private bool checkBiStability(List <double> optPValuesArray, List <string> pNames, int checkParamIndex,
int speciesIndex)
{
bool isBiStable = false;
int numOfParameters = optPValuesArray.Count;
double tempCheckParamValue;
var decFloatingSpeciesArray = new double[20];
var incFloatingSpeciesArray = new double[20];
double speciesValsSum = 0.0;
double[] speciesConcArray;
//Set the parameter values to Optimized Parameter Values
for (int i = 0; i < pNames.Count; i++)
{
rr.setValue(pNames[i], optPValuesArray[i]);
}
rr.setTimeStart(0);
rr.setTimeEnd(simulationTime);
BringToSteadyStateOrThrow();
//Now decrement the parameter value and simulate untill steady state is reached.
//Do this 20 times and store the species concentration in an array.
for (int i = 0; i < 20; i++)
{
//Now Decrement the ith parameter value and calculate the species conc. at steady state
tempCheckParamValue = (1.00 - 0.01 * (i + 1)) * optPValuesArray[checkParamIndex];
rr.setValue(pNames[checkParamIndex], tempCheckParamValue);
BringToSteadyStateOrThrow();
speciesConcArray = rr.getFloatingSpeciesConcentrations();
decFloatingSpeciesArray[i] = speciesConcArray[speciesIndex];
}
rr.reset();
rr.setValue(pNames[checkParamIndex], optPValuesArray[checkParamIndex]);
rr.setTimeStart(0);
rr.setTimeEnd(simulationTime);
BringToSteadyStateOrThrow(1);
//Now increment the parameter value and simulate untill steady state is reached.
//Do this 20 times and store the species concentration in an array.
for (int i = 0; i < 20; i++)
{
//Now Increment the ith parameter value and calculate the species conc. at steady state
tempCheckParamValue = (1.00 + 0.01 * (i + 1)) * optPValuesArray[checkParamIndex];
rr.setValue(pNames[checkParamIndex], tempCheckParamValue);
BringToSteadyStateOrThrow();
speciesConcArray = rr.getFloatingSpeciesConcentrations();
incFloatingSpeciesArray[i] = speciesConcArray[speciesIndex];
}
speciesValsSum = 0.0;
for (int i = 2; i < 20; i++)
{
speciesValsSum = speciesValsSum + decFloatingSpeciesArray[i];
}
double decFloatSpeciesMean = speciesValsSum / 18;
speciesValsSum = 0.0;
for (int i = 2; i < 20; i++)
{
speciesValsSum = speciesValsSum + incFloatingSpeciesArray[i];
}
double incFloatSpeciesMean = speciesValsSum / 18;
if (decFloatSpeciesMean > 2 * incFloatSpeciesMean || incFloatSpeciesMean > 2 * decFloatSpeciesMean)
{
isBiStable = true;
}
return(isBiStable);
}
private void cmdSteadyState_Click(object sender, EventArgs e)
{
thread.QueueItem(() =>
{
if (m_sSBML != null)
{
if (m_sSBML.Length > 0)
{
try
{
if (sim == null)
{
sim = new RoadRunner();
}
sim.loadSBML(m_sSBML);
sim.simulate();
double steadyState = sim.steadyState();
if (
MessageBox.Show(
"Found steady state with sums of squares: " + steadyState +
". Do you want to use this state to be used?", "Steady state calculated",
MessageBoxButtons.YesNo, MessageBoxIcon.Question) != DialogResult.Yes)
{
return;
}
sim.simulate();
ArrayList floatingSpeciesNames = sim.getFloatingSpeciesNames();
double[] speciesConcentrations1 = sim.getFloatingSpeciesConcentrations();
ArrayList boundarySpeciesNames = sim.getBoundarySpeciesNames();
double[] speciesConcentrations2 = sim.getBoundarySpeciesConcentrations();
ArrayList parameterTupleList = sim.getAllGlobalParameterTupleList();
NOM.loadSBML(m_sSBML);
for (int index = 0; index < floatingSpeciesNames.Count; ++index)
{
NOM.setValue((string)floatingSpeciesNames[index], speciesConcentrations1[index]);
}
for (int index = 0; index < boundarySpeciesNames.Count; ++index)
{
NOM.setValue((string)boundarySpeciesNames[index], speciesConcentrations2[index]);
}
foreach (ArrayList arrayList in parameterTupleList)
{
NOM.setValue((string)arrayList[0], (double)arrayList[1]);
}
m_sSBML = NOM.getSBML();
loadSBML(m_sSBML);
return;
}
catch (Exception ex)
{
MessageBox.Show("Could not compute steady state due to: " + ex.Message,
"Steady state could not be computed ...", MessageBoxButtons.OK, MessageBoxIcon.Hand);
return;
}
}
}
MessageBox.Show("There is no model to analyze. Load a model first.", "No Model loaded",
MessageBoxButtons.OK, MessageBoxIcon.Hand);
});
}