r.selections = list(
itertools.chain(
["time"], r.model.getBoundarySpeciesIds(), r.model.getFloatingSpeciesIds(), r.model.getReactionIds()
)
)
print(r.selections)
absTol = 1e-6 * min(r.model.getCompartmentVolumes())
relTol = 1e-6
r.reset()
r.reset(SelectionRecord.ALL)
r.reset(SelectionRecord.INITIAL_GLOBAL_PARAMETER)
t_duration = 5;
peak_status = 0
// Rule for PP_S
PP_S := peak_status * 1.0
// Event to trigger the peak
E0: at(time>=0): peak_status=0;
E1: at(time>=t_peak): peak_status=1;
E2: at(time>=t_peak+t_duration): peak_status=0;
end
"""
model = antimony.loadString(model_txt)
sbml_file = 'event_timepoint.xml'
antimony.writeSBMLFile(sbml_file, 'event_timepoint')
r = roadrunner.RoadRunner(sbml_file)
print(r.getSBML())
r.selections = ['time'] + r.model.getBoundarySpeciesIds() \
+ r.model.getFloatingSpeciesIds() \
+ r.model.getReactionIds()
print(r.selections)
# tolerances & integration
absTol = 1E-12 *min(r.model.getCompartmentVolumes())
relTol = 1E-12
# variable step size integration (reset just to be sure)
r.reset()
r.reset(SelectionRecord.ALL)
// Rule for the function
PP_S := 1/(sigma *sqrt(2*pi)) * exp(-(time-mu)^2/(2*sigma^2));
//PP_S' = -(time - mu)/(sigma^3*sqrt(2*pi)) * exp(- (time-mu)^2/(2*sigma^2));
// PP_S := sin(time);
// Additional events for triggering re-integration
E1: at(time>=t_peak-4*sigma): K1=K1;
end
"""
model = antimony.loadString(model_txt)
out_dir = os.path.dirname(os.path.abspath(__file__))
sbml_path = str(os.path.join(out_dir, "time_peak.xml"))
print("SBML path:", sbml_path)
antimony.writeSBMLFile(sbml_path, "time_peak")
r = roadrunner.RoadRunner(sbml_path)
# display the generated and parsed SBML
# print(r.getSBML())
print("default selections:", r.selections)
r.selections = ["time"] + r.model.getBoundarySpeciesIds() + r.model.getFloatingSpeciesIds() + r.model.getReactionIds()
print("floating species:", r.model.getFloatingSpeciesIds())
print("selections:", r.selections)
# tolerances & integration
absTol = 1e-12 * min(r.model.getCompartmentVolumes())
relTol = 1e-12
print("absTol:", absTol, "; relTol:", relTol)
print("Naive VarStep")
"""
Create the SBML model.
"""
import antimony
model_id = 'vanderpol'
# ----------------------------
model_str = '''
model {}
var species x = -2;
var species y = 0;
const mu = 1;
J1: -> x; y
J2: -> y; mu *(1-x^2)*y - x
end
'''.format(model_id)
# ----------------------------
antimony.setBareNumbersAreDimensionless(True)
antimony.loadAntimonyString(model_str)
model_file = './vanderpol-sbml.xml'
antimony.writeSBMLFile(model_file, model_id)
print(model_file)