def ensembleTimeCourse(model_col):
"""
"""
r = te.loada(model_col[0])
T = np.empty((len(model_col), 100, r.getNumFloatingSpecies()))
for i in range(len(model_col)):
r = te.loada(model_col[i])
T[i] = r.simulate(0, 100, 100)[:, 1:]
return T
def ensembleReactionRates(model_col):
"""
"""
r = te.loada(model_col[0])
J = np.empty((len(model_col), r.getNumReactions()))
for i in range(len(model_col)):
r = te.loada(model_col[i])
r.steadyState()
J[i] = r.getReactionRates()
return J
def ensembleSteadyState(model_col):
"""
"""
r = te.loada(model_col[0])
SS = np.empty((len(model_col), r.getNumFloatingSpecies()))
for i in range(len(model_col)):
r = te.loada(model_col[i])
r.steadyState()
SS[i] = r.getFloatingSpeciesConcentrations()
return SS
def ensembleFluxControlCoefficient(model_col):
"""
"""
r = te.loada(model_col[0])
F = np.empty((len(model_col), r.getNumReactions(), r.getNumReactions()))
for i in range(len(model_col)):
r = te.loada(model_col[i])
r.steadyState()
F[i] = r.getScaledFluxControlCoefficientMatrix()
return F
def simulate_pscan(param, param_range: np.ndarray, ini_volume, selections,
ss_param_dict: dict):
mod = te.loada(cf.MECHANICAL_SIZE_CONTROL_MOD)
ss_finder = SteadyStateFinder(cf.SIZE_REGULATION_MOD)
ia_dict, rules_dict = mrt.get_ia_and_rules(mod)
return p_scan(param, param_range, ss_finder, ia_dict, rules_dict,
ss_param_dict, selections, mod, ini_volume)
def identifiability(best_estimated_parameters: Dict[str, float], num_points: int = 10):
# we reload roadrunner here to prevent potential unintended consequences of modifying r inplace
r = te.loada(ANTIMONY_STRING)
# We make a copy of the original free parameters here
# since we'll need to modify which parameters are estimated later
# and put the original values back before each parameter
original_free_parameters = r.freeParameters()
# somewhere to store the results
results = dict()
for parameter in r.freeParameters():
print("Running profile likelihood for parameter ", parameter)
# get best estimated value for parameter
if parameter not in best_estimated_parameters.keys():
raise ValueError(f"Parameter {parameter} not in best estimated parameters: {best_estimated_parameters}")
# reset our model back to the best parameter set
for k, v in best_estimated_parameters.items():
setattr(r, k, v)
# we can use the interface from above but we need to update the
# freeParameters method to contain only 'parameter'. In profile
# likelihood, many parameter estimations are conducted, staring
# from the best estimated parameter set. The difference is that
# we fix 1 parameter (say k1) to a calculated value and reoptimize
# all the others. Then we repeat, but with a different value of k1.
def freeParameters(self):
return [p for p in original_free_parameters if p != parameter]
# tell roadrunner which parameters to estimate during reoptimization
r.freeParameters = freeParameters
# calculate the boundaries of the proile likelihood in logspace
best_estimated_value = best_estimated_parameters[parameter]
lb = best_estimated_value / 1000
ub = best_estimated_value * 1000
# these are the values that we will set fix parameter to
x = np.logspace(np.log10(lb), np.log10(ub), num_points)
best_rss_for_parameter_fixed_at_x = [] # for collecting the best rss values for each run
list_of_best_params = [] # collect the best parameters for each run
for fixed_parameter_value in x:
print("scanning parameter value of: ", fixed_parameter_value)
# 1) set the fixed parameter value
setattr(r, parameter, fixed_parameter_value)
# 2) repeat the parameter estimation.
objective_values_for_this_run, x_sim, y_sim, sel, best_parameters = do_estimation(ngen=50)
best_rss_for_parameter_fixed_at_x.append(objective_values_for_this_run[-1])
list_of_best_params.append(best_parameters)
results[parameter] = dict(
x=x,
list_of_best_params=list_of_best_params,
best_rss_for_parameter_fixed_at_x=best_rss_for_parameter_fixed_at_x
)
return results
def testCombMotif(flatComb, motifList):
try:
combMotif = te.loada(
flatComb
) # If it fails here, the combined model is not formatted correctly
SS = combMotif.steadyState()
except:
raise AssertionError('Failed to create a combined model! Check code.')
try:
SS = combMotif.steadyState()
print('Model reaches Steady-State!')
except:
print(
'Model Fails to reach Steady-state. Retrying with new parameter values.'
)
global SSFAILED
SSFAILED = True
motifList = []
motifListDir = motifsFromScratch()
motifList = chooseDupMotif(motifListDir)
combined = combineMotifs()
flatComb = flattenMotif(combined)
testCombMotif(flatComb, motifList)
if SS == 0:
print('Steady-state = 0. Retrying with new parameter values.')
global SSFAILED
SSFAILED = True
motifList = []
motifListDir = motifsFromScratch()
chooseDupMotif(motifListDir)
combined = combineMotifs()
flatComb = flattenMotif(combined)
testCombMotif(flatComb, motifList)
return (combMotif, SSFAILED)
def test_truth_table(testmodel, input_ids, output_ids, truth_table,
ht=0.8, lt=0.2, delay=99, plot=False):
import tellurium as te
r = te.loada(testmodel)
sims = []
for row in truth_table:
message = ['When']
for i, input_val in enumerate(row[0]):
message.append(input_ids[i] + ':' + str(input_val))
r[input_ids[i]] = input_val
sim = r.simulate(0, delay + 1, delay + 1, ['time'] + input_ids + output_ids)
sims.append(sim)
for i, output_val in enumerate(row[1]):
offset = len(input_ids) + 1 # Time + length of inputs
ind = i + offset
full_message = ' '.join(message + [
'then',
output_ids[i] + ':' + str(output_val),
'; Found %s = %f' % (output_ids[i], sim[delay][ind])
])
print full_message
if output_val == 0:
assert sim[delay][ind] < lt, full_message
else:
assert sim[delay][ind] > ht, full_message
return r, sims
def exportAsCombine(self, outputPath, execute=False):
""" Creates COMBINE archive for given antimony and phrasedml files.
If execute=True all phrasedml are executed and the results written
:param exportPath: full path of the combine zip file to create
:type exportPath: str
"""
# Create empty archive
m = tecombine.CombineArchive()
# Add antimony models to archive
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
m.addAntimonyStr(aStr, "{}.xml".format(name))
# Add phrasedml models to archive
for k, phrasedmlStr in enumerate(self.phrasedmlList):
phrasedml.clearReferencedSBML()
self._setReferencedSBML(phrasedmlStr)
m.addPhraSEDMLStr(phrasedmlStr, self._phrasedmlFileName(k), master=True)
phrasedml.clearReferencedSBML()
# Add README.md to archive
readmeStr = self.createReadmeString(outputPath)
m.addStr(readmeStr, location='README.md', filetype='md')
# add output files to archive
if execute:
for phrasedmlStr in self.phrasedmlList:
# execute in temporary directory
workingDir = tempfile.mkdtemp(suffix="_sedml")
execStr = self._toPython(phrasedmlStr, workingDir=workingDir)
exec execStr
# Add output files to archive
files = [f for f in os.listdir(workingDir)]
for f in files:
filepath = os.path.join(workingDir, f)
if f.endswith('.xml'):
# SBML or SEDML resulting from antimony/phrasedml (already in archive)
pass
elif f.endswith('.md'):
# README.md (already in archive)
pass
elif f.endswith('.png'):
# outputPlot2D | outputPlot3D
m.addFile(filepath, filetype="png")
elif f.endswith('.csv'):
# outputReport
m.addFile(filepath, filetype="csv")
else:
warnings.warn('Unsupported file type not written in COMBINE archive: {}'.format(filepath))
# remove temporary workingDir
shutil.rmtree(workingDir)
# Write archive
m.write(outputPath)
def test_getSeed(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
seed = r.getSeed()
self.assertIsNotNone(seed)
def test_setSeed(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
r.setSeed(123)
self.assertEqual(123, r.getSeed())
def fed_batch_model_mu():
mu_model = '''
model *IDModel()
######## Set the compartment to 1, otherwise it will be multiplied by the compounds.
compartment comp1;
comp1 =1;
######## Specify the species in the compartment
glucose in comp1; biomass in comp1; serine in comp1; #acetate in comp1
######## Constants
mu_max = 0.2477 # [1/h]
Ks = 1.4344 # [g/L]
Ks_qs = 2.6784 # [g/L]
Ki = 688309 # [g/L]
qs_max = 1.4075 # (g/(g*h))
F0 = 0.3
mu_set = 0.02
alpha = 1.5007
beta = 2.7714
######## Initial conditions
V = 0.1021
glucose = 0 # 0.149770*V # [g]
biomass = 0.209504 #5.092*V # [g]
serine = 0 # [g]
######## Feed function
Fin := F0*exp(mu_set*time)/1000 # [L/h]
######## Function for volume in fed-batch
EqVolume: -> V; Fin # [L/h]
######## Initial concentrations
c_glucose := glucose/V # [g/L]
c_glufeed = 415 # [g/L]
c_biomass := biomass/V
######## Functions
mu = 0
qs := qs_max*c_glucose/(Ks_qs+c_glucose) # [g_substrate/g_biomass h]
qp := alpha*mu/(mu+beta)
######## Mass Balances
eq_biomass: -> biomass; mu*biomass # [g/h]
eq_glucose: -> glucose; -qs*biomass + Fin*c_glufeed # [g/h]
eq_serine: -> serine; qp*biomass # [g/h]
end
'''
r = te.loada(mu_model)
return r
def run(self,func=None):
"""Allows the user to set the data from a File
This data is to be compared with the simulated data in the process of parameter estimation
Args:
func: An Optional Variable with default value (None) which by default run differential evolution
which is from scipy function. Users can provide reference to their defined function as argument.
Returns:
The Value of the parameter(s) which are estimated by the function provided.
.. sectionauthor:: Shaik Asifullah <*****@*****.**>
"""
self._parameter_names = self.bounds.keys()
self._parameter_bounds = self.bounds.values()
self._model_roadrunner = te.loada(self.model.model)
x_data = self.data[:,0]
y_data = self.data[:,1:]
arguments = (x_data,y_data)
if(func is not None):
result = differential_evolution(self._SSE, self._parameter_bounds, args=arguments)
return(result.x)
else:
result = func(self._SSE,self._parameter_bounds,args=arguments)
return(result.x)
def simulationSandbox(setup, ant_str, r_comb):
'''
Function to parallelize simulations due to memory leak issue.
Sandbox anything that has to do with antimony and kill it off after an
iteration
'''
antimony.clearPreviousLoads()
rr = te.loada(ant_str)
rr.resetAll() # ALWAYS RESET
rr.conservedMoietyAnalysis = True
pert_i = rr.steadyStateNamedArray() # Initial steady state
# Put initial steady state and species ids
#pert_init.append(pert_i[0])
# Pertubation for rate constants
k_pert_output_i = np.empty([len(r_comb), setup.num_float])
for i in range(len(r_comb)):
k_pert_output_i[i] = util.perturbRate(rr, r_comb[i], setup.k_pert)
antimony.clearPreviousLoads()
return pert_i.tolist(), k_pert_output_i.tolist()
def test_plot(self):
""" Regression tests for plotting.
The following calls should work. """
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
s = r.simulate(0, 100, 21)
# no argument version
r.plot()
# plot with data
r.plot(s)
# plot with named data
r.plot(result=s)
# plot without legend
r.plot(s, loc=False)
# plot without showing
r.plot(s, show=False)
r.plot(s, show=True) # no show
# plot with label, title, axis and legend
r.plot(s,
xlabel="x",
ylabel="y",
xlim=[0, 10],
ylim=[0, 10],
grid=True)
# plot with additional plot settings from matplotlib
r.plot(s, color="blue", alpha=0.1, linestyle="-", marker="o")
def test_getSeed(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
seed = r.getSeed()
self.assertIsNotNone(seed)
def pathway(promoters, decay=True):
antinom = modelHeader()
if decay:
antinom += modelTemplate(1, decay)
antinom += modelTemplate(1)
antinom += modelTemplate(None)
antinom += "model *Big_Model()"+"\n"
for i in np.arange(len(promoters)):
p = promoters[i]
if p is not None:
if i == 0 and decay:
antinom += "\t"+"m%d: Prom_Upstream_Model();" % (i+1,)
else:
antinom += "\t"+"m%d: Prom_Model();" % (i+1,)
else:
antinom += "\t"+"m%d: Noprom_Model();" % (i+1,)
antinom += "\n"
for i in np.arange(len(promoters)-1):
antinom += "\t"+"m%d.Product is m%d.Substrate;" % (i+1, i+2)
antinom += "\n"
for i in np.arange(1,len(promoters)):
p = promoters[i]
if p is None:
antinom += "\t"+"m%d.Activated_promoter is m%d.Activated_promoter" %(i+1,i)
antinom += "\n"
antinom += "end\n"
return te.loada(antinom)
def runSSA(N, k, runs, std):
# P, Ss.
i_mean = np.array([20, 0])
i_std = np.array([5, 0])
# kb, kd, kout, kin.
k_mean = np.array([1, 0.01, k, k])
k_std = np.array([std, 0.001, 0, 0])
s_stack = np.zeros(N+2)
for i in range(runs):
# Errors may be thrown out here if a negative value is drawn.
initials = np.random.normal(i_mean,i_std, size = (N,len(i_mean)))
rates = np.random.normal(k_mean,k_std, size = (N,len(k_mean)))
# Rewrite Antimony file for N population cells.
writeBirthDeath(initials.astype(int), rates, N)
path = 'birthdeath.ant'
r = te.loada(path)
r.integrator = 'gillespie'
selections = ['time'] + r.getFloatingSpeciesIds()
r.integrator.variable_step_size = False
r.resetToOrigin()
s = r.simulate(0, 1000, 100, selections=selections)
s_stack = np.vstack((s_stack, s))
s_stack = s_stack[1:]
s_stack_df = pd.DataFrame(s_stack, columns = s.colnames)
s_stack_df['N'] = np.repeat(N,runs*100)
s_stack_df['k'] = np.repeat(k,runs*100)
s_stack_df['std'] = np.repeat(std,runs*100)
return s_stack_df
def test_plot(self):
""" Regression tests for plotting.
The following calls should work. """
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
print(type(r))
s = r.simulate(0, 100, 21)
# no argument version
r.plot()
# plot with data
r.plot(s)
# plot with named data
r.plot(result=s)
# plot without legend
r.plot(s)
# plot without showing
r.plot(s, show=False)
r.plot(s, show=True) # no show
# plot with label, title, axis and legend
r.plot(s, xlabel="x", ylabel="y", xlim=[0, 10], ylim=[0, 10], grid=True)
# plot with additional plot settings from matplotlib
r.plot(s, alpha=0.1, color="blue", linestyle="-", marker="o")
def run(self, func=None):
"""Allows the user to set the data from a File
This data is to be compared with the simulated data in the process of parameter estimation
Args:
func: An Optional Variable with default value (None) which by default run differential evolution
which is from scipy function. Users can provide reference to their defined function as argument.
Returns:
The Value of the parameter(s) which are estimated by the function provided.
.. sectionauthor:: Shaik Asifullah <*****@*****.**>
"""
self._parameter_names = self.bounds.keys()
self._parameter_bounds = self.bounds.values()
self._model_roadrunner = te.loada(self.model.model)
x_data = self.data[:, 0]
y_data = self.data[:, 1:]
arguments = (x_data, y_data)
if (func is not None):
result = differential_evolution(self._SSE,
self._parameter_bounds,
args=arguments)
return (result.x)
else:
result = func(self._SSE, self._parameter_bounds, args=arguments)
return (result.x)
def runSimulation(sim_time=SIM_TIME,
num_points=NUM_POINTS,
parameters=None,
road_runner=ROAD_RUNNER,
model=MODEL):
"""
Runs the simulation model rr for the parameters.
:param int sim_time: time to run the simulation
:param int num_points: number of timepoints simulated
:param lmfit.Parameters parameters:
:param ExtendedRoadRunner road_runner:
:param str model:
:return named_array:
"""
if road_runner is None:
road_runner = te.loada(model)
else:
road_runner.reset()
if parameters is not None:
parameter_dict = parameters.valuesdict()
# Set the simulation constants for all parameters
for constant in parameter_dict.keys():
stmt = "road_runner.%s = parameter_dict['%s']" % (constant,
constant)
exec(stmt)
return road_runner.simulate(0, sim_time, num_points)
def _adjustNames(self, antimonyModel:str, observedTS:NamedTimeseries) \
->typing.Tuple[NamedTimeseries, list]:
"""
Antimony exports can change the names of floating species
by adding a "_" at the end. Check for this and adjust
the names in observedTS.
Return
------
NamedTimeseries: newObservedTS
list: newSelectedColumns
"""
rr = te.loada(antimonyModel)
dataNames = rr.simulate().colnames
names = ["[%s]" % n for n in observedTS.colnames]
missingNames = [n[1:-1] for n in set(names).difference(dataNames)]
newSelectedColumns = list(self.selectedColumns)
if len(missingNames) > 0:
newObservedTS = observedTS.copy()
self.logger.exception("Missing names in antimony export: %s" %
str(missingNames))
for name in observedTS.colnames:
missingName = "%s_" % name
if name in missingNames:
newObservedTS = newObservedTS.rename(name, missingName)
newSelectedColumns.remove(name)
newSelectedColumns.append(missingName)
else:
newObservedTS = observedTS
return newObservedTS, newSelectedColumns
def testme():
""" Call this method to try out the methods in this module"""
r = _te.loada("""
J1: $Xo -> S1; k1*Xo - k11*S1;
J2: S1 -> S2; k2*S1 - k22*S2;
J3: S2 -> S3; k3*S2 - k33*S3;
J4: S3 -> S4; k3*S3 - k44*S4;
J5: S4 -> S5; k4*S4 - k44*S5;
J6: S5 -> S6; k5*S5 - k55*S6;
J7: S6 -> S7; k4*S6 - k44*S7;
J8: S7 -> S8; k3*S7 - k33*S8;
J9: S8 -> ; k4*S8;
k1 = 0.3; k11 = 0.26;
k2 = 0.5; k22 = 0.41;
k3 = 0.27; k33 = 0.12;
k4 = 0.9; k44 = 0.56
k5 = 0.14; k55 = 0.02
Xo = 10;
""")
r.steadyState()
plotting.plotFloatingSpecies(r, width=6, height=3)
plotting.plotConcentrationControlIn3D(r)
plotting.plotFluxControlIn3D(r, lowerLimit=0)
plotting.plotConcentrationControlHeatMap(r)
plotting.plotFluxControlHeatMap(r)
def generateNetworkWithSteadyState(num_node, num_bound, num_input, knownr=1):
"""
Generate network topology that has steady state solution
:param num_node: total number of species
:param num_bound: total number of boundary species
:param num_input: number of input boundary species
:rtype: array
"""
import antimony
import tellurium as te
i = 0
while i < 2:
try:
test_net = generateRandomNetwork(num_node, num_bound, num_input)
k_count = np.count_nonzero(test_net)
s_init = generateInitialSpecies(num_node, 5)
k_init = generateInitialRateConstants(k_count, 1)
ant_str = generateAntimony(test_net, s_init, k_init, num_node,
num_bound)
antimony.clearPreviousLoads()
rr = te.loada(ant_str)
rr.resetToOrigin() # ALWAYS RESET
rr.steadyStateNamedArray() # Test steady state
i += 1
except ValueError:
pass
except RuntimeError:
pass
antimony.clearPreviousLoads()
return test_net, s_init, k_init
def __init__(self,
model,
trueParameterDct,
startTime=0,
endTime=None,
numPoint=None):
"""
Parameters
----------
model: str/ExtendedAntimony
parameter values are the true values
trueParameterDct: dict
True values of parameters for the model
key: parameter name
value: value of parameter
Returns
-------
"""
self.startTime = startTime
self.endTime = endTime
self.numPoint = numPoint
self.trueParameterDct = trueParameterDct
if isinstance(model, str):
self.antimonyModel = model
self.roadrunnerModel = te.loada(self.antimonyModel)
else:
self.roadrunnerModel = model
self.antimonyModel = self.roadrunnerModel.getAntimony()
self.baseArr = self._getFlatValues(self.trueParameterDct)
self.nrmseNrm = np.sqrt(np.sum(self.baseArr**2))
self.simDF = None # Results of last simulation experiments
self.simTable = None # 2 parameter pivot table created in plot
def test_setSeed(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
r.setSeed(123)
self.assertEqual(123, r.getSeed())
def createSBML(antimony_str):
"""
:param str antimony_str: antimony model
:return str SBML:
"""
rr = te.loada(antimony_str)
sbmlstr = rr.getSBML()
return sbmlstr
def load_model(model_file,parameter_dictionary):
'''
Load a model and set its parameters
'''
model = te.loada(model_file)
update_model(model,parameter_dictionary)
return model
def _initializeTests(title, modelStr):
global _testCount
global _failedTest
_testCount = 0
_failedTest = []
r = _te.loada (modelStr)
sbmlStr = r.getSBML()
print ('\nBegin Report: ' + title)
return _simplesbml.loadSBMLStr (sbmlStr)
def spark_work(model_with_parameters):
import tellurium as te
if(antimony == "antimony"):
model_roadrunner = te.loada(model_with_parameters[0])
else:
model_roadrunner = te.loadSBMLModel(model_with_parameters[0])
parameter_scan_initilisation = te.ParameterScan(model_roadrunner,**model_with_parameters[1])
simulator = getattr(parameter_scan_initilisation, function_name)
return(simulator())
def to_roadrunner(self) -> rr.ExecutableModel:
"""
Construct a roadrunner model via the tellurium
interface using the current antimony string
Returns:
"""
return te.loada(self.to_antimony())
def _init():
global _known_parameters
rr = _te.loada(_known_model_part)
_known_parameters = dict(
zip(rr.model.getGlobalParameterIds(),
rr.model.getGlobalParameterValues()))
global _all_regs
_all_regs = _generate_all_regs()
def test_draw(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
try:
import pygraphviz
r.draw()
except ImportError:
pass
def test_loada(self):
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
self.assertIsNotNone(rr.getModel())
def test_draw(self):
r = te.loada("""
S1 -> S2; k1*S1;
k1 = 0.1; S1 = 40; S2 = 0.0;
""")
try:
import pygraphviz
r.draw()
except ImportError:
pass
def dynamic_simulate(self):
if self.model_str is None:
print("Error simulation: Model definition missing")
return None
self.loada_str = self.preamble_str + self.model_str + self.input_str
self.r = te.loada(self.loada_str)
self.r.selections = self.output_vars
self.result = self.r.simulate(0, self.real_time, self.n_times)
self.X = np.array(self.result).T # time along shape[1]
self.U = np.array(self.input_tracks)
def test_loada(self):
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
self.assertIsNotNone(rr.getModel())
def classify(setup, s_arr, c_arr):
"""
Ground truth classification. Returns initial perturbation response,
perturbation response, classification, and reaction index
:param g_truth: ground truth network matrix
:param s_truth: ground truth species concentrations
:param k_truth: ground truth rate constants
:param num_node: ground truth numbder of nodes
:param num_bound: ground truth numbder of boundary species
:param k_pert: perturbation amount
:param Thres: classification threshold
:rtype: list
"""
antimony.clearPreviousLoads()
# Strip and translate to string
t_s = setup.t_s.astype('str')
t_k = setup.t_k[setup.t_k != np.array(0)].astype('str')
#t_k_count = np.count_nonzero(setup.t_net)
t_ant = generate.generateAntimonyNew(setup.t_net, t_s, t_k, s_arr, c_arr)
#r_ind = np.array(np.where(setup.t_net != np.array(0))).T
r_ind = util.getPersistantOrder(setup.t_net, setup.p_net)
rr = te.loada(t_ant)
rr.reset() # ALWAYS RESET
rr.conservedMoietyAnalysis = True
pert_i = rr.steadyStateNamedArray() # Initial steady state
r_comb = clustering.getListOfCombinations(r_ind)
# Pertubation for rate constants
k_pert_output_i = np.empty([len(r_comb), setup.num_float])
for i in range(len(r_comb)):
k_pert_output_i[i] = util.perturbRate(rr, r_comb[i], setup.k_pert)
# Classification for rate constants
k_class_i = np.empty([len(r_comb), setup.num_float], dtype=int)
for i in range(len(r_comb)):
for j in range(setup.num_float):
k_diff = (k_pert_output_i[i][j] - pert_i[0][j])
if (np.abs(k_diff) > setup.Thres):
if k_diff < 0.:
k_class_i[i][j] = 1
else:
k_class_i[i][j] = 2
else:
k_class_i[i][j] = 0
antimony.clearPreviousLoads()
return pert_i[0], k_pert_output_i, k_class_i
def fromAntimony(cls, antimonyStr, location, master=None):
""" Create SBMLAsset from antimonyStr
:param antimonyStr:
:type antimonyStr:
:param location:
:type location:
:return:
:rtype:
"""
r = te.loada(antimonyStr)
raw = r.getSBML()
return cls.fromRaw(raw=raw, location=location, filetype='sbml', master=master)
def fromAntimony(cls, antimonyStr, location, master=None):
""" Create SBMLAsset from antimonyStr
:param antimonyStr:
:type antimonyStr:
:param location:
:type location:
:return:
:rtype:
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
r = te.loada(antimonyStr)
raw = r.getSBML()
return cls.fromRaw(raw=raw, location=location, filetype='sbml', master=master)
def test_README_example(self):
""" Tests the source example in the main README.md. """
import tellurium as te
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
result = rr.simulate(0, 40, 500)
te.plotArray(result)
def stochastic_work(model_object):
import tellurium as te
if model_type == "antimony":
model_roadrunner = te.loada(model_object.model)
else:
model_roadrunner = te.loadSBMLModel(model_object.model)
model_roadrunner.integrator = model_object.integrator
# seed the randint method with the current time
random.seed()
# it is now safe to use random.randint
model_roadrunner.setSeed(random.randint(1000, 99999))
model_roadrunner.integrator.variable_step_size = model_object.variable_step_size
model_roadrunner.reset()
simulated_data = model_roadrunner.simulate(model_object.from_time, model_object.to_time, model_object.step_points)
return([simulated_data.colnames,np.array(simulated_data)])
def _setReferencedSBML(self, phrasedmlStr):
""" Set phrasedml referenced SBML for given phrasedml String. """
modelNames = []
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
modelNames.append(name)
sources = self._modelsFromPhrasedml(phrasedmlStr)
for source, name in sources.iteritems():
# not a antimony model
if name not in modelNames:
continue
# set as referenced model
aStr = self.antimonyList[modelNames.index(name)]
phrasedml.setReferencedSBML(source, te.antimonyToSBML(aStr))
def test_seed(self):
r = te.loada('''
S1 -> S2; k1*S1; k1 = 0.1; S1 = 40; S2 = 0;
''')
# Simulate from time zero to 40 time units
result = r.gillespie(0, 40, 11)
# Simulate on a grid with 10 points from start 0 to end time 40
result = r.gillespie(0, 40, 10)
# Simulate from time zero to 40 time units using the given selection list
# This means that the first column will be time and the second column species S1
result = r.gillespie(0, 40, 11, ['time', 'S1'])
# Simulate from time zero to 40 time units, on a grid with 20 points
# using the give selection list
result = r.gillespie(0, 40, 20, ['time', 'S1'])
def test_plot2DParameterScan(self):
"""Test plot2DParameterScan."""
import tellurium as te
from tellurium.analysis.parameterscan import plot2DParameterScan
r = te.loada("""
model test
J0: S1 -> S2; Vmax * (S1/(Km+S1))
S1 = 10; S2 = 0;
Vmax = 1; Km = 0.5;
end
""")
s = r.simulate(0, 50, 101)
# r.plot(s)
import numpy as np
plot2DParameterScan(r,
p1='Vmax', p1Range=np.linspace(1, 10, num=5),
p2='Vmax', p2Range=np.linspace(0.1, 1.0, num=5),
start=0, end=50, points=101)
def test_complex_simulation(self):
""" Test complex simulation. """
model = '''
model feedback()
// Reactions:
J0: $X0 -> S1; (VM1 * (X0 - S1/Keq1))/(1 + X0 + S1 + S4^h);
J1: S1 -> S2; (10 * S1 - 2 * S2) / (1 + S1 + S2);
J2: S2 -> S3; (10 * S2 - 2 * S3) / (1 + S2 + S3);
J3: S3 -> S4; (10 * S3 - 2 * S4) / (1 + S3 + S4);
J4: S4 -> $X1; (V4 * S4) / (KS4 + S4);
// Species initializations:
S1 = 0; S2 = 0; S3 = 0;
S4 = 0; X0 = 10; X1 = 0;
// Variable initialization:
VM1 = 10; Keq1 = 10; h = 10; V4 = 2.5; KS4 = 0.5;
end
'''
r = te.loada(model)
result = r.simulate(0, 40, 101)
r.plot(result)
#Output requested: Amount of people in each state for years 1-10.
#
#This implementation uses a flattened model separated to M=Male and F=Female
import tellurium as te
r = te.loada ('''
MJ00: MH -> MS; MH*0.2
MJ02: MH -> MD; MH*0.01
MJ10: MS -> MH; MS*0.1
MJ12: MS -> MD; MS*0.3
FJ00: FH -> FS; FH*0.1
FJ02: FH -> FD; FH*0.01
FJ10: FS -> FH; FS*0.1
FJ12: FS -> FD; FS*0.3
MH = 50
MS = 0
MD = 0
FH = 50
FS = 0
FD = 0
''')
# This will create the SBML XML file
te.saveToFile ('Example3.xml', r.getSBML())
r.setIntegrator('gillespie')
r.integrator.variable_step_size = True
"""
Some testing with ndarrays for storage
"""
import numpy as np
import tellurium as te
r = te.loada("""
model test()
J0: S1 -> S2; k1*S1;
S1=10.0; S2=0.0;
k1=0.1;
end
""")
print(r)
N1 = 3
N2 = 4
N3 = 5
test = np.empty(shape=(N1, N2, N3), dtype=object)
for k in range(N1):
r.reset()
s = r.simulate(start=0, end=5, steps=5)
test[k, 0, 0] = s
# -*- coding: utf-8 -*-
"""
Simple UniUni reaction with first-order mass-action kinetics.
"""
from __future__ import print_function
import tellurium as te
model = '''
model pathway()
S1 -> S2; k1*S1
# Initialize values
S1 = 10; S2 = 0
k1 = 1
end
'''
# load model
r = te.loada(model)
# carry out a time course simulation
# arguments are: start time, end time, number of points
result = r.simulate(0, 10, 100)
# plot results
r.plotWithLegend(result)
# Sniffers, buzzers, toggles and blinkers.
# Tyson Model 2c - Substrate-depletion oscillator
import tellurium as te
import matplotlib.pyplot as plt
r = te.loada ('''
J1: $src -> X; k1*S;
J2: X -> R; (kop + ko*EP)*X;
J3: R -> $waste; k2*R;
J4: E -> EP; Vmax_1*R*E/(Km_1 + E);
J5: EP -> E; Vmax_2*EP/(Km_2 + EP);
src = 0; kop = 0.01; ko = 0.4;
k1 = 1; k2 = 1; R = 1;
EP = 1; S = 0.2; Km_1 = 0.05;
Km_2 = 0.05; Vmax_2 = 0.3; Vmax_1 = 1;
''')
m = r.simulate (0, 300, 1000, ["Time", "R", "X", "EP", "E"]);
plt.plot(m[:,0], m[:,1], 'r-', label="R", linewidth=2)
plt.plot(m[:,0], m[:,2], 'g-', label="X", linewidth=2)
plt.legend(loc='upper right')
plt.xlabel('Time', fontsize=16)
plt.ylabel('Concentration', fontsize=16)
plt.show()
r = te.loada ('''
#J1: S1 -> S2; Activator*kcat1*S1/(Km1+S1);
J1: S1 -> S2; SE2*kcat1*S1/(Km1+S1);
J2: S2 -> S1; Vm2*S2/(Km2+S2);
J3: T1 -> T2; S2*kcat3*T1/(Km3+T1);
J4: T2 -> T1; Vm4*T2/(Km4+T2);
J5: -> E2; Vf5/(Ks5+T2^h5);
J6: -> E3; Vf6*T2^h6/(Ks6+T2^h6);
#J7: -> E1;
J8: -> S; kcat8*E1
J9: E2 -> ; k9*E2;
J10:E3 -> ; k10*E3;
J11: S -> SE2; E2*kcat11*S/(Km11+S);
J12: S -> SE3; E3*kcat12*S/(Km12+S);
J13: SE2 -> ; SE2*kcat13;
J14: SE3 -> ; SE3*kcat14;
Km1 = 0.01; Km2 = 0.01; Km3 = 0.01; Km4 = 0.01; Km11 = 1; Km12 = 0.1;
S1 = 6; S2 =0.1; T1=6; T2 = 0.1;
SE2 = 0; SE3=0;
S=0;
E2 = 0; E3 = 0;
kcat1 = 0.1; kcat3 = 3; kcat8 =1; kcat11 = 1; kcat12 = 1; kcat13 = 0.1; kcat14=0.1;
E1 = 1;
k9 = 0.1; k10=0.1;
Vf6 = 1;
Vf5 = 3;
Vm2 = 0.1;
Vm4 = 2;
h6 = 2; h5=2;
Ks6 = 1; Ks5 = 1;
Activator = 0;
at (time > 100): Activator = 5;
''')
r = te.loada("""
model normalized_species()
# conversion between active (SA) and inactive (SI)
J1: SA -> SI; k1*SA - k2*SI;
k1 = 0.1; k2 = 0.02;
# species
species SA, SI, ST;
SA = 10.0; SI = 0.0;
const ST := SA + SI;
SA is "active state S";
SI is "inactive state S";
ST is "total state S";
# normalized species calculated via assignment rules
species SA_f, SI_f;
SA_f := SA/ST;
SI_f := SI/ST;
SA_f is "normalized active state S";
SI_f is "normalized inactive state S";
# parameters for your function
P = 0.1;
tau = 10.0;
nA = 1.0;
nI = 2.0;
kA = 0.1;
kI = 0.2;
# now just use the normalized species in some math
F := ( (1-(SI_f^nI)/(kI^nI+SI_f^nI)*(kI^nI+1) ) * ( (SA_f^nA)/(kA^nA+SA_f^nA)*(kA^nA+1) ) -P)*tau;
end
""")
# ### Consecutive UniUni reactions using first-order mass-action kinetics
# Model creation and simulation of a simple irreversible chain of reactions S1 -> S2 -> S3 -> S4.
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
r = te.loada('''
model pathway()
S1 -> S2; k1*S1
S2 -> S3; k2*S2
S3 -> S4; k3*S3
# Initialize values
S1 = 5; S2 = 0; S3 = 0; S4 = 0;
k1 = 0.1; k2 = 0.55; k3 = 0.76
end
''')
result = r.simulate(0, 20, 51)
te.plotArray(result);
# In[2]:
k10 = random.uniform(0.0001, 1)
k11 = random.uniform(0.0001, 1)
k12 = random.uniform(1.0 / 2500.0, 1.0 / 10000000.0)
Km9 = random.uniform(0.0001, 0.01)
Km10 = random.uniform(0.0001, 0.01)
Km11 = random.uniform(0.0001, 0.01)
inter = 0.0
S1 = 10.0
constants_ref = {'k1': str(k1), 'k2': str(k2), 'k3': str(k3), 'k4': str(k4),
'k5': str(k5), 'k6': str(k6), 'k7': str(k7), 'k9': str(k9),
'k10': str(k10), 'k11': str(k11), 'k12': str(k12), 'Km9' : str(Km9),
'Km10': str(Km10), 'Km11': str(Km11), 'inter': str(inter), 'k8': str(k8),
'S1': str(S1)}
rr = te.loada(model.format(**constants))
rr.getSteadyStateValues()
S4_ref = rr.S4
print 'S4_ref =', S4_ref
inter = random.uniform(0.0000000001, 1.0)
constants = {'k1': str(k1), 'k2': str(k2), 'k3': str(k3), 'k4': str(k4),
'k5': str(k5), 'k6': str(k6), 'k7': str(k7), 'k9': str(k9),
'k10': str(k10), 'k11': str(k11), 'k12': str(k12), 'Km9' : str(Km9),
'Km10': str(Km10), 'Km11': str(Km11), 'inter': str(inter), 'k8': str(k8),
'S1': str(S1)}
rr = te.loada(model.format(**constants))
rr.getSteadyStateValues()
S4 = rr.S4
def simulate(antModelStr, constants):
rr = te.loada(antModelStr.format(**constants))
rr.simulate(0, 800000, 100)
rr.plot()
print "P =", rr.P
# Copyright (c) 2017 Kiri Choi
import os, sys
import tellurium as te
import matplotlib
import matplotlib.pyplot as plt
import seaborn as sb
import numpy as np
workingDir = os.getcwd()
f = open('ant_str.txt','r')
ant_str = f.read()
f.close()
r = te.loada(ant_str)
results = r.simulate(0, 30, 31)
ind_1 = np.shape(results)[1]/2
#ind_2 = np.sqrt((np.shape(results)[1] - 2)/2)
ind_2 = 38
grid = []
for i in range(len(results[:,1:-ind_1])):
grid.append(results[:,1:-ind_1][i].reshape(-1, int(ind_2)))
sb.set_style("white")
plt.figure()
cmap = matplotlib.colors.ListedColormap(['black','white'])
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
import matplotlib.pyplot as plt
import tellurium as te
import numpy as np
from roadrunner import Config
Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True)
r = te.loada('''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;
S2 -> $X1; k3*S2;
vo = 1
k1 = 2; k2 = 0; k3 = 3;
''')
p = te.SteadyStateScan(r,
value = 'k3',
startValue = 2,
endValue = 3,
numberOfPoints = 20,
selection = ['S1', 'S2']
)
p.plotArray()
Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, False)
def simulate(antModelStr, constants):
rr = te.loada(antModelStr.format(**constants))
rr.simulate(0, 800000, 1000)
rr.plot()
rr.getSteadyStateValues()
return rr.P
# coding: utf-8
# Back to the main [Index](../index.ipynb)
# ### Simple Example
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
r = te.loada('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10')
r.simulate(0, 50, 100)
r.plot();
# ### More Complex Example
# Stochastic simulation of a linear chain.
# In[2]:
import tellurium as te
import numpy as np
r = te.loada('''
J1: S1 -> S2; k1*S1;
J2: S2 -> S3; k2*S2 - k3*S3
# J2_1: S2 -> S3; k2*S2
# J2_2: S3 -> S2; k3*S3;
J3: S3 -> S4; k4*S3;