class Earm10ODESuite(object):
def setup(self):
self.nsims = 100
self.timer = timeit.default_timer
self.model = earm_1_0.model
self.model.reset_equations()
self.parameter_set = np.repeat(
[[p.value for p in self.model.parameters]], self.nsims, axis=0)
integrator_options_common = {
'model': self.model,
'tspan': np.linspace(0, 1000, 101),
'atol': 1e-6,
'rtol': 1e-6,
'mxsteps': 20000,
'param_values': self.parameter_set
}
self.sim_lsoda = ScipyOdeSimulator(integrator='lsoda',
**integrator_options_common)
self.sim_cupsoda = CupSodaSimulator(**integrator_options_common)
def time_scipy_lsoda(self):
self.sim_lsoda.run()
def time_cupsoda(self):
self.sim_cupsoda.run()
def setup(self):
self.nsims = 100
self.timer = timeit.default_timer
self.model = earm_1_0.model
self.model.reset_equations()
self.parameter_set = np.repeat(
[[p.value for p in self.model.parameters]], self.nsims, axis=0)
integrator_options_common = {
'model': self.model,
'tspan': np.linspace(0, 20000, 101),
'param_values': self.parameter_set
}
self.sim_lsoda = ScipyOdeSimulator(
integrator='lsoda',
compiler='cython',
integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'mxstep': 20000},
**integrator_options_common
)
self.sim_lsoda_no_compiler_directives = ScipyOdeSimulator(
integrator='lsoda',
compiler='cython',
cython_directives={},
integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'mxstep': 20000},
**integrator_options_common
)
self.sim_cupsoda = CupSodaSimulator(
integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'max_steps': 20000},
**integrator_options_common
)
def setup(self):
self.nsims = 100
self.timer = timeit.default_timer
self.model = earm_1_0.model
self.model.reset_equations()
self.parameter_set = np.repeat(
[[p.value for p in self.model.parameters]], self.nsims, axis=0)
integrator_options_common = {
'model': self.model,
'tspan': np.linspace(0, 20000, 101),
'param_values': self.parameter_set
}
self.sim_lsoda = ScipyOdeSimulator(integrator='lsoda',
compiler='cython',
integrator_options={
'atol': 1e-6,
'rtol': 1e-6,
'mxstep': 20000
},
**integrator_options_common)
self.sim_lsoda_no_compiler_directives = ScipyOdeSimulator(
integrator='lsoda',
compiler='cython',
cython_directives={},
integrator_options={
'atol': 1e-6,
'rtol': 1e-6,
'mxstep': 20000
},
**integrator_options_common)
self.sim_cupsoda = CupSodaSimulator(integrator_options={
'atol': 1e-6,
'rtol': 1e-6,
'max_steps': 20000
},
**integrator_options_common)
elif parameter_idx in [91]:
samples = np.random.uniform(low=602214.086, high=1806642.258, size=size)
return samples
else:
raise ValueError('Distribution is not defined for parameter index {}'.format(parameter_idx))
parameters = np.array([p.value for p in model.parameters])
nsamples = 50000
repeated_parameter_values = np.tile(parameters, (nsamples, 1))
for par_idx in kr_pars_to_sample:
repeated_parameter_values[:, par_idx] = sample_kr_uniform(nsamples)
for kf_idx, kr_idx in zip(kf_pars_to_calculate, kr_pars_to_sample):
repeated_parameter_values[:, kf_idx] = repeated_parameter_values[:, kr_idx] / sample_kd_uniform(kr_idx, nsamples)
np.save('pars_sampled_kd_bcl2.npy', repeated_parameter_values)
#
tspan = np.linspace(0, 20000, 100)
vol= 1e-19
integrator_opt = {'rtol': 1e-6, 'atol': 1e-6, 'mxsteps': 20000}
sims = CupSodaSimulator(model, tspan=tspan, gpu=0, memory_usage='shared_constant', vol=vol,
integrator_options=integrator_opt).run(param_values=repeated_parameter_values)
sims.save('simulations_sampled_kd_bcl2.h5')
signatures = run_tropical_multi(model=model, simulations=sims, cpu_cores=20, verbose=True)
with open('signatures_sampled_kd_bcl2.pickle', 'wb') as handle:
pickle.dump(signatures, handle, protocol=pickle.HIGHEST_PROTOCOL)
def cupsoda(model, start=0, finish=10, points=10, path='/opt/conda/bin/'):
set_path('cupsoda', path)
return CupSodaSimulator(model, linspace(start, finish,
points + 1)).run().dataframe
unique_pars = unique_pars[max_idx[:5000]]
par_set_calibrated = np.copy(param_values)
all_par_set_calibrated = np.tile(par_set_calibrated, (len(unique_pars), 1))
all_par_set_calibrated[:, rates_of_interest_mask] = 10**unique_pars
tspan = np.linspace(0, 60, 100)
arrestin_idx = 44
kcat_idx = [36, 37]
tspan_eq = np.linspace(0, 100, 100)
integrator_opt = {'rtol': 1e-6, 'atol': 1e-6, 'mxsteps': 20000}
cupsoda_solver = CupSodaSimulator(model,
tspan=tspan_eq,
gpu=0,
obs_species_only=False,
memory_usage='shared_constant',
integrator_options=integrator_opt)
pars_eq = np.copy(all_par_set_calibrated)
pars_eq[:, kcat_idx] = 0
conc_eq = pre_equilibration(cupsoda_solver, param_values=pars_eq)[1]
sims_final = CupSodaSimulator(model,
tspan=tspan,
gpu=0,
obs_species_only=False,
memory_usage='shared_constant',
integrator_options=integrator_opt).run(
param_values=all_par_set_calibrated,
initials=conc_eq)
max_arrestin = 100
arrestin_initials = np.linspace(0, max_arrestin, n_conditions)
par_clus1 = par_set_calibrated
arrestin_idx = 44
kcat_idx = [36, 37]
repeated_parameter_values = np.tile(par_clus1, (n_conditions, 1))
repeated_parameter_values[:, arrestin_idx] = arrestin_initials
np.save('arrestin_diff_IC_par0.npy', repeated_parameter_values)
tspan_eq = np.linspace(0, 100, 100)
integrator_opt = {'rtol': 1e-6, 'atol': 1e-6, 'mxsteps': 20000}
cupsoda_solver = CupSodaSimulator(model,
tspan=tspan_eq,
gpu=0,
obs_species_only=False,
memory_usage='shared_constant',
integrator_options=integrator_opt)
pars_eq = np.copy(repeated_parameter_values)
pars_eq[:, kcat_idx] = 0
conc_eq = pre_equilibration(cupsoda_solver, param_values=pars_eq)[1]
sims_final = CupSodaSimulator(model,
tspan=tspan,
gpu=0,
obs_species_only=False,
memory_usage='shared_constant',
integrator_options=integrator_opt).run(
param_values=repeated_parameter_values,
initials=conc_eq)