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Running the Simulation

Starting the Application​

In the hosted or local website, open an experiment from Your projects and wait for the 3D arena to say it is ready. The first load can take longer because the Godot web runtime is downloaded. Choose 2 Run above the arena. Developers can instead open project.godot in Godot 4.7.1 and choose Run Project for the standalone interface.

Simulation Controls​

The application provides controls for managing simulation execution.

Start​

Choose Start in the Run toolbar to begin or resume. The button changes to Pause while a run is active.

Pause​

Choose Pause to stop advancing steps without clearing the current state. Step advances exactly one simulation step while paused.

Reset​

Reset returns the simulation to its starting state and restores the configured starting doors. Check the displayed seed afterward: some experiment configurations enable a new random seed on reset. To reproduce an earlier run, explicitly restore its saved seed and configuration.

Simulation Speed​

Choose 1x, 10x, 100x or Max. These control how quickly fixed steps are processed, not the length of a simulated step. Max is limited by a frame-time budget so the interface can respond.

The simulation uses fixed time steps, meaning that changing the display speed should not change the underlying simulation behaviour.

Simulation Steps​

The simulation can operate using discrete simulation steps.

Step-based execution is important for scheduled events such as stimulus activation and treatment administration.

For example:

Simulation Step 0
       ↓
Simulation Step 1
       ↓
Simulation Step 2
       ↓
Scheduled Stimulus
       ↓
Simulation Step 3

Stimuli and other scheduled events are activated according to simulation steps rather than the frame rate of the application.

Observing the Simulation​

During a simulation, users can observe the current demonstration agent and its interaction with the virtual arena. Its movement is a platform test, not a validated behavioural prediction.

The integrated Sprint 1 application includes:

  • Rat movement
  • Arena regions
  • Environmental stimuli
  • Barriers
  • Shelter
  • Other arena structures

Use the camera selector for Orbit, Free fly or Follow agent. Reset view restores a usable viewpoint. View options contains labels and camera settings. Hide controls makes the arena wider; Focus on arena fills the screen while keeping compact Start/Pause and permitted door controls. Press Escape or Exit focus view to return.

If your project role includes Arena, choose a route in the Run Doors strip and select Open door or Close door. This is a live intervention: it does not reset the trial and is recorded on the next step. Set the initial door state in Setup → Arena instead if it should be part of the starting configuration. If the door control is disabled, check whether you have arena-edit permission and whether the simulator is ready.

Reproducibility​

The simulation uses a random seed and fixed simulation time steps to support reproducibility.

Running the same experiment with the same configuration and random seed should produce the same simulation behaviour.

Changing display speed alone should not change the result for the same configuration, seed and sequence of interventions. A different seed, changed door, edited treatment or modified plugin can change the run. This reproducibility claim is about the software, not real-world animal behaviour.

AI Attribution: This document was drafted and edited with AI assistance, including ChatGPT and OpenAI Codex. The team reviewed it against the implemented project.