Sensitivity Analysis Added

tellurium/__init__.py

@@ -86,12 +86,13 @@
 # Distributed computing
 from .analysis.stochasticmodel import StochasticSimulationModel
 from .analysis.parameterestimation import ParameterEstimation
+from .analysis.sensitivityanalysis import SensitivityAnalysis
 
 from .tellurium import (
     # distrib. parameter scan
     distributed_parameter_scanning, sample_plot, plotImage,
     # distrib. stochastic sims & fitting
-    distributed_stochastic_simulation, plot_distributed_stochastic, plot_stochastic_result
+    distributed_stochastic_simulation, plot_distributed_stochastic, plot_stochastic_result, distributed_sensitivity_analysis
     )
 
 # Bifurcations

tellurium/analysis/sensitivityanalysis.py

@@ -0,0 +1,89 @@
+class SensitivityAnalysis(object):
+    def __init__(self,model=None,sbml=False,conservedMoietyAnalysis=True):
+        self._model = model
+        self._sbml = sbml
+        self._conservedMoietyAnalysis = conservedMoietyAnalysis
+        self._preprocessingFunc = None
+        self._bounds = None
+        self._args = None
+
+
+    @property
+    def model(self):
+        return self._model
+
+    @model.setter
+    def model(self, value):
+        self._model = value
+
+    @model.deleter
+    def model(self):
+        del self._model
+
+    @property
+    def sbml(self):
+        return self._sbml
+
+    @sbml.setter
+    def sbml(self, value):
+        self._sbml = value
+
+    @sbml.deleter
+    def sbml(self):
+        del self._sbml
+
+    @property
+    def conservedMoietyAnalysis(self):
+        return self._conservedMoietyAnalysis
+
+    @conservedMoietyAnalysis.setter
+    def conservedMoietyAnalysis(self, value):
+        self._conservedMoietyAnalysis = value
+
+    @conservedMoietyAnalysis.deleter
+    def conservedMoietyAnalysis(self):
+        del self._conservedMoietyAnalysis
+
+
+    @property
+    def preprocessingFunc(self):
+        return self._preprocessingFunc
+
+    @preprocessingFunc.setter
+    def preprocessingFunc(self, value):
+        self._preprocessingFunc = value
+
+    @preprocessingFunc.deleter
+    def preprocessingFunc(self):
+        del self._preprocessingFunc
+
+
+    @property
+    def bounds(self):
+        return self._bounds
+
+    @bounds.setter
+    def bounds(self, value):
+        self._bounds = value
+
+    @bounds.deleter
+    def bounds(self):
+        del self._bounds
+
+    @property
+    def args(self):
+        return self._args
+
+    @args.setter
+    def args(self, value):
+        self._args = value
+
+    @args.deleter
+    def args(self):
+        del self._args
+
+
+    def setPreProcessingFunction(self,func,*args):
+        self._preprocessingFunc = func
+        self._args = args
+

tellurium/metastore_db/README_DO_NOT_TOUCH_FILES.txt

@@ -0,0 +1,9 @@
+
+# *************************************************************************
+# ***              DO NOT TOUCH FILES IN THIS DIRECTORY!                ***
+# *** FILES IN THIS DIRECTORY AND SUBDIRECTORIES CONSTITUTE A DERBY     ***
+# *** DATABASE, WHICH INCLUDES THE DATA (USER AND SYSTEM) AND THE       ***
+# *** FILES NECESSARY FOR DATABASE RECOVERY.                            ***
+# *** EDITING, ADDING, OR DELETING ANY OF THESE FILES MAY CAUSE DATA    ***
+# *** CORRUPTION AND LEAVE THE DATABASE IN A NON-RECOVERABLE STATE.     ***
+# *************************************************************************

tellurium/metastore_db/log/README_DO_NOT_TOUCH_FILES.txt

@@ -0,0 +1,8 @@
+
+# *************************************************************************
+# ***              DO NOT TOUCH FILES IN THIS DIRECTORY!                ***
+# *** FILES IN THIS DIRECTORY ARE USED BY THE DERBY DATABASE RECOVERY   ***
+# *** SYSTEM. EDITING, ADDING, OR DELETING FILES IN THIS DIRECTORY      ***
+# *** WILL CAUSE THE DERBY RECOVERY SYSTEM TO FAIL, LEADING TO          ***
+# *** NON-RECOVERABLE CORRUPT DATABASES.                                ***
+# *************************************************************************

tellurium/metastore_db/seg0/README_DO_NOT_TOUCH_FILES.txt

@@ -0,0 +1,8 @@
+
+# *************************************************************************
+# ***              DO NOT TOUCH FILES IN THIS DIRECTORY!                ***
+# *** FILES IN THIS DIRECTORY ARE USED BY THE DERBY DATABASE TO STORE   *** 
+# *** USER AND SYSTEM DATA. EDITING, ADDING, OR DELETING FILES IN THIS  ***
+# *** DIRECTORY WILL CORRUPT THE ASSOCIATED DERBY DATABASE AND MAKE     ***
+# *** IT NON-RECOVERABLE.                                               ***
+# *************************************************************************

tellurium/metastore_db/service.properties

@@ -0,0 +1,23 @@
+#/home/shaik/gsoc/tellurium/tellurium/metastore_db
+# ********************************************************************
+# ***                Please do NOT edit this file.                 ***
+# *** CHANGING THE CONTENT OF THIS FILE MAY CAUSE DATA CORRUPTION. ***
+# ********************************************************************
+#Wed Jun 28 09:27:25 PDT 2017
+SysschemasIndex2Identifier=225
+SyscolumnsIdentifier=144
+SysconglomeratesIndex1Identifier=49
+SysconglomeratesIdentifier=32
+SyscolumnsIndex2Identifier=177
+SysschemasIndex1Identifier=209
+SysconglomeratesIndex3Identifier=81
+SystablesIndex2Identifier=129
+SyscolumnsIndex1Identifier=161
+derby.serviceProtocol=org.apache.derby.database.Database
+SysschemasIdentifier=192
+derby.storage.propertiesId=16
+SysconglomeratesIndex2Identifier=65
+derby.serviceLocale=en_US
+SystablesIdentifier=96
+SystablesIndex1Identifier=113
+#--- last line, don't put anything after this line ---

tellurium/tellurium.py

@@ -354,6 +354,72 @@ def spark_work(model_with_parameters):
 
     return(sc.parallelize(list_of_models,len(list_of_models)).map(spark_work).collect())
 
+def distributed_sensitivity_analysis(sc,senitivity_analysis_model):
+    def spark_sensitivity_analysis(model_with_parameters):
+        import tellurium as te
+
+        sa_model = model_with_parameters[0]
+        parameters = model_with_parameters[1]
+
+        if(sa_model.sbml):
+            model_roadrunner = te.loadAntimonyModel(te.sbmlToAntimony(sa_model.model))
+        else:
+            model_roadrunner = te.loadAntimonyModel(sa_model.model)
+
+        model_roadrunner.conservedMoietyAnalysis = sa_model.conservedMoietyAnalysis
+
+        #Performing PreSimulation
+        if(sa_model.preprocessingFunc is None):
+            pre_simulator = getattr(model_roadrunner, "simulate")
+        else:
+            pre_simulator = getattr(model_roadrunner, sa_model.preprocessingFunc)
+
+        pre_simulator(*sa_model.args)
+        ANALYSIS = ""
+        #Setting the Parameter Variables
+        for i_param,param_names in enumerate(sa_model.bounds.keys()):
+            ANALYSIS += ("\nSetting Value of {0} as {1}".format(param_names,parameters[i_param]))
+            setattr(model_roadrunner, param_names, parameters[i_param])
+
+
+        fig1a_local = model_roadrunner.getCC('PP_K', 'r1b_k2')
+        ANALYSIS += ('\nFigure 1A: local value = {}'.format(fig1a_local))
+
+
+        fig1b_local = model_roadrunner.getCC('PP_K', 'r8a_a8')
+        ANALYSIS += ('\nFigure 1B: local value = {}'.format(fig1b_local))
+
+
+        fig1c_local = model_roadrunner.getCC('PP_K', 'r10a_a10')
+        ANALYSIS += ('\nFigure 1C: local value = {}'.format(fig1c_local))
+        return(ANALYSIS)
+
+
+    if(senitivity_analysis_model.bounds is  None):
+        print("Bounds are Undefined.")
+        return
+
+    params = []
+    for bound_values in senitivity_analysis_model.bounds.values():
+        if(len(bound_values) > 2):
+            params.append(np.linspace(bound_values[0], bound_values[1], bound_values[2]))
+        elif(len(bound_values == 2)):
+            params.append(np.linspace(bound_values[0], bound_values[1], 3))
+        else:
+            print("Improper Boundaries Defined")
+            return;
+    samples = perform_sampling(np.meshgrid(*params))
+    samples = zip([senitivity_analysis_model]*len(samples),samples)
+    return(sc.parallelize(samples,len(samples)).map(spark_sensitivity_analysis).collect())
+
+def perform_sampling(mesh):
+    samples = []
+    mesh = [items.flatten() for items in mesh]
+    for i in range(len(mesh[0])):
+        samples.append([items[i] for items in mesh])
+    return(samples)
+
+
 def loada(ant):
     """Load model from Antimony string.