0.30
750
15
0.25
0.70
Population: 0 | Time: 0.0s
State: Initializing...

Welcome to the Petri Dish Simulator!

Concept: This simulation models how organisms (like bacteria or yeast) colonize a surface (agar) in a petri dish. Growth starts from initial points you place and spreads outwards, forming colonies. Density naturally increases in the center and limits further growth there, pushing expansion outwards.

How to Use:

  1. Toggle Controls: Use the "Show/Hide Controls" button at the bottom-left to access simulation parameters.
  2. View Controls (3D Area):
    • Mouse: Left-Click+Drag = Tilt/Orbit, Right-Click+Drag = Pan, Scroll Wheel = Zoom.
    • Touch: One finger = Tilt/Orbit, Two fingers pinch = Zoom, Two fingers drag = Pan.
  3. Seed Organisms: Click or tap on the beige agar surface inside the dish to place the initial "founder" organisms (blue spheres). You need at least one to start. (Do this when controls are hidden for full view).
  4. Adjust Parameters (in Controls Panel):
    • Growth Rate: Base chance for an organism to reproduce each step.
    • Max Population: The carrying capacity of the dish.
    • Sim Speed: How many simulation steps occur per second.
    • Spread Distance: How far a *new* organism can appear from its parent. Smaller values create tighter colonies.
    • Density Effect: How much local crowding reduces the growth rate. Higher values lead to more defined colony edges.
  5. Run: Press 'Start' in the controls panel. New organisms (green spheres) will appear.
  6. Control: Use 'Pause', 'Reset', and 'Instructions' buttons in the controls panel.

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OrganismSim

Explore how seeded organisms spread across a 3D Petri dish in this educational colony-growth simulation.

What this tool does

OrganismSim models organisms colonizing a flat agar surface. You place founder organisms, start the simulation, and watch new organisms reproduce and spread outward while local crowding reduces growth.

Who this is for

How to use this tool

  1. Review the on-page instructions and open the controls if they are hidden
  2. Click or tap the beige agar surface to place one or more blue founder organisms
  3. Adjust growth rate, simulation speed, spread distance, and density effect as needed
  4. Press Start, then use Pause or Reset to compare runs

Inputs

Inputs include seed positions on the agar surface and four simulation parameters: growth rate, simulation speed, spread distance, and density effect. The maximum population and organism size are built into the model.

Outputs

The 3D dish shows blue founder organisms and green organisms added during growth. The status display reports the live population, elapsed simulation time, and whether the run is ready, running, paused, or complete.

Example use cases

Limitations

This is a simplified educational model, not a biological growth forecast. Its reproduction, crowding, and spread rules do not represent a specific organism, laboratory condition, or experimental result.

Explore more SolvProb simulations

Frequently asked questions

Is OrganismSim a real biology simulator?

No. It is a simplified visual model for learning and experimentation with growth rules, not a validated biological simulator.

How do I start a simulation?

Place at least one seed on the agar surface, choose your settings, and press Start. New organisms appear as the model advances.

What does the density effect control?

It controls how strongly nearby organisms reduce reproduction probability. Higher values generally create more defined colony edges.

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