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Team:BCCS-Bristol/Modeling/HowBSimWorks
From 2009.igem.org
BCCS-Bristol
iGEM 2009
iGEM 2009
How BSim works
How BSim should work
particles.add( new Bacterium(position: 0 1 0, radius: 1), new Bacterium(position: 0 1 0, radius: 1), new Bacterium(position: 0 1 0, radius: 1), new Bead(position: 0 1 0), ); b = new Bacterium() b.grn(new GRN(dy/dx = -2x; dx/dz = y^2)) particles.add(b); chemicalFields.add( new ChemicalField(chemical: aspartate), new ChemicalField(chemical: AHL) ) boundaries(..) dt(..) simulationTime(..) renderer(new ProcessingRenderer()) exporters.add( new FileExporter(), new MovieExporter(), new ScreenshotExporter() ) gui()
How AgentCell works
A very cut down version of Example.java in agentcell.runs:
public class Example {
private static List cellArrayList;
public Example() {
super();
}
// Setup and run a model.
public static void main(String args[]) {
final ChemotaxisModel model = new ChemotaxisModel();
model.setDt(0.01);
model.setStopTime(4.0); //2000.0);
double equilibrationTime=2.0; //1000.0;
final World world = new World();
model.setWorld(world);
world.setModel(model);
BoundaryConditions boundaryConditions = new BoundaryConditions(world);
world.setBoundaryConditions(boundaryConditions);
// Set the chemical gradient.
double aspartateGradient = 1.0E-8; // M / micrometer
world.setConcentrationField(new ConcentrationFieldConstantGradientWithBounds(
Molecule.ASPARTATE, // type
new Vect3(0, 0, 0), // origin
0, // concentration at origin in Mol
new Vect3(0, 0, aspartateGradient), 0, // min Level
1.0E-2)); // max level
//Create the cells
cellArrayList = RunSetupUtils.findMatchingDirectories(new File(ChemotaxisModel.runDirAbsolutePath), "cell");
model.setAgentCellNumberOfCells(String.valueOf(cellArrayList.size()));
for (int i = 0; i < cellArrayList.size(); i++) {
double zpos = 100.0; //position chosen for the cell to be in 1 uM aspartate
Vect position = new Vect3(0, 0, zpos);
Orientation orientation = new Orientation(); //local and global axes are aligned
orientation.randomize();
double volume = 1.41E-15;
ChemotacticCell cell = new ChemotacticCell(world, position,
orientation, new Copynumber(Molecule.CHEYP), volume);
cell.setPath( new File(cellArrayList.get(i).toString()).getAbsolutePath());
cell.setEquilibrationTime(equilibrationTime);
Receptors receptors = new Receptors(cell);
receptors.getDissociationConstants().put("{asp}",new Double(1.71E-6));
receptors.getDissociationConstants().put("{asp*}",new Double(12E-6));
cell.setReceptors(receptors);
// Create a Network
cell.setChemotaxisNetwork( new ChemotaxisNetwork(cell, "STCHSTC.INI",
(new File(cell.getPath(), "network1") + File.separator + "Input")) );
cell.getChemotaxisNetwork().getCopynumber(cell.getCheYp());
int initialMotorState;
if (cell.getCheYp().getLevel() > cheYpThreshold.getLevel()) {
initialMotorState = Motor.CW;
} else {
initialMotorState = Motor.CCW;
}
double minCWDuration = 0.1; // seconds
double minCCWDuration = 0.1; // seconds
double boxcarTimeWidth = 0.3; //seconds
cell.setMotor(new AveragedCheYpThresholdMotor(cell,
initialMotorState, minCWDuration, minCCWDuration,
cheYpThreshold,
(int) Math.round(boxcarTimeWidth / model.getDt())));
// Create a flagella group
int flagellaState = Flagella.INVALIDSTATE;
if (cell.getMotor().getState() == Motor.CCW) {
flagellaState = Flagella.BUNDLED;
} else {
flagellaState = Flagella.APART;
}
//cell.setFlagella(new TetheredFlagellum(cell,flagellaState));
cell.setFlagella(new SwimmingFlagella(cell, flagellaState));
// Create a motion stepper with run and tumble states.
RunTumbleStepper motionStepper = new RunTumbleStepper(cell);
//Motion:
double runSpeed = 20;
double runRotationalDiffusion = 0.0620577;
motionStepper.setRun(new Run(motionStepper, runSpeed,
runRotationalDiffusion));
//Tumble that fits the distribution in
//Fig. 3, p. 501 from Berg and Brown, Nature, 239, 500 (1972)
double shape = 4;
double scale = 18.32045567939674;
double location = -4.606176605609249;
motionStepper.setTumble(new TumbleGammaDistribution(motionStepper,
shape, scale, location));
// motionStepper.setTumble(new TumbleCosinusDistribution(motionStepper));
cell.setMotionStepper(motionStepper);
//print info about cell
System.out.println("Initial position of cell " +
cell.getIdentifier() + " is :" + cell.getPosition());
// Add the new cell to the world.
world.getCells().add(cell);
}
// Create a new time schedule.
model.setSchedule(new Schedule());
// Schedule each of the cells to run.
model.getSchedule().scheduleActionAtIntervalRnd(model.getDt(),
((List) model.getWorld().getCells()), ChemotacticCell.class, "step");
// Run the model.
BatchController control = new BatchController(new Vector());
model.setController(control);
control.setModel(model);
model.addSimEventListener(control);
control.begin();
}
}
