def rad_cell_dr(samplefile, radii, end_time, sample_size, percent, specList,
suppress=False, dr_species=['rad_cell', 1,1],
modelfiles = ['IFN_alpha_altSOCS_ppCompatible','IFN_beta_altSOCS_ppCompatible']):
from pysb.export import export
# Write modelfiles
print("Importing models")
alpha_model = __import__(modelfiles[0])
py_output = export(alpha_model.model, 'python')
with open('ODE_system_alpha.py','w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1])
py_output = export(beta_model.model, 'python')
with open('ODE_system_beta.py','w') as f:
f.write(py_output)
alpha_responses = [[] for i in range(len(specList))]
beta_responses = [[] for i in range(len(specList))]
for r in radii:
courses = rad_cell_point(samplefile, r, end_time, sample_size, percent, specList,
suppress=True, dose_species=dr_species)
# courses = [[IFNa spec 1], [IFNb spec 1], [IFNa spec 2], [IFNb spec 2]]
# [IFNa spec 1] = [[mean], [low], [high]]
courses = [[l[-1] for l in s] for s in courses]
# courses = [[mean dose, low, high]_IFNaS1, [mean dose, low, high]_IFNbS1, ...
for i in range(len(specList)):
alpha_responses[i].append(courses[i*2])
beta_responses[i].append(courses[i*2+1])
alpha_responses = [[[el[0] for el in alpha_responses[s]],[el[1] for el in alpha_responses[s]],[el[2] for el in alpha_responses[s]]] for s in range(len(alpha_responses))]
beta_responses = [[[el[0] for el in beta_responses[s]], [el[1] for el in beta_responses[s]], [el[2] for el in beta_responses[s]]] for s in range(len(alpha_responses))]
return [alpha_responses, beta_responses]
def main():
plt.close('all')
t=linspace(0,3600,num=100)
testDose = ['I',6.022e18*logspace(-14,-2,num=50)]
# kSOCS
yscan = 1e-6*logspace(-2,2,num=50)
t=linspace(0,3600,num=500)
# Write modelfile
import IFN_simplified_model_alpha_ppCompatible as alpha_model
py_output = export(alpha_model.model, 'python')
writeFile = "ODE_system_alpha.py"
with open(writeFile, 'w') as f:
f.write(py_output)
import IFN_simplified_model_beta_ppCompatible as beta_model
py_output = export(beta_model.model, 'python')
writeFile = "ODE_system_beta.py"
with open(writeFile, 'w') as f:
f.write(py_output)
# Run scans
# =============================================================================
k3k4_DRparamScan("IFN_simplified_model_alpha_ppCompatible", 'alpha', ['kSOCSon',yscan],
testDose, t, [['TotalpSTAT',"Total pSTAT"]],
Norm=10000, doseNorm=6.022e18)
def main():
plt.close('all')
modelfiles = [
"ifnmodels.IFN_detailed_model_alpha_ppCompatible",
"ifnmodels.IFN_detailed_model_beta_ppCompatible"
]
# Write modelfiles
print("Importing models")
alpha_model = __import__(modelfiles[0], fromlist=['ifnmodels'])
py_output = export(alpha_model.model, 'python')
with open('ODE_system_alpha.py', 'w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1], fromlist=['ifnmodels'])
py_output = export(beta_model.model, 'python')
with open('ODE_system_beta.py', 'w') as f:
f.write(py_output)
p0 = [['kpa', 1, 0.1, 'log'], ['kSTATbinding', 1E-6, 0.4, 'log'],
['kSOCSon', 1.70E-6, 0.1, 'log'], ['kd4', 0.87, 0.2, 'log'],
['k_d4', 0.86, 0.5, 'log'], ['delR', -1878, 500, 'linear'],
['meanR', 2000, 300, 'linear'], ['kloc', 1.23E-3, 0.1, 'log'],
['kSOCSmRNA', 1E-3, 0.1, 'log'], ['mRNAdeg', 5E-4, 0.1, 'log'],
['mRNAtrans', 1E-3, 0.1, 'log'], ['kSOCS', 5E-3, 0.1, 'log']]
our_priors_dict = {
'R1': [100, 12000, None, None],
'R2': [100, 12000, None, None],
'kpa': [1.5E-8, 10, np.log(1), 4],
'kSOCSon': [1.5E-11, 0.07, np.log(1E-6), 4],
'k_d4': [4E-5, 0.9, np.log(0.006), 1.8],
'kd4': [0.002, 44, np.log(0.3), 1.8],
'kSTATbinding': [1E-11, 1, np.log(1E-6), 4],
'kloc': [1E-5, 10, np.log(1.25E-3), 4],
'kSOCSmRNA': [1E-7, 10, np.log(1E-3), 4],
'mRNAdeg': [5E-8, 10, np.log(5E-4), 4],
'mRNAtrans': [1E-7, 10, np.log(1E-3), 4],
'kSOCS': [5E-7, 10, np.log(5E-3), 4]
}
# (n, theta_0, beta, rho, chains, burn_rate=0.1, down_sample=1, max_attempts=6,
# pflag=True, cpu=None, randomize=True)
MCMC(1000,
p0,
our_priors_dict,
2,
1,
5,
burn_rate=0.2,
down_sample=40,
max_attempts=6)
def export_memi(model, formats, version):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'MEMI%s.%s' % (version, extension)
with open(fname, 'wb') as fh:
fh.write(model_export)
def check_convert(model, format):
""" Test exporters run without error """
exported_file = None
try:
exported_file = export.export(model, format)
except export.ExpressionsNotSupported:
pass
except export.CompartmentsNotSupported:
pass
except Exception as e:
# Some example models are deliberately incomplete, so here we
# will treat any of these "expected" exceptions as a success.
model_base_name = model.name.rsplit('.', 1)[1]
exception_class = expected_exceptions.get(model_base_name)
if exception_class and isinstance(e, exception_class):
pass
else:
raise
if exported_file is not None:
if format == 'python':
# linspace arguments picked to avoid VODE warning
exec(
exported_file +
'Model().simulate(tspan=numpy.linspace(0,1,501))\n',
{'_use_inline': False})
elif format == 'pysb_flat':
exec(exported_file, {'__name__': model.name})
def export_memi(model, formats, version):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'MEMI%s.%s' % (version, extension)
with open(fname, 'wb') as fh:
fh.write(model_export)
def export_pomi(model, formats):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'POMI1.0.%s' % extension
with open(fname, 'wt') as fh:
fh.write(model_export)
def export_pomi(model, formats):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'POMI1.0.%s' % extension
with open(fname, 'wt') as fh:
fh.write(model_export)
def export_hello(model, formats):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'hello_indra_model.%s' % extension
with open(fname, 'wb') as fh:
fh.write(model_export.encode('utf-8'))
def export_hello(model, formats):
for f in formats:
model_export = export(model, f)
extension = (f if f != 'pysb_flat' else 'py')
fname = 'hello_indra_model.%s' % extension
with open(fname, 'wb') as fh:
fh.write(model_export)
def _prepare_kappa(model):
"""Return a Kappa STD with the model loaded."""
import kappy
kappa = kappy.KappaStd()
model_str = export(model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
return kappa
def _prepare_kappa(model):
"""Return a Kappa STD with the model loaded."""
import kappy
kappa = kappy.KappaStd()
model_str = export(model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
return kappa
def profile(processes):
if processes[0] != 1:
print("Must test serial time. Please ensure processes[0]==1")
return 1
test_priors = {
'kpa': [1.5E-9, 1, np.log(1), 4],
'kSOCSon': [1.5E-11, 0.07, np.log(1E-6), 4],
'k_d4': [4E-5, 0.9, np.log(0.006), 1.8],
'kd4': [0.002, 44, np.log(0.3), 1.8],
'R1': [100, 12000, None, None],
'R2': [100, 12000, None, None]
}
plt.close('all')
modelfiles = [
'ifnmodels.IFN_alpha_altSOCS_ppCompatible',
'ifnmodels.IFN_beta_altSOCS_ppCompatible'
]
# Write modelfiles
alpha_model = __import__(modelfiles[0], fromlist=['ifnmodels'])
py_output = export(alpha_model.model, 'python')
with open('ODE_system_alpha.py', 'w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1], fromlist=['ifnmodels'])
py_output = export(beta_model.model, 'python')
with open('ODE_system_beta.py', 'w') as f:
f.write(py_output)
p0 = [['kpa', 1E-6, 0.1, 'log'], ['kSOCSon', 1E-6, 0.1, 'log'],
['kd4', 0.3, 0.2, 'log'], ['k_d4', 0.006, 0.5, 'log'],
['delR', 0, 500, 'linear'], ['meanR', 2000, 300, 'linear']]
# ==========================================================
times = []
for p in processes:
tic = time.clock()
MCMC(50, p0, test_priors, 8, 1, 8, burn_rate=0.1, down_sample=2, cpu=p)
toc = time.clock()
times.append(toc - tic)
fig, ax = plt.subplots()
ax.scatter([1] + processes[1:],
[1] + [times[0] / times[i] for i in range(1, len(times))],
'b',
markersize=64)
ax.set_title('Profiling MCMC')
ax.set_xlabel('Number of Threads')
ax.set_ylabel('Speed up')
plt.savefig('speedup.pdf')
plt.show()
def check_convert(model, format):
""" Test exporters run without error """
exported_file = None
try:
exported_file = export.export(model, format)
except export.ExpressionsNotSupported:
pass
except export.CompartmentsNotSupported:
pass
except Exception as e:
# Some example models are deliberately incomplete, so here we
# will treat any of these "expected" exceptions as a success.
exception_class = expected_exceptions.get(base_name(model))
if not exception_class or not isinstance(e, exception_class):
raise
if exported_file is not None:
if format == 'python':
# linspace arguments picked to avoid VODE warning
exec(exported_file + 'Model().simulate(tspan=numpy.linspace(0,1,501))\n', {'_use_inline': False})
elif format == 'pysb_flat':
exec(exported_file, {'__name__': model.name})
elif format == 'sbml':
# Skip the simulation comparison if roadrunner not available
if roadrunner is None:
raise SkipTest("SBML Simulation test skipped (requires roadrunner)")
roadrunner.Logger.setLevel(roadrunner.Logger.LOG_ERROR)
# Simulate SBML using roadrunner
rr = roadrunner.RoadRunner(exported_file)
rr.timeCourseSelections = \
['__s{}'.format(i) for i in range(len(model.species))] + \
['__obs{}'.format(i) for i in range(len(model.observables))]
rr_result = rr.simulate(0, 10, 100)
# Simulate original using PySB
df = ScipyOdeSimulator(model).run(tspan=np.linspace(0, 10, 100)).dataframe
# Compare species' trajectories
for sp_idx in range(len(model.species)):
rr_sp = rr_result[:, sp_idx]
py_sp = df.iloc[:, sp_idx]
is_close = np.allclose(rr_sp, py_sp, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_sp, pysb=py_sp)))
raise ValueError('Model {}, species __s{} trajectories do not match:'.format(
model.name, sp_idx))
# Compare observables' trajectories
for obs_idx in range(len(model.observables)):
rr_obs = rr_result[:, obs_idx + len(model.species)]
py_obs = df.iloc[:, obs_idx + len(model.species)]
is_close = np.allclose(rr_obs, py_obs, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_obs, pysb=py_obs)))
raise ValueError('Model {}, observable__o{} "{}" trajectories do not match:'.format(
model.name, obs_idx, model.observables[obs_idx].name))
def make_contact_map(pysb_model):
"""Return a Kappa contact map."""
kappa = kappy.KappaStd()
model_str = export(pysb_model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
cmap = kappa.analyses_contact_map()
cm = cm_json_to_graph(cmap)
return cm
def make_contact_map(pysb_model):
"""Return a Kappa contact map."""
kappa = kappy.KappaStd()
model_str = export(pysb_model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
cmap = kappa.analyses_contact_map()
cm = cm_json_to_graph(cmap)
return cm
def build_model(self, name):
if name == '':
return None
else:
model_code = __import__('ifnmodels.' + name, fromlist=['ifnmodels'])
py_output = export(model_code.model, 'python')
ODE_filename = "ODE_system_{}_{}.py".format(time.strftime("%Y%m%d-%H%M%S"), randint(100000, 999999))
with open(ODE_filename, 'w') as f:
f.write(py_output)
ODE_system = __import__(ODE_filename[:-3])
model_obj = ODE_system.Model()
os.remove(ODE_filename)
return model_obj
def make_influence_map(pysb_model):
"""Return a Kappa influence map."""
kappa = kappy.KappaStd()
model_str = export(pysb_model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
imap = kappa.analyses_influence_map()
im = im_json_to_graph(imap)
for param in pysb_model.parameters:
try:
im.remove_node(param.name)
except:
pass
return im
def make_influence_map(pysb_model):
"""Return a Kappa influence map."""
kappa = kappy.KappaStd()
model_str = export(pysb_model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
imap = kappa.analyses_influence_map()
im = im_json_to_graph(imap)
for param in pysb_model.parameters:
try:
im.remove_node(param.name)
except:
pass
return im
def generate_im(self, model):
"""Return a graph representing the influence map generated by Kappa
Parameters
----------
model : pysb.Model
The PySB model whose influence map is to be generated
Returns
-------
graph : networkx.MultiDiGraph
A MultiDiGraph representing the influence map
"""
kappa = kappy.KappaStd()
model_str = export.export(model, 'kappa')
kappa.add_model_string(model_str)
kappa.project_parse()
imap = kappa.analyses_influence_map(accuracy='medium')
graph = im_json_to_graph(imap)
return graph
xmlfile = bnglfile.replace('.bngl', '.xml')
gdatfile = bnglfile.replace('.bngl', '.gdat')
rxnfile = bnglfile.replace('.bngl', '.rxns.tsv')
paramsfile = bnglfile.replace('.bngl', '.params.tsv')
# write all model parameters to a separate file
with open(paramsfile, 'w') as file:
file.write('parameter\tvalue\n')
for param in model.parameters:
file.write(f'{param.name}\t{param.value}\n')
# compress the params file
sp.run(['gzip', '-f', paramsfile.split('/')[-1]], cwd=outdir)
# write BNGL file
with open(bnglfile, 'w') as file:
file.write(export(model, 'bngl'))
# convert BNGL file to XML for NFSim input
sp.run(['BNG2.pl', '--xml', '--outdir', outdir, bnglfile])
# parameters for NFsim
equilibrium_time = 0 # seconds
tstop = str(1000000) # seconds
maxcputime = str(100 * 60) # seconds
osteps = str(100) # number of samples
seed = str(111) # random number initial seed
gml = str(1000000) # max num of mol allowed in simulation
utl = '3' # max number of bonds to traverse during simulation
network = '-connect' # whether to infer reaction network connectivity
# print NFSim command
def to_potterswheel(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'potterswheel'))
return None
def save_model(self, name):
file_text = export(self.model, 'bng_net')
print(file_text)
with open(name, 'w') as f:
f.write(file_text)
def to_bngnet(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'bng_net'))
return None
def IFN_2Dscan(modelfile, param1, param2, t_list, spec, custom_params=False,
cpu=None, doseNorm=1, suppress=False, verbose=1):
# initialization
jobs = Queue()
result = JoinableQueue()
if cpu == None or cpu >= cpu_count():
NUMBER_OF_PROCESSES = cpu_count()-1
else:
NUMBER_OF_PROCESSES = cpu
if verbose != 0: print("Using {} threads".format(NUMBER_OF_PROCESSES))
# build task list
params=[]
if verbose != 0: print("Building tasks")
if type(custom_params) == list:
for val1 in param1[1]:
for val2 in param2[1]:
params.append([[param1[0],val1],[param2[0],val2]]+[c for c in custom_params])
else:
for val1 in param1[1]:
for val2 in param2[1]:
params.append([[param1[0],val1],[param2[0],val2]])
# Write modelfile
imported_model = __import__(modelfile,fromlist=['ifnmodels'])
py_output = export(imported_model.model, 'python')
with open('ODE_system.py','w') as f:
f.write(py_output)
tasks = [[modelfile, t_list, spec, p] for p in params]
# put jobs on the queue
if verbose != 0: print("There are {} tasks to compute".format(len(params)))
if verbose != 0: print("Putting tasks on the queue")
for w in tasks:
jobs.put(w)
if verbose != 0: print("Computing scan")
# start up the workers
[Process(target=IFN_2Dscan_helper, args=(i, jobs, result)).start()
for i in range(NUMBER_OF_PROCESSES)]
# pull in the results from each worker
pool_results=[]
for t in range(len(tasks)):
r = result.get()
pool_results.append(r)
result.task_done()
# tell the workers there are no more jobs
for w in range(NUMBER_OF_PROCESSES):
jobs.put(None)
# close all extra threads
result.join()
jobs.close()
result.close()
if verbose != 0: print("Done scan")
response_image = image_builder(pool_results, doseNorm, (len(param1[1]),len(param2[1])))
# plot heatmap if suppress==False
if suppress==False:
IFN_heatmap(response_image, "response image - {}".format(param1[0]), param2[0])
#return the scan
return response_image
Model()
import EGFR_to_RAS_dim as EGFR_to_RAS
EGFR_to_RAS.monomers()
EGFR_to_RAS.KRAS_activation()
EGFR_to_RAS.SOS_dephosphorylation()
EGFR_to_RAS.declare_observables()
import BRAF_module
BRAF_module.monomers()
BRAF_module.BRAF_dynamics()
BRAF_module.observables()
import MEK_ERK_phosphorylation
MEK_ERK_phosphorylation.monomers()
MEK_ERK_phosphorylation.by_BRAF_mut()
MEK_ERK_phosphorylation.MEK_phosphorylates_ERK()
MEK_ERK_phosphorylation.DUSP_phospatase()
MEK_ERK_phosphorylation.PP2A_phosphatase()
MEK_ERK_phosphorylation.ERK_feedback()
MEK_ERK_phosphorylation.MEK_inhibitor()
MEK_ERK_phosphorylation.declare_observables()
from pysb.export import export
matlab_output = export(model, 'matlab')
with open('matlab_files/run_timecourse_test.m', 'w') as f:
f.write(matlab_output)
def check_convert(model, format):
""" Test exporters run without error """
exported_file = None
try:
if format == 'json':
exported_file = JsonExporter(model).export(include_netgen=True)
else:
exported_file = export.export(model, format)
except export.ExpressionsNotSupported:
pass
except export.CompartmentsNotSupported:
pass
except export.LocalFunctionsNotSupported:
pass
except Exception as e:
# Some example models are deliberately incomplete, so here we
# will treat any of these "expected" exceptions as a success.
exception_class = expected_exceptions.get(base_name(model))
if not exception_class or not isinstance(e, exception_class):
raise
if exported_file is not None:
if format == 'python':
# linspace arguments picked to avoid VODE warning
exec(
exported_file +
'Model().simulate(tspan=numpy.linspace(0,1,501))\n',
{'_use_inline': False})
elif format == 'pysb_flat':
exec(exported_file, {'__name__': model.name})
elif format == 'sbml':
# Skip the simulation comparison if roadrunner not available
if roadrunner is None:
raise SkipTest(
"SBML Simulation test skipped (requires roadrunner)")
roadrunner.Logger.setLevel(roadrunner.Logger.LOG_ERROR)
# Simulate SBML using roadrunner
rr = roadrunner.RoadRunner(exported_file)
rr.timeCourseSelections = \
['__s{}'.format(i) for i in range(len(model.species))] + \
['__obs{}'.format(i) for i in range(len(model.observables))]
rr_result = rr.simulate(0, 10, 100)
# Simulate original using PySB
df = ScipyOdeSimulator(model).run(
tspan=np.linspace(0, 10, 100)).dataframe
# Compare species' trajectories
for sp_idx in range(len(model.species)):
rr_sp = rr_result[:, sp_idx]
py_sp = df.iloc[:, sp_idx]
is_close = np.allclose(rr_sp, py_sp, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_sp, pysb=py_sp)))
raise ValueError(
'Model {}, species __s{} trajectories do not match:'.
format(model.name, sp_idx))
# Compare observables' trajectories
for obs_idx in range(len(model.observables)):
rr_obs = rr_result[:, obs_idx + len(model.species)]
py_obs = df.iloc[:, obs_idx + len(model.species)]
is_close = np.allclose(rr_obs, py_obs, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_obs, pysb=py_obs)))
raise ValueError(
'Model {}, observable__o{} "{}" trajectories do not match:'
.format(model.name, obs_idx,
model.observables[obs_idx].name))
elif format == 'json':
# Round-trip the model by re-importing the JSON
m = model_from_json(exported_file)
# Check network generation and force RHS evaluation
if model.name not in ('pysb.examples.tutorial_b',
'pysb.examples.tutorial_c'):
ScipyOdeSimulator(m, compiler='cython')
if sys.version_info.major >= 3:
# Only check on Python 3 to avoid string-to-unicode encoding
# issues
check_model_against_component_list(m,
model.all_components())
elif format == 'bngl':
if model.name.endswith('tutorial_b') or \
model.name.endswith('tutorial_c'):
# Models have no rules
return
with tempfile.NamedTemporaryFile(suffix='.bngl',
delete=False) as tf:
tf.write(exported_file.encode('utf8'))
# Cannot have two simultaneous file handled on Windows
tf.close()
try:
m = model_from_bngl(tf.name)
# Generate network and force RHS evaluation
ScipyOdeSimulator(m, compiler='cython')
finally:
os.unlink(tf.name)
def to_pysb(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'pysb_flat'))
return None
def to_kappa(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'kappa'))
return None
def to_stochkit(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'stochkit'))
return None
# # Limited Internalization Sim
# posterior_filename = 'MCMC_Results-03-11-2018\\Reanalysis\\posterior_sample_reanalysis.csv'
# priors_dict={'R1':[100,12000,None,None],'R2':[100,12000,None,None],
# 'kSOCSon':[1.5E-11,0.07,np.log(1E-6),4],
# 'k_d4':[4E-5,0.9,np.log(0.006),1.8],
# 'krec_a1':[3E-7,3E-1,None,None],'krec_a2':[5E-6,5E0,None,None],
# 'krec_b1':[1E-7,1E-1,None,None],'krec_b2':[1E-6,1E0,None,None]}
# modelfiles = ['ifnmodels.IFN_alpha_altSOCS_Internalization_ppCompatible','ifnmodels.IFN_beta_altSOCS_Internalization_ppCompatible']
# =============================================================================
# Make sure modelfile is up to date
# Write modelfiles
from pysb.export import export
alpha_model = __import__(modelfiles[0],fromlist=['ifnmodels'])
py_output = export(alpha_model.model, 'python')
with open('ODE_system_alpha.py','w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1],fromlist=['ifnmodels'])
py_output = export(beta_model.model, 'python')
with open('ODE_system_beta.py','w') as f:
f.write(py_output)
# Global data import since this script will be used exclusively on IFN data
IFN_exps = [ED.data.loc[(ED.data.loc[:,'Dose (pM)']==10) & (ED.data.loc[:,'Interferon']=="Alpha"),['0','5','15','30','60']].values[0],
ED.data.loc[(ED.data.loc[:,'Dose (pM)']==10) & (ED.data.loc[:,'Interferon']=="Beta"),['0','5','15','30','60']].values[0],
ED.data.loc[(ED.data.loc[:,'Dose (pM)']==90) & (ED.data.loc[:,'Interferon']=="Alpha"),['0','5','15','30','60']].values[0],
ED.data.loc[(ED.data.loc[:,'Dose (pM)']==90) & (ED.data.loc[:,'Interferon']=="Beta"),['0','5','15','30','60']].values[0],
ED.data.loc[(ED.data.loc[:,'Dose (pM)']==600) & (ED.data.loc[:,'Interferon']=="Alpha"),['0','5','15','30','60']].values[0],
ED.data.loc[(ED.data.loc[:,'Dose (pM)']==600) & (ED.data.loc[:,'Interferon']=="Beta"),['0','5','15','30','60']].values[0]]
def to_json(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'json'))
return None
def main():
plt.close('all')
# modelfiles = ['ifnmodels.IFN_alpha_altSOCS_ppCompatible','ifnmodels.IFN_beta_altSOCS_ppCompatible']
modelfiles = [
'ifnmodels.IFN_alpha_altSOCS_Internalization_ppCompatible',
'ifnmodels.IFN_beta_altSOCS_Internalization_ppCompatible'
]
# Write modelfiles
print("Importing models")
alpha_model = __import__(modelfiles[0], fromlist=['ifnmodels'])
py_output = export(alpha_model.model, 'python')
with open('ODE_system_alpha.py', 'w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1], fromlist=['ifnmodels'])
py_output = export(beta_model.model, 'python')
with open('ODE_system_beta.py', 'w') as f:
f.write(py_output)
# =============================================================================
# altSOCS model:
# p0=[['kpa',1.79E-5,0.1,'log'],['kSOCSon',1.70E-6,0.1,'log'],['kd4',0.87,0.2,'log'],
# ['k_d4',0.86,0.5,'log'],['delR',-1878,500,'linear'],['meanR',2000,300,'linear']]
#
# our_priors_dict={'R1':[100,12000,None,None],'R2':[100,12000,None,None],
# 'kpa':[1.5E-9,1,np.log(1),4],'kSOCSon':[1.5E-11,0.07,np.log(1E-6),4],
# 'k_d4':[4E-5,0.9,np.log(0.006),1.8],'kd4':[0.002,44,np.log(0.3),1.8]}
# =============================================================================
# altSOCS model with internalization
p0_int = [['kpa', 1.79E-5, 0.1, 'log'], ['kSOCSon', 1.70E-6, 0.2, 'log'],
['kd4', 0.87, 0.2, 'log'], ['k_d4', 0.86, 0.5, 'log'],
['delR', -1878, 500, 'linear'], ['meanR', 2000, 300, 'linear'],
['kIntBasal_r1', 1E-4, 0.1, 'log'],
['kIntBasal_r2', 2E-4, 0.1, 'log'],
['kint_IFN', 5E-4, 0.1, 'log'], ['krec_a1', 3E-4, 0.1, 'log'],
['krec_a2', 5E-3, 0.1, 'log'], ['krec_b1', 1E-4, 0.1, 'log'],
['krec_b2', 1E-3, 0.1, 'log']]
int_priors_dict = {
'R1': [100, 12000, None, None],
'R2': [100, 12000, None, None],
'kpa': [1.5E-9, 1, np.log(1), 4],
'kSOCSon': [1.5E-11, 0.07, np.log(1E-6), 4],
'k_d4': [4E-5, 0.9, np.log(0.006), 1.8],
'kd4': [0.002, 44, np.log(0.3), 1.8],
'kIntBasal_r1': [1E-7, 1E-1, None, None],
'kIntBasal_r2': [2E-7, 2E-1, None, None],
'kint_IFN': [5E-7, 5E-1, None, None],
'krec_a1': [3E-7, 3E-1, None, None],
'krec_a2': [5E-6, 5E0, None, None],
'krec_b1': [1E-7, 1E-1, None, None],
'krec_b2': [1E-6, 1E0, None, None]
}
# (n, theta_0, beta, rho, chains, burn_rate=0.1, down_sample=1, max_attempts=6,
# pflag=True, cpu=None, randomize=True)
MCMC(50,
p0_int,
int_priors_dict,
5,
1,
3,
burn_rate=0.0,
down_sample=1,
max_attempts=0)
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 19 08:49:04 2018
@author: Duncan
Export to STAN
"""
from pysb.export import export
modelfiles = [
'ifnmodels.IFN_alpha_altSOCS_Internalization_ppCompatible',
'ifnmodels.IFN_beta_altSOCS_Internalization_ppCompatible'
]
alpha_model = __import__(modelfiles[0], fromlist=['ifnmodels'])
py_output = export(alpha_model.model, 'stan')
with open('STAN_alpha.stan', 'w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1], fromlist=['ifnmodels'])
py_output = export(beta_model.model, 'stan')
with open('STAN_beta.stan', 'w') as f:
f.write(py_output)
def to_mathematica(model, outfile):
with open(outfile, 'w') as outfile:
outfile.write(export(model, 'mathematica'))
return None
def k3k4_DRparamScan(modelfile, typeIFN, param2, testDose, t_list, spec,
custom_params=None, Norm=False, cpu=None, suppress=False, doseNorm=1):
# build k3 and k4 parameters, performing a sanity check at the same time
k4scan=[]
k3scan=[]
if typeIFN=='alpha':
k4scan = 0.3*logspace(-3,3,num=len(param2[1]))
k3scan = 3E-4*logspace(-3,3,num=len(param2[1]))
elif typeIFN=='beta':
k4scan = 0.0006*logspace(-3,3,num=len(param2[1]))
k3scan = 1.2e-5*logspace(-3,3,num=len(param2[1]))
else:
print("Expected type of interferon to be either alpha or beta")
return 1
# initialization
jobs = Queue()
result = JoinableQueue()
if cpu == None or cpu >= cpu_count():
NUMBER_OF_PROCESSES = cpu_count()-1
else:
NUMBER_OF_PROCESSES = cpu
print("using {} processors".format(NUMBER_OF_PROCESSES))
# build task list
params=[]
print("building tasks")
if typeIFN=='alpha':
if custom_params == None:
for val1 in range(len(k4scan)):
for val2 in param2[1]:
params.append([['kd3',k3scan[val1]],['kd4',k4scan[val1]],[param2[0],val2]])
else:
for val1 in range(len(k4scan)):
for val2 in param2[1]:
params.append([['kd3',k3scan[val1]],['kd4',k4scan[val1]],[param2[0],val2]]+[c for c in custom_params])
elif typeIFN=='beta':
if custom_params == None:
for val1 in range(len(k4scan)):
for val2 in param2[1]:
params.append([['k_d3',k3scan[val1]],['k_d4',k4scan[val1]],[param2[0],val2]])
else:
for val1 in range(len(k4scan)):
for val2 in param2[1]:
params.append([['k_d3',k3scan[val1]],['k_d4',k4scan[val1]],[param2[0],val2]]+[c for c in custom_params])
# Write modelfile
imported_model = __import__(modelfile)
py_output = export(imported_model.model, 'python')
with open('ODE_system.py','w') as f:
f.write(py_output)
# put jobs on the queue
tasks = [[modelfile, testDose, t_list, spec, Norm, p] for p in params]
print("There are {} tasks to compute".format(len(params)))
print("putting tasks on the queue")
for w in tasks:
jobs.put(w)
print("computing scan")
# start up the workers
[Process(target=p_DRparamScan_helper, args=(i, jobs, result)).start()
for i in range(NUMBER_OF_PROCESSES)]
# pull in the results from each worker
pool_results=[]
for t in range(len(tasks)):
r = result.get()
pool_results.append(r)
result.task_done()
# tell the workers there are no more jobs
for w in range(NUMBER_OF_PROCESSES):
jobs.put(None)
# close all extra threads
result.join()
jobs.close()
result.close()
print("done scan")
# plot heatmap if suppress==False
if suppress==False:
dose_image, response_image = image_builder(pool_results, doseNorm, (len(k4scan),len(param2[1])))
if typeIFN=='alpha':
IFN_heatmap(response_image, ['Response_EC50_alpha_k4',k4scan], param2)
IFN_heatmap(dose_image, ['Dose_EC50_alpha_k4',k4scan], param2)
else:
IFN_heatmap(response_image, ['Response_EC50_beta_k4',k4scan], param2)
IFN_heatmap(dose_image, ['Dose_EC50_beta_k4',k4scan], param2)
#return the scan
return pool_results
# -*- coding: utf-8 -*-
"""
Spyder Editor
This is a temporary script file.
"""
from pysb.export import export
import numpy as np
import matplotlib.pyplot as plt
modelfiles = [
'IFN_detailed_alt_SOCS_alpha_ppCompatible',
'IFN_detailed_alt_SOCS_beta_ppCompatible'
]
alpha_model = __import__(modelfiles[0])
py_output = export(alpha_model.model, 'sbml')
with open('detailed_SBML_alpha.sbml', 'w') as f:
f.write(py_output)
beta_model = __import__(modelfiles[1])
py_output = export(beta_model.model, 'sbml')
with open('detailed_SBML_beta.sbml', 'w') as f:
f.write(py_output)
# =============================================================================
# import ODE_system_alpha as m
# mA = m.Model()
# alpha_parameters=[]
# for p in mA.parameters:
# if p[0]=='kd4':
# alpha_parameters.append(0.485)
# elif p[0]=='kSOCSon':
def check_convert(model, format):
""" Test exporters run without error """
exported_file = None
try:
exported_file = export.export(model, format)
except export.ExpressionsNotSupported:
pass
except export.CompartmentsNotSupported:
pass
except export.LocalFunctionsNotSupported:
pass
except Exception as e:
# Some example models are deliberately incomplete, so here we
# will treat any of these "expected" exceptions as a success.
exception_class = expected_exceptions.get(base_name(model))
if not exception_class or not isinstance(e, exception_class):
raise
if exported_file is not None:
if format == 'python':
# linspace arguments picked to avoid VODE warning
exec(
exported_file +
'Model().simulate(tspan=numpy.linspace(0,1,501))\n',
{'_use_inline': False})
elif format == 'pysb_flat':
exec(exported_file, {'__name__': model.name})
elif format == 'sbml':
# Skip the simulation comparison if roadrunner not available
if roadrunner is None:
raise SkipTest(
"SBML Simulation test skipped (requires roadrunner)")
roadrunner.Logger.setLevel(roadrunner.Logger.LOG_ERROR)
# Simulate SBML using roadrunner
rr = roadrunner.RoadRunner(exported_file)
rr.timeCourseSelections = \
['__s{}'.format(i) for i in range(len(model.species))] + \
['__obs{}'.format(i) for i in range(len(model.observables))]
rr_result = rr.simulate(0, 10, 100)
# Simulate original using PySB
df = ScipyOdeSimulator(model).run(
tspan=np.linspace(0, 10, 100)).dataframe
# Compare species' trajectories
for sp_idx in range(len(model.species)):
rr_sp = rr_result[:, sp_idx]
py_sp = df.iloc[:, sp_idx]
is_close = np.allclose(rr_sp, py_sp, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_sp, pysb=py_sp)))
raise ValueError(
'Model {}, species __s{} trajectories do not match:'.
format(model.name, sp_idx))
# Compare observables' trajectories
for obs_idx in range(len(model.observables)):
rr_obs = rr_result[:, obs_idx + len(model.species)]
py_obs = df.iloc[:, obs_idx + len(model.species)]
is_close = np.allclose(rr_obs, py_obs, rtol=1e-4)
if not is_close:
print(pd.DataFrame(dict(rr=rr_obs, pysb=py_obs)))
raise ValueError(
'Model {}, observable__o{} "{}" trajectories do not match:'
.format(model.name, obs_idx,
model.observables[obs_idx].name))
