public override void GlobalContext()
{
base.GlobalContext();
_induction = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.INDUCTION).DowncastTo <InductionProcess>());
_induction.Name = "Induction";
_induction.Parameter(CoreConstantsForSpecs.Parameter.EC50).Value = 10;
_compound.AddProcess(_induction);
_irreversibleInhibiton = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.IRREVERSIBLE_INHIBITION).DowncastTo <InhibitionProcess>());
_irreversibleInhibiton.Name = "IrreversibleProcess";
_irreversibleInhibiton.Parameter(CoreConstantsForSpecs.Parameter.KINACT).Value = 10;
_compound.AddProcess(_irreversibleInhibiton);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound }, new[] { _protocol })
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
_simulation.InteractionProperties.AddInteraction(new InteractionSelection {
CompoundName = _compound.Name, MoleculeName = _enzyme.Name, ProcessName = _induction.Name
});
_simulation.InteractionProperties.AddInteraction(new InteractionSelection {
CompoundName = _compound.Name, MoleculeName = _enzyme.Name, ProcessName = _irreversibleInhibiton.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_otherCompound = DomainFactoryForSpecs.CreateStandardCompound().WithName("OtherCompound");
_otherProtocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("OtherProtocol");
var liverClearance = addLiverPlasmaClearanceTo(_compound);
addLiverPlasmaClearanceTo(_otherCompound);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound, _otherCompound }, new[] { _protocol, _otherProtocol, })
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
CompoundName = _compound.Name, ProcessName = liverClearance.Name, ProcessType = liverClearance.SystemicProcessType
});
_simulation.CompoundPropertiesFor(_otherCompound.Name)
.Processes
.MetabolizationSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
CompoundName = _otherProtocol.Name, ProcessName = liverClearance.Name, ProcessType = liverClearance.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_transporterContainerTemplateRepository = IoC.Resolve <ITransporterContainerTemplateRepository>();
var allTransporters = _transporterContainerTemplateRepository.TransportersFor(_individual.Species.Name, CoreConstants.Organ.Brain);
var influxBBB = allTransporters.Where(x => x.MembraneLocation == MembraneLocation.BloodBrainBarrier)
.FirstOrDefault(x => x.TransportType == TransportType.Influx);
_transporter = _transporterFactory.CreateFor(_individual).DowncastTo <IndividualTransporter>().WithName("TRANS");
var transportContainer = _transporter.ExpressionContainer(CoreConstants.Organ.Brain).DowncastTo <TransporterExpressionContainer>();
transportContainer.UpdatePropertiesFrom(influxBBB);
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
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 void should_be_able_to_create_a_simulation()
{
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
var simEvent = _simulation.Model.Root.EntityAt <IContainer>(Constants.EVENTS, "Event");
simEvent.ShouldNotBeNull();
}
public override void GlobalContext()
{
base.GlobalContext();
_transporter = _transporterFactory.CreateFor(_individual, "TRANS", TransportType.Efflux).DowncastTo <IndividualTransporter>();
var transportContainer = _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(_transporter)
.First(x => x.LogicalContainer.IsNamed(CoreConstants.Organ.BRAIN));
transportContainer.TransportDirection = TransportDirectionId.InfluxBrainPlasmaToInterstitial;
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection
{
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
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);
}
public override void GlobalContext()
{
base.GlobalContext();
_otherCompound = DomainFactoryForSpecs.CreateStandardCompound().WithName("OtherCompound");
_otherProtocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("OtherProtocol");
_otherCompound.AddProcess(_cloneManager.Clone(_metabolizationProcess));
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound, _otherCompound }, new[] { _protocol, _otherProtocol, })
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
_simulation.CompoundPropertiesFor(_otherCompound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _otherCompound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound, _metabolite }, new[] { _protocol, null }).DowncastTo <IndividualSimulation>();
ProcessSelectionFor(_parentMetabolizationCYP3A4).MetaboliteName = _metabolite.Name;
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_buildConfigurationTask = IoC.Resolve <IBuildConfigurationTask>();
_entityPathResolver = IoC.Resolve <IEntityPathResolver>();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
var cloneManager = IoC.Resolve <ICloneManager>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = enzymeFactory.AddMoleculeTo(_individual, "CYP").DowncastTo <IndividualEnzyme>();
_metabolizationProcess = cloneManager.Clone(compoundProcessRepository
.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
const string transporterName = "Tr1";
var individual = DomainFactoryForSpecs.CreateStandardIndividual();
var transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
var transporter = transporterFactory.CreateFor(individual).WithName(transporterName);
individual.AddMolecule(transporter);
var compound = DomainFactoryForSpecs.CreateStandardCompound().WithName(_drugName);
var cloneManager = IoC.Resolve <ICloneManager>();
var compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
var transportProcess = cloneManager.Clone(compoundProcessRepository.ProcessByName(CompoundTransportName))
.WithName(_transportProcessName);
compound.AddProcess(transportProcess);
var protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(individual, compound, protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new ProcessSelection {
ProcessName = transportProcess.Name, MoleculeName = transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _iv).DowncastTo <IndividualSimulation>();
_simulation.AllowAging = true;
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepo = IoC.Resolve <ICompoundProcessRepository>();
_interactionTask = IoC.Resolve <IInteractionTask>();
var cloner = IoC.Resolve <ICloneManager>();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
var inhibitor = DomainFactoryForSpecs.CreateStandardCompound().WithName("Inhibitor");
var protocol2 = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("IV2");
var allPartialProcesses = PartialProcesses.ToList();
foreach (var metaTemplate in allPartialProcesses)
{
var moleculeName = "Molecule_" + metaTemplate.Name;
if (metaTemplate as EnzymaticProcess != null)
{
var individualProtein = enzymeFactory.CreateFor(_individual).WithName(moleculeName);
_individual.AddMolecule(individualProtein.DowncastTo <IndividualEnzyme>().WithName(moleculeName));
}
else
{
var individualProtein = transporterFactory.CreateFor(_individual).WithName(moleculeName);
_individual.AddMolecule(individualProtein.DowncastTo <IndividualTransporter>().WithName(moleculeName));
}
var process = cloner.Clone(metaTemplate).DowncastTo <PartialProcess>();
process.Name = "Process " + moleculeName;
process.MoleculeName = moleculeName;
_compound.AddProcess(process);
var inhibitionTemplate = _compoundProcessRepo.ProcessByName <InteractionProcess>(InhibitionProcessName);
var inhibitionProcess = cloner.Clone(inhibitionTemplate);
inhibitionProcess.Name = "InhibitionProcess " + moleculeName;
inhibitionProcess.MoleculeName = moleculeName;
inhibitor.AddProcess(inhibitionProcess);
}
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(
_individual, new[] { _compound, inhibitor }, new[] { _protocol, protocol2 }).DowncastTo <IndividualSimulation>();
foreach (var inhibitionProcess in inhibitor.AllProcesses <InteractionProcess>())
{
var interactionSelection = new InteractionSelection {
CompoundName = inhibitor.Name, MoleculeName = inhibitionProcess.MoleculeName, ProcessName = inhibitionProcess.Name
};
_simulation.InteractionProperties.AddInteraction(interactionSelection);
}
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
protected IndividualSimulation CreateSimulationWithCalculatedSpecificPintFor(CalculationMethod intestinalPermeabilityMethod)
{
var modelProperties = DomainFactoryForSpecs.CreateDefaultModelPropertiesFor(_individual);
_compound.RemoveCalculationMethodFor(CoreConstants.Category.IntestinalPermeability);
_compound.AddCalculationMethod(intestinalPermeabilityMethod);
var simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol, modelProperties).DowncastTo <IndividualSimulation>();
DomainFactoryForSpecs.AddModelToSimulation(simulation);
return(simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var templateIndividual = DomainFactoryForSpecs.CreateStandardIndividual();
var compound = DomainFactoryForSpecs.CreateStandardCompound();
var protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = enzymeFactory.CreateFor(templateIndividual).DowncastTo <IndividualEnzyme>().WithName("CYP");
templateIndividual.AddMolecule(_enzyme);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(templateIndividual, compound, protocol).DowncastTo <IndividualSimulation>();
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_compound2 = DomainFactoryForSpecs.CreateStandardCompound().WithName("C2");
_protocol2 = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("IV2");
var modelProps = DomainFactoryForSpecs.CreateModelPropertiesFor(_individual, CoreConstants.Model.TwoPores);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(
_individual, new[] { _compound, _compound2 }, new[] { _protocol, _protocol2 }, modelProps) as IndividualSimulation;
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
_compound1Name = _compound.Name;
_compound2Name = _compound2.Name;
}
public override void GlobalContext()
{
base.GlobalContext();
_kidneyProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstants.Process.KIDNEY_CLEARANCE).DowncastTo <SystemicProcess>());
_kidneyProcess.Name = "My Kidney Process";
_kidneyProcess.Parameter(ConverterConstants.Parameter.PlasmaClearance).Value = 10;
_compound.AddProcess(_kidneyProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _kidneyProcess.Name, ProcessType = _kidneyProcess.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_processGFR = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.GLOMERULAR_FILTRATION).DowncastTo <SystemicProcess>());
_processGFR.Name = "My GFR Process";
_processGFR.Parameter(CoreConstants.Parameters.GFR_FRACTION).Value = 0.8;
_compound.AddProcess(_processGFR);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _processGFR.Name, ProcessType = _processGFR.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_process = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(ProcessName).DowncastTo <SystemicProcess>());
_process.Name = "My Liver Process";
_process.Parameter(ConverterConstants.Parameter.CLspec).Value = 1;
_compound.AddProcess(_process);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _process.Name, ProcessType = _process.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
var enzymeFactory = IoC.Resolve<IIndividualEnzymeFactory>();
var individualProtein = enzymeFactory.CreateFor(_individual).WithName(_enzymeName);
individualProtein.Ontogeny = new UserDefinedOntogeny() {Table = createOntogenyTable()};
_individual.AddMolecule(individualProtein.DowncastTo<IndividualEnzyme>().WithName(_enzymeName));
var containerTask = IoC.Resolve<IContainerTask>();
_individual.OriginData.Age = 2;
_allDistributedParameter = containerTask.CacheAllChildren<IDistributedParameter>(_individual);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol) as IndividualSimulation;
_simulation.AllowAging = true;
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
_allAgeDependentParameters = containerTask.CacheAllChildren<IParameter>(_simulation.Model.Root);
}
protected float[][][] _binParticlesFractionPerSegment; //no of particles fraction[particles bin][lumen segment][time]
public override void GlobalContext()
{
base.GlobalContext();
_compound.Name = "C1";
_protocol = DomainFactoryForSpecs.CreateStandardOralProtocol();
_formulation = DomainFactoryForSpecs.CreateParticlesFormulation(NumberOfBins);
//user defined actions in the building blocks
SetupBuildingBlocks();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(
_individual, _compound, _protocol, allowAging: false, formulation: _formulation) as IndividualSimulation;
//setup compound processes
SetupProcesses();
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
//user defined actions in simulations, different for every test scenario
SetupSimulation();
if (DisableIntestinalAbsorptionAndLuminalFlow)
{
//disable intestinal absorption and luminal flow to feces for easier mass balance checks
MoleculeProperties(CoreConstants.Parameters.INTESTINAL_PERMEABILITY).Value = 0;
IntestinalTransitRateFor(CoreConstants.Compartment.Rectum).Value = 0;
}
//store initial drug mass
_appliedDrugMass = Application.Container(CoreConstants.ContainerName.ProtocolSchemaItem)
.Parameter(CoreConstantsForSpecs.Parameter.DRUG_MASS).Value.ToFloat();
//Get paths for output quantities of interest
(var lumenPaths, var binSolidDrugPaths, var binInsolubleDrugPaths,
var binSolidDrugPerSegmentPaths, var binParticlesFractionPerSegmentPaths) = outputPaths(NumberOfBins);
//add quantities of interest to the simulation outputs
addOutputs(lumenPaths, binSolidDrugPaths, binInsolubleDrugPaths, binSolidDrugPerSegmentPaths, binParticlesFractionPerSegmentPaths);
RunSimulation(_simulation).Wait();
//fill simulation output times and values required for all further tests
fillSimulationOutputs(lumenPaths, binSolidDrugPaths, binInsolubleDrugPaths, binSolidDrugPerSegmentPaths, binParticlesFractionPerSegmentPaths);
}
public override void GlobalContext()
{
base.GlobalContext();
_enzyme.TissueLocation = TissueLocation.ExtracellularMembrane;
_enzyme.MembraneLocation = MembraneLocation.Apical;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_allExpressionParameters[CoreConstants.Organ.BONE].Value = _relExpBone;
_allExpressionParameters[CoreConstants.Compartment.DUODENUM].Value = _relExpDuo;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
protected IndividualSimulation CreateSimulationWithSetSpecificPintFor(CalculationMethod intestinalPermeabilityMethod)
{
var modelProperties = DomainFactoryForSpecs.CreateDefaultModelPropertiesFor(_individual);
_compound.RemoveCalculationMethodFor(CoreConstants.Category.IntestinalPermeability);
_compound.AddCalculationMethod(intestinalPermeabilityMethod);
_alternativeIntestinalPermParam.Value = 1.2345E-3;
var simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol, modelProperties).DowncastTo <IndividualSimulation>();
simulation.CompoundPropertiesList.First().CompoundGroupSelections.First(
cgs => cgs.GroupName.Equals(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY))
.AlternativeName = _intestinalPermAlternativeName;
DomainFactoryForSpecs.AddModelToSimulation(simulation);
return(simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
var modelConfig = _modelConfigurationRepository.AllFor(_individual.Species).First(x => x.ModelName == CoreConstants.Model.TWO_PORES);
var twoPoreModelProperties = _modelPropertiesTask.DefaultFor(modelConfig, _individual.OriginData);
_compound.Parameter(Constants.Parameters.IS_SMALL_MOLECULE).Value = 0;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol, twoPoreModelProperties)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_enzyme.TissueLocation = TissueLocation.Intracellular;
_enzyme.IntracellularVascularEndoLocation = IntracellularVascularEndoLocation.Interstitial;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Organ.Bone).Value = _relExpBoneNorm;
_enzyme.GetRelativeExpressionParameterFor(CoreConstants.Organ.Bone).Value = _relExpBone;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Duodenum).Value = _relExpDuoNorm;
_enzyme.GetRelativeExpressionParameterFor(CoreConstants.Compartment.Duodenum).Value = _relExpDuo;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_population, _compound, _iv, allowAging: true).DowncastTo <PopulationSimulation>();
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}