public override void GlobalContext()
{
base.GlobalContext();
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Periportal).Value = 1;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
var objectPatFactory = new ObjectPathFactoryForSpecs();
var path = objectPatFactory.CreateObjectPathFrom(Constants.ORGANISM,
CoreConstants.Organ.Liver,
CoreConstants.Compartment.Pericentral,
CoreConstants.Compartment.Intracellular,
CoreConstants.Molecule.ProcessProductName(_compound.Name, _enzyme.Name, CoreConstants.Molecule.Metabolite),
CoreConstants.Observer.ObserverNameFrom(CoreConstants.Observer.FRACTION_OF_DOSE, _compound.Name));
var quantitySelection = new QuantitySelection(path.ToString(), QuantityType.Metabolite);
_simulation.OutputSelections.AddOutput(quantitySelection);
}
public static IDistributedParameter NormalDistributedParameter(double defaultMean = 0, double defaultDeviation = 1, double defaultPercentile = 0.5, bool isDefault = false, bool distributionParameterIsDefault = true)
{
var parameter = new DistributedParameter().WithId("P1");
parameter.IsDefault = isDefault;
var pathFactory = new ObjectPathFactoryForSpecs();
var meanParameter = new Parameter {
Name = Constants.Distribution.MEAN
}.WithFormula(new ConstantFormula(defaultMean).WithId("MeanFormula")).WithId("Mean");
meanParameter.IsDefault = distributionParameterIsDefault;
addDimensionTo(meanParameter);
var stdParameter = new Parameter {
Name = Constants.Distribution.DEVIATION
}.WithFormula(new ConstantFormula(defaultDeviation).WithId("DeviationFormula")).WithId("Deviation");
stdParameter.IsDefault = distributionParameterIsDefault;
addDimensionTo(stdParameter);
var percentileParameter = new Parameter {
Name = Constants.Distribution.PERCENTILE
}.WithFormula(new ConstantFormula(defaultPercentile).WithId("PercentileFormula")).WithId("Percentile");
percentileParameter.IsDefault = distributionParameterIsDefault;
addDimensionTo(percentileParameter);
parameter.Add(meanParameter);
parameter.Add(stdParameter);
parameter.Add(percentileParameter);
parameter.Formula = new NormalDistributionFormula().WithId("NormalDistributionFormula");
parameter.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(parameter, meanParameter));
parameter.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(parameter, stdParameter));
addDimensionTo(parameter);
return(parameter);
}
public override void GlobalContext()
{
base.GlobalContext();
_allExpressionParameters[CoreConstants.Compartment.PLASMA].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.BLOOD_CELLS].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.VASCULAR_ENDOTHELIUM].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.PERIPORTAL].Value = 1;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection
{
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
var objectPatFactory = new ObjectPathFactoryForSpecs();
var path = objectPatFactory.CreateObjectPathFrom(Constants.ORGANISM,
CoreConstants.Organ.LIVER,
CoreConstants.Compartment.PERICENTRAL,
CoreConstants.Compartment.INTRACELLULAR,
CoreConstants.Molecule.ProcessProductName(_compound.Name, _enzyme.Name, CoreConstants.Molecule.Metabolite),
CoreConstants.Observer.ObserverNameFrom(CoreConstants.Observer.FRACTION_OF_DOSE, _compound.Name));
var quantitySelection = new QuantitySelection(path.ToString(), QuantityType.Metabolite);
_simulation.OutputSelections.AddOutput(quantitySelection);
}
protected override void Context()
{
base.Context();
var objectPathFactory = new ObjectPathFactoryForSpecs();
_oneParameter = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1").WithId("1");
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName("toto").WithId("2");
_parameter.Formula = new ExplicitFormula("2*3").WithId("p");
_container.Add(_oneParameter);
_container.Add(_parameter);
_parameter.Formula.AddObjectPath(objectPathFactory.CreateRelativeFormulaUsablePath(_parameter, _oneParameter));
_parameter.Value = 10;
}
