public static void main(String[] args) {
// 1) Prepare the environment :
// get a reference to the extracelular matrix (ECM)
ECM ecm = ECM.getInstance();
// add additional PhysicalNodes (for diffusion)
int nbOfAdditionalNodes = 100;
for (int i = 0; i < nbOfAdditionalNodes; i++) {
double[] coord = randomNoise(500, 3);
ecm.getPhysicalNodeInstance(coord);
}
// 2) Create some artificial chemical gradients
// horizontal gaussian (peak concentration, peak coordinate, variance)
ecm.addArtificialGaussianConcentrationZ(new Substance("A", Color.red), 1, 300, 100);
ecm.addArtificialGaussianConcentrationZ(new Substance("B", Color.blue), 1, 00, 100);
ecm.addArtificialGaussianConcentrationZ(new Substance("C", Color.green), 1, -300, 100);
// horizontal linerar gradient
ecm.addArtificialLinearConcentrationZ(new Substance("D", Color.cyan), 1, 300, -300);
// vertical gaussian
ecm.addArtificialGaussianConcentrationX(new Substance("E", Color.red), 1, 0, 100);
ecm.addArtificialGaussianConcentrationX(new Substance("F", Color.green), 1, 300, 100);
// 3) Create a 4-uple Cell-SomaElement-PhysicalSphere-SpaceNode at the desired location
double[] cellLocation = new double[] {0, 0, 0};
Cell cell = CellFactory.getCellInstance(cellLocation);
cell.setColorForAllPhysicalObjects(Param.RED);
// 4) Extend an axon from the cell
NeuriteElement neurite = cell.getSomaElement().extendNewNeurite(new double[] {0, 0, 1});
neurite.getPhysical().setDiameter(1.0);
neurite.getPhysicalCylinder().setDiameter(3);
// 5) Put a movementReceptor
X_Movement_Module r = new X_Movement_Module();
r.linearDiameterDecrease = 0.01;
r.addAttractant("A");
neurite.addLocalBiologyModule(r);
// 6) Simulate
Scheduler.simulate();
}
