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Multi-Heart-Model Documentation Index

This index provides a comprehensive guide to understanding the Multi-Heart-Model codebase architecture and structure.

Documentation Files

Quick Start & References (Read These First)

  1. QUICK_REFERENCE.md - Start here for quick answers

    • Quick start code examples
    • Key files and their purposes
    • Parameter ranges and defaults
    • Common usage patterns
    • Troubleshooting guide
    • Best for: Developers familiar with the project or quick lookups

  2. CODEBASE_ANALYSIS_SUMMARY.md - Executive overview

    • High-level summary of architecture
    • Key findings and strengths
    • Technical specifications
    • Next steps for integration
    • Best for: Project managers and system architects

Detailed Technical Documentation (Read For Deep Understanding)

  1. ARCHITECTURE_OVERVIEW.md - Comprehensive technical guide

    • Complete module descriptions
    • All existing models and their specifications
    • Architecture patterns and design decisions
    • Coupling and integration mechanisms
    • Testing framework details
    • Extensibility patterns
    • Best for: Developers implementing new features

  2. ARCHITECTURE_DIAGRAM.txt - Visual reference

    • System architecture diagrams (ASCII)
    • Data flow illustrations
    • Component relationship diagrams
    • Testing infrastructure overview
    • Configuration structure
    • Best for: Understanding system flow visually

Original Project Documentation

  1. architecture.md - Original architecture document

    • Mathematical formulation
    • Subsystem responsibilities
    • Configuration flow
    • Output specifications

  2. hbcm_overview.md - HBCM model overview

    • Core mathematical formulation
    • Model capabilities
    • Use cases and applications
    • Workflow integration

  3. microprocessor_motorhand_integration.md - Hardware integration details

    • Primal Logic Processor specifications
    • MotorHandPro integration
    • Hardware deployment information

  4. NODERED_NODEJS_INTEGRATION.md - Node-RED and Node.js integration architecture

    • Node-RED orchestration patterns
    • Node.js API gateway design
    • OpenSim biomechanical integration
    • WebSocket bridging and real-time data
    • IoT device aggregation
    • Implementation roadmap
    • Best for: Developers adding web services, IoT integration, or OpenSim coupling

How to Navigate This Documentation

I'm a New Developer

  1. Start with QUICK_REFERENCE.md (5 min read)
  2. Review ARCHITECTURE_DIAGRAM.txt for visual understanding (10 min)
  3. Read ARCHITECTURE_OVERVIEW.md for complete context (30 min)
  4. Examine code in src/ directory
  5. Run tests: pytest tests/ -v

I'm Adding a New Organ System

  1. Review ARCHITECTURE_OVERVIEW.md section "10. PATTERNS FOR ORGAN CHIP SYSTEM INTEGRATION"
  2. Check QUICK_REFERENCE.md "Integration Testing Checklist"
  3. Study existing models in src/cardiac/ and src/neural/
  4. Follow the modular composition pattern
  5. Add comprehensive tests

I'm Optimizing for Performance

  1. Read ARCHITECTURE_OVERVIEW.md section "9. PERFORMANCE CHARACTERISTICS"
  2. Review QUICK_REFERENCE.md "Performance Tips"
  3. Profile using Python's cProfile or pytest-benchmark
  4. Consider upgrading from Euler to RK4 integration
  5. Evaluate vectorization opportunities

I'm Preparing for Hardware Deployment

  1. Review CODEBASE_ANALYSIS_SUMMARY.md "Hardware Deployment Ready"
  2. Study src/integration/motorhand_bridge.py for QUANT interface
  3. Review Arduino code generation in generate_arduino_interface()
  4. Read QUICK_REFERENCE.md "Hardware Deployment Path"
  5. Follow integration testing checklist

I'm Debugging an Issue

  1. Check QUICK_REFERENCE.md "Troubleshooting" section
  2. Review relevant test file for expected behavior
  3. Consult ARCHITECTURE_OVERVIEW.md for implementation details
  4. Check parameter ranges in QUICK_REFERENCE.md

Key Concepts Quick Links

Models

  • Neural Model: See ARCHITECTURE_OVERVIEW.md § 2.B
  • Cardiac Model: See ARCHITECTURE_OVERVIEW.md § 2.A
  • Coupling Model: See ARCHITECTURE_OVERVIEW.md § 2.C

Systems

  • Primal Logic Processor: See ARCHITECTURE_OVERVIEW.md § 2.D
  • Motor Integration: See ARCHITECTURE_OVERVIEW.md § 2.E

Patterns

  • Model Interface: See ARCHITECTURE_OVERVIEW.md § 3.A
  • Coupling Pattern: See ARCHITECTURE_OVERVIEW.md § 3.B
  • Extensibility Pattern: See ARCHITECTURE_OVERVIEW.md § 10

Testing

  • Unit Tests: See ARCHITECTURE_OVERVIEW.md § 6
  • Integration Tests: See ARCHITECTURE_DIAGRAM.txt "TESTING & VALIDATION"

Configuration

  • YAML Configuration: See ARCHITECTURE_DIAGRAM.txt "CONFIGURATION SYSTEM"
  • Parameter Ranges: See QUICK_REFERENCE.md "Parameter Ranges & Defaults"

Code Navigation

Source Code Structure

src/
├── cardiac/         → VanDerPolOscillator model
├── neural/          → FitzHughNagumo model
├── coupling/        → HeartBrainCouplingModel orchestrator
├── microprocessor/  → PrimalLogicProcessor controller
└── integration/     → MotorHandBridge interface

Test Files

tests/
├── test_models.py                           → Unit tests
└── integration/test_microprocessor_motorhand.py  → Integration tests

Configuration

config/
└── default.yaml     → YAML parameters

Examples

examples/
└── microprocessor_motorhand_demo.py  → Complete demo script

Quick Facts

Metric Value
Total Python LOC 1,153
Test Coverage ~100% of production code
Test Methods 30+
Main Modules 5
Dependencies NumPy (core only)
Default Timestep 0.01s (100 Hz)
Integration Pattern Explicit Euler
State Dimensionality 4D (extendable)
Control Performance 75% jerk reduction
Hardware Target SkyWater 90nm

Documentation Quality Levels

Level 1: Quick Answers (QUICK_REFERENCE.md)

  • Quick start examples
  • Parameter tables
  • Common patterns
  • Troubleshooting

Level 2: Executive Overview (CODEBASE_ANALYSIS_SUMMARY.md)

  • High-level architecture
  • Key findings
  • Next steps
  • Conclusions

Level 3: Technical Details (ARCHITECTURE_OVERVIEW.md)

  • Complete module descriptions
  • All equations and mathematics
  • Data structures
  • Integration mechanisms

Level 4: Visual Understanding (ARCHITECTURE_DIAGRAM.txt)

  • ASCII diagrams
  • Data flow illustrations
  • Component relationships

Level 5: Deep Dive (Original documentation)

  • Research background
  • Mathematical derivations
  • Hardware specifications

Common Tasks & Documentation

Task: Understand basic model structure

Read: QUICK_REFERENCE.md → Module Relationships Time: 5 minutes

Task: Add a new organ system

Read: ARCHITECTURE_OVERVIEW.md § 10 → QUICK_REFERENCE.md § Integration Testing Checklist Time: 30 minutes planning + implementation

Task: Modify coupling parameters

Read: QUICK_REFERENCE.md § Parameter Ranges & Defaults Time: 5 minutes

Task: Optimize for performance

Read: ARCHITECTURE_OVERVIEW.md § 9 → QUICK_REFERENCE.md § Performance Tips Time: 20 minutes analysis + optimization

Task: Deploy to hardware

Read: CODEBASE_ANALYSIS_SUMMARY.md → QUICK_REFERENCE.md § Hardware Deployment Path Time: 2-4 hours

Task: Debug simulation divergence

Read: QUICK_REFERENCE.md § Troubleshooting → ARCHITECTURE_OVERVIEW.md relevant section Time: 10-30 minutes

References to Code

When reading documentation, you can jump to actual code files:

  • Cardiac model: /src/cardiac/van_der_pol.py
  • Neural model: /src/neural/fhn.py
  • Coupling model: /src/coupling/hbcm.py
  • Primal Logic: /src/microprocessor/primal_processor.py
  • Control utilities: /src/microprocessor/control_system.py
  • Motor bridge: /src/integration/motorhand_bridge.py
  • Unit tests: /tests/test_models.py
  • Integration tests: /tests/integration/test_microprocessor_motorhand.py
  • Example: /examples/microprocessor_motorhand_demo.py

How Documentation Connects

QUICK_REFERENCE.md (Start here)
    ↓
    ├→ ARCHITECTURE_DIAGRAM.txt (Visual overview)
    │   ↓
    └→ ARCHITECTURE_OVERVIEW.md (Deep technical details)
        ↓
        └→ CODEBASE_ANALYSIS_SUMMARY.md (Executive summary)
            ↓
            └→ Original documentation (Research details)

Feedback & Updates

This documentation was generated on: November 12, 2025

For updates or clarifications:

  1. Check original .md files in the docs/ directory
  2. Review relevant code files in src/
  3. Run test suite to validate understanding
  4. Refer to example scripts in examples/

Version Information

  • Documentation Version: 1.0
  • Repository: Multi-Heart-Model
  • License: MIT
  • Patent: U.S. Provisional Patent Application No. 63/842,846
  • Status: Production-ready

Last Updated: November 12, 2025 Total Documentation Pages: 4 comprehensive guides + this index Total Words: ~30,000 Code References: 100+ specific file references Diagrams: 5+ ASCII diagrams