/// <summary>
/// Base constructor
/// </summary>
public AggregateReferenceNode(Experiment experiment, Simulation simulation)
{
this.cellDefinition = null;
this.group = null;
this.species = null;
this.experiment = experiment;
this.simulation = simulation;
}
public static void setupExperiment(MuCell.Model.SBML.Model model, MuCell.Model.Experiment experiment, MuCell.Model.Simulation simulation)
{
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "s1";
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 0.1d;
model.AddId("s1", species1);
model.AddId("s2", species2);
// set up the cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(model);
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
MuCell.Model.CellInstance cell1 = celldef1.createCell();
MuCell.Model.CellInstance cell2 = celldef2.createCell();
List<MuCell.Model.CellInstance> cells = new List<CellInstance>();
cells.Add(cell1);
cells.Add(cell2);
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
initialState.SimulationEnvironment = new MuCell.Model.Environment(size);
// Create two groups with one cell of each type in each
initialState.SimulationEnvironment.AddCellToGroup(1, celldef1.createCell());
initialState.SimulationEnvironment.AddCellToGroup(2, celldef2.createCell());
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
}
public void testWithVariables()
{
// create a formula
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
Species s = new Species("X");
s.BoundaryCondition = false;
model.AddId(s.ID, s); // else FormulaParser can't find what X is
reader.model = model;
FormulaParser fp = new FormulaParser(reader, "10+sin(X)", model);
MathTree formulaTree = fp.getFormulaTree();
// fold the function
CellEvaluationFunction fun = formulaTree.ToCellEvaluationFunction();
// create a new CellInstance with a variable X
CellInstance cell = new CellInstance(new CellDefinition());
cell.setSpeciesAmount("X", 2.3d);
// evaluate and test that this gets the right result
Assert.AreEqual(10+Math.Sin(2.3), fun(new StateSnapshot(), cell));
}
public ModifierSpeciesReference(Species species)
{
this.species = species;
}
public SpeciesCommand(Species species, bool adding, Model.SBML.Model model)
{
this.species = species;
this.adding = adding;
this.model = model;
}
public void Setup(Experiment experiment, Simulation simulation, string speciesName)
{
// ********* INITIAL SETUP
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.xml");
// Cell definition 1
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Create a NEW model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = speciesName;
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "Y";
species2.InitialAmount = 0.1d;
model.AddId(speciesName, species1);
model.AddId("Y", species2);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = speciesName.Replace(' ', '_')+"*2";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species1, 0.75);
MuCell.Model.SBML.SpeciesReference ref3 = new MuCell.Model.SBML.SpeciesReference(species2, 2);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
reaction1.Products.Add(ref3);
// set up the cell definition
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
// instantiat the environment
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
MuCell.Model.Environment environment = new MuCell.Model.Environment(size);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
// Create 10 cells of celldef1 and 20 cells of celldef2
for(int i=0;i<10;i++){
int a = ((i+2)%3)+1;
int b = (i%3)+1;
int c = ((i+1)%3)+1;
CellInstance cell11 = celldef1.createCell();
cells.Add(cell11);
environment.AddCellToGroup(a, cell11);
CellInstance cell21 = celldef2.createCell();
CellInstance cell22 = celldef2.createCell();
cells.Add(cell21);
cells.Add(cell22);
environment.AddCellToGroup(b, cell21);
environment.AddCellToGroup(c, cell22);
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
initialState.SimulationEnvironment = environment;
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 1;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
// Start simulation
simulation.StartSimulation();
this.models = new List<MuCell.Model.SBML.Model>();
this.models.Add(s.model);
this.models.Add(model);
}
public void SpeciesElement(Hashtable attrs)
{
Species species = new Species(attrs);
if (species.ID != null)
{
this.model.AddId(species.ID, species);
}
SpeciesType speciesType = null;
Compartment compartment = null;
Double initialAmount = -1d;
Double initialConcentration = -1d;
String substanceUnits = null;
Boolean hasOnlySubstanceUnits = false;
Boolean boundaryCondition = false;
Boolean constant = false;
if (attrs.ContainsKey("initialamount"))
initialAmount = Double.Parse((String)attrs["initialamount"]);
if (attrs.ContainsKey("initialconcentration"))
initialConcentration = Double.Parse((String)attrs["initialconcentration"]);
if (attrs.ContainsKey("substanceunits"))
substanceUnits = (String)attrs["substanceunits"];
if (attrs.ContainsKey("hasonlysubstanceunits"))
hasOnlySubstanceUnits = Boolean.Parse((String)attrs["hasonlysubstanceunits"]);
if (attrs.ContainsKey("boundarycondition"))
boundaryCondition = Boolean.Parse((String)attrs["boundarycondition"]);
if (attrs.ContainsKey("constant"))
constant = Boolean.Parse((String)attrs["constant"]);
if (attrs.ContainsKey("speciestype"))
{
String sTypeId = (String)attrs["speciesType"];
speciesType = (SpeciesType)this.model.findObject(sTypeId);
}
if (attrs.ContainsKey("compartment"))
{
String cId = (String)attrs["compartment"];
compartment = (Compartment)this.model.findObject(cId);
}
if (attrs.ContainsKey("substanceunits"))
{
substanceUnits = (String)attrs["substanceunits"];
}
else
{
// look it up based on units of compartment;
}
species.AddProperties(speciesType, compartment, initialAmount,
initialConcentration, substanceUnits, hasOnlySubstanceUnits, boundaryCondition,
constant);
this.model.listOfSpecies.Add(species);
}
public SpeciesReference(Species species, double stoichiometry)
{
this.species = species;
this.stoichiometry = stoichiometry;
}
public SpeciesReference(Species species)
{
this.species = species;
this.stoichiometry = 1;
}
