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Calcium Simulator -- Interface Map

Project Structure

calcium_simulator/
  __init__.py              # Package docstring + version
  main.py                  # Entry point: creates QApplication, CalciumModel, MainWindow
  calcium_model.py         # CalciumModel: reaction-diffusion solver (222 lines)
  gui.py                   # MainWindow: PyQt5 tabbed GUI with parameter controls (537 lines)
  pyproject.toml           # Package metadata and dependencies
  requirements.txt         # Pinned dependency versions
  configs/                 # Predefined cell state JSON files
    default_state.json
    high_calcium_state.json
    low_calcium_state.json
  examples/                # Example usage
  tests/
    test_calcium_model.py  # Smoke tests for CalciumModel

Key Classes

Class File Purpose
CalciumModel calcium_model.py 2D reaction-diffusion solver: IP3R gating, SERCA, ER/mito compartments, buffering
MainWindow gui.py PyQt5 GUI: tabbed image views, parameter sliders, IP3 uncaging, state save/load

Data Flow

  1. main.py creates CalciumModel and passes it to MainWindow
  2. MainWindow.timer calls update_simulation() at 20fps
  3. Each tick calls CalciumModel.step() which updates calcium, ER, mito, IP3, buffers
  4. GUI reads model arrays and displays via pyqtgraph ImageView
  5. JSON state files in configs/ store/restore parameter sets