public override void GlobalContext()
{
base.GlobalContext();
_simulation = _simulationPersister.LoadSimulation(HelperForSpecs.DataFile("S1.pkml"));
_concurrentRunSimulationBatch = new ConcurrentRunSimulationBatch
(
_simulation,
new SimulationBatchOptions
{
VariableMolecules = new[]
{
new[] { "Organism", "Kidney", "Intracellular", "Caffeine" }.ToPathString()
},
VariableParameters = new[]
{
new[] { "Organism", "Liver", "Volume" }.ToPathString(),
new[] { "Organism", "Hematocrit" }.ToPathString(),
}
}
);
sut.AddSimulationBatch(_concurrentRunSimulationBatch);
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
var pkParametersTask = Api.GetPKParameterTask();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 2, VariationRange = 0.2
};
//Should calculate CMax/100
_userDefinedPKParameter = new UserDefinedPKParameter {
Name = "Toto", NormalizationFactor = 100, StandardPKParameter = StandardPKParameter.C_max
};
pkParametersTask.AddUserDefinedPKParameter(_userDefinedPKParameter);
_userDefinedCLParameter = new UserDefinedPKParameter {
Name = "MyCL", StandardPKParameter = StandardPKParameter.CL
};
pkParametersTask.AddUserDefinedPKParameter(_userDefinedCLParameter);
var containerTask = Api.GetContainerTask();
var liverVolumes = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume");
_sensitivityAnalysis.AddParameterPaths(liverVolumes.Select(x => x.ConsolidatedPath()));
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = _simulationPersister.LoadSimulation(HelperForSpecs.DataFile("not_ok_sim.pkml"));
var containerTask = Api.GetContainerTask();
containerTask.AddQuantitiesToSimulationOutputByPath(_simulation, "DERMAL_APPLICATION_AREA|skin_compartment|SC_skin_sublayer|comp10_1|layer1|permeant");
_simulationBatch = new ConcurrentRunSimulationBatch
(
_simulation,
new SimulationBatchOptions
{
VariableParameters = new[]
{
"DERMAL_APPLICATION_AREA|skin_compartment|SC_skin_sublayer|SC_total_thickness",
}
}
);
_parValues = new SimulationBatchRunValues
{
ParameterValues = new[] { 0.0002 }
};
_simulationBatch.AddSimulationBatchRunValues(_parValues);
sut.AddSimulationBatch(_simulationBatch);
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = _simulationPersister.LoadSimulation(HelperForSpecs.DataFile("S1.pkml"));
_simulationBatch = new ConcurrentRunSimulationBatch
(
_simulation,
new SimulationBatchOptions
{
VariableParameters = new[]
{
new[] { "Organism", "Liver", "Volume" }.ToPathString(),
new[] { "Organism", "Hematocrit" }.ToPathString(),
}
}
);
_parValues1 = new SimulationBatchRunValues
{
ParameterValues = new[] { 3.5, 0.53 }
};
_parValues2 = new SimulationBatchRunValues
{
ParameterValues = new[] { 3.4, 0.50 }
};
_simulationBatch.AddSimulationBatchRunValues(_parValues1);
sut.AddSimulationBatch(_simulationBatch);
sut.RunConcurrently();
sut.Dispose();
}
protected override void Context()
{
base.Context();
_simulationFile = FileHelper.GenerateTemporaryFileName();
var fileName = HelperForSpecs.DataFile("S1.pkml");
_simulation = sut.LoadSimulation(fileName);
}
protected override void Context()
{
sut = Api.GetSimulationResultsTask();
_simulationPersister = Api.GetSimulationPersister();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
_simulation = _simulationPersister.LoadSimulation(simulationFile);
}
public override void GlobalContext()
{
base.GlobalContext();
var tmpFile = FileHelper.GenerateTemporaryFileName();
_outputFolder = new FileInfo(tmpFile).DirectoryName;
_populationFile = HelperForSpecs.DataFile("pop_5.csv");
}
public override void GlobalContext()
{
base.GlobalContext();
_simulationFile = HelperForSpecs.DataFile("S1.pkml");
_simulationPersister = Api.GetSimulationPersister();
_simulationBatchFactory = Api.GetSimulationBatchFactory();
_simulation = _simulationPersister.LoadSimulation(_simulationFile);
}
protected override void Context()
{
base.Context();
sut.AddSimulation(_simulationPersister.LoadSimulation(HelperForSpecs.DataFile("S1.pkml")));
sut.AddSimulation(_simulationPersister.LoadSimulation(HelperForSpecs.DataFile("simple.pkml")));
sut.AddSimulation(_simulationPersister.LoadSimulation(HelperForSpecs.DataFile("simple.pkml")));
sut.AddSimulation(_simulationPersister.LoadSimulation(HelperForSpecs.DataFile("multiple_dosing.pkml")));
}
public override void GlobalContext()
{
base.GlobalContext();
_populationFile = HelperForSpecs.DataFile("pop_10.csv");
_populationFileWithUnitInParameterName = HelperForSpecs.DataFile("pop_10_parameter_with_unit.csv");
_simulationFile = HelperForSpecs.DataFile("S1.pkml");
_simulationPersister = Api.GetSimulationPersister();
sut = Api.GetPopulationTask();
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
var containerTask = Api.GetContainerTask();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_liverVolume = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume").First();
}
public override void GlobalContext()
{
base.GlobalContext();
_populationFile = HelperForSpecs.DataFile("pop_10.csv");
_simulationFile = HelperForSpecs.DataFile("S1.pkml");
_simulationPersister = Api.GetSimulationPersister();
_populationTask = Api.GetPopulationTask();
sut = Api.GetSimulationRunner();
_simulation = _simulationPersister.LoadSimulation(_simulationFile);
}
public override void GlobalContext()
{
base.GlobalContext();
var populationFile = HelperForSpecs.DataFile("pop_5_sparse_id.csv");
var populationTask = Api.GetPopulationTask();
_population = populationTask.ImportPopulation(populationFile);
_result = _simulationRunner.Run(new SimulationRunArgs {
Simulation = _simulation, Population = _population
});
}
protected override void Context()
{
base.Context();
var simulationFile = HelperForSpecs.DataFile("multiple_dosing.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_result = _simulationRunner.Run(new SimulationRunArgs {
Simulation = _simulation
});
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("simple.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 1, VariationRange = 0.2
};
}
public override void GlobalContext()
{
base.GlobalContext();
var populationFile = HelperForSpecs.DataFile("pop_5.csv");
var populationTask = Api.GetPopulationTask();
_population = populationTask.ImportPopulation(populationFile);
//negative volumes ensures that we have one simulation crashing
_population.SetValues("Organism|Liver|Volume", new[] { 2.3, 2.3, 2.3, 2.3, -10 });
_result = _simulationRunner.Run(new SimulationRunArgs {
Simulation = _simulation, Population = _population
});
}
public override void GlobalContext()
{
base.GlobalContext();
_outputPath = "Organism|PeripheralVenousBlood|Caffeine|Plasma (Peripheral Venous Blood)";
_pkParameterFile = HelperForSpecs.DataFile("20 Values for peripheral venous blood.csv");
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_simulationRunner = Api.GetSimulationRunner();
_pkParameterTask = Api.GetPKParameterTask();
sut = Api.GetPKAnalysisTask();
}
protected override void Context()
{
base.Context();
var simulationFile = HelperForSpecs.DataFile("Simple.pkml");
_simulation = _simulationPersister.LoadSimulation(simulationFile);
var simulationRunner = Api.GetSimulationRunner();
_results = simulationRunner.Run(new SimulationRunArgs {
Simulation = _simulation
});
_csvFile = FileHelper.GenerateTemporaryFileName();
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 2, VariationRange = 0.2
};
var containerTask = Api.GetContainerTask();
var liverVolumes = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume");
_sensitivityAnalysis.AddParameterPaths(liverVolumes.Select(x => x.ConsolidatedPath()));
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 2, VariationRange = 0.2
};
var containerTask = Api.GetContainerTask();
var liverVolumes = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume");
_sensitivityAnalysis.AddParameters(liverVolumes);
_sensitivityAnalysisRunner = Api.GetSensitivityAnalysisRunner();
_sensitivityAnalysisRunResult = _sensitivityAnalysisRunner.Run(_sensitivityAnalysis);
_allPKParameterSensitivities = _sensitivityAnalysisRunResult.AllPKParameterSensitivities;
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = _simulationPersister.LoadSimulation(HelperForSpecs.DataFile("sc_model_2c.pkml"));
_simulationRunner = Api.GetSimulationRunner();
_containerTask = Api.GetContainerTask();
_containerTask.AddQuantitiesToSimulationOutputByPath(_simulation, "DERMAL_APPLICATION_AREA|permeant|Mass_balance_observer");
_containerTask.AddQuantitiesToSimulationOutputByPath(_simulation, "DERMAL_APPLICATION_AREA|permeant|Stratum_corneum_observer");
_containerTask.AddQuantitiesToSimulationOutputByPath(_simulation, "DERMAL_APPLICATION_AREA|permeant|Vehicle_observer");
_simulationBatch = new ConcurrentRunSimulationBatch
(
_simulation,
new SimulationBatchOptions
{
VariableParameters = new[]
{
"DERMAL_APPLICATION_AREA|skin_compartment|SC_skin_sublayer|SC_total_thickness",
"DERMAL_APPLICATION_AREA|skin_compartment|Hydrated SC",
}
}
);
_parValues = new SimulationBatchRunValues
{
ParameterValues = new[]
{
0.0002, 1
}
};
_simulationBatch.AddSimulationBatchRunValues(_parValues);
sut.AddSimulationBatch(_simulationBatch);
}
protected override void Context()
{
base.Context();
_resultsFile = HelperForSpecs.DataFile("res_10.csv");
}
protected override void Context()
{
base.Context();
_simulationFile = HelperForSpecs.DataFile("S1.pkml");
}
protected override void Context()
{
base.Context();
_junkFile = HelperForSpecs.DataFile("pop_10.csv");
}
