Human Biology - Computational Model

A comprehensive, type-safe computational model of human biology built in Rust for simulation, analysis, and diagnosis of biological systems.

Project Status

• ✅ Compilation: Clean build
• ✅ Tests: 1698 passing
• ✅ Systems: 3 complete computational systems, 9 scaffolds

Organ Systems

✅ Complete Computational Models

• Cardiovascular: Cardiac mechanics, hemodynamics, electrophysiology
• Nervous: Hodgkin-Huxley action potentials, synaptic transmission, circadian rhythms
• Respiratory: Gas exchange, pulmonary mechanics, oxygen transport kinetics

🚧 Scaffolds

• Immune: Cytokine networks, immune cells
• Endocrine: Hormones, feedback loops
• Renal: Filtration, acid-base balance
• Digestive: GI tract, absorption
• Sensory: Vision, hearing
• Integumentary: Skin layers
• Reproductive: Reproductive anatomy
• Muscular: Muscle contraction
• Lymphatic: Lymph nodes, vessels

What Actually Works

Computational Models (Ready to Use)

• Cardiac Mechanics: LaPlace's law, Frank-Starling curves, MVO2, ischemia detection
• Action Potentials: Complete Hodgkin-Huxley equations with gating variables
• Respiratory Mechanics: Compliance, resistance, V/Q matching, surfactant dynamics
• Mitochondrial Function: ETC, OXPHOS, ROS production
• ALDH2 Metabolism: Acetaldehyde processing with genetic variants
• Inflammation Markers: Cytokine levels, acute phase response

Clinical Validation (Ground-Truth Data)

• 20+ Medical Domains: Cardiovascular, metabolic, renal, etc. with peer-reviewed references
• Evidence-Based: PMID/DOI citations for expected ranges
• Biomarker Simulation: Cancer markers, inflammation, Alzheimer's biomarkers

Genetics & Ancestry

• 50+ Genes: Externalized TOML data with population variants
• Ancestry Models: African, Asian, European genetic variants
• Pharmacogenomics: Drug metabolism (ALDH2, CYP2D6, etc.)

Quick Start

use human_biology::{Human, BiologicalSex};

// Create a human model
let person = Human::new_adult_male(
    "john_doe",
    30.0,  // age
    175.0, // height (cm)
    75.0   // weight (kg)
);

// Get health metrics
let bmi = person.bmi();
let cardiac_output = person.cardiac_output_l_per_min();
let gfr = person.gfr_ml_per_min();

Installation

git clone https://github.com/lantos1618/open_human_ontology
cd open_human_ontology
cargo build --release
cargo test
cargo doc --open

Architecture

src/
├── biology/          # Cellular, molecular, genetics, neural, immunology
├── systems/          # 13 organ systems (cardiovascular, nervous, etc.)
├── physiology/       # Stress, aging, inflammation, thermoregulation
├── simulation/       # Multi-system integration engine
├── chemistry/        # Reactions, equilibrium
├── physics/          # Mechanics, forces, thermodynamics
└── human.rs          # Main integrated model

Examples - Real Computational Models

# Cardiovascular: Cardiac ischemia detection
cargo run --example cardiac_ischemia_detector --release

# Nervous: Hodgkin-Huxley action potential
cargo run --example hodgkin_huxley_action_potential --release

# Respiratory: COPD vs Pulmonary Fibrosis
cargo run --example respiratory_pathology --release

# Metabolism: Alcohol pharmacokinetics
cargo run --example alcohol_pharmacokinetics --release

# Endocrine: Insulin-glucose feedback
cargo run --example insulin_glucose_feedback --release

# Clinical: Biomarker analyzer
cargo run --example clinical_biomarker_analyzer --release

Technology

• Rust 2021 edition
• nalgebra for linear algebra
• serde for serialization
• rayon for parallelization
• proptest for property-based testing

Development Status

Completed Refactoring

Phase 1: Honest Documentation

• Corrected claims about system completeness
• Distinguished scaffolds from working implementations

Phase 2: Remove Fake Simulations

• Deleted hardcoded println-based examples
• Retained ground-truth validated simulations

Phase 3: Externalize Data

• Moved genetic data to TOML files
• Validated cancer risk data against peer-reviewed sources (NCI, BOADICEA, GeneReviews)

Phase 4: Simplify Module Structure

• Fixed all ambiguous glob reexports
• Removed warning suppressions

Future Work

• Disease progression modeling
• Pharmacokinetics/pharmacodynamics
• Clinical validation framework

Testing

cargo test                    # Run all 1698 tests
cargo test --lib             # Library tests only
cargo test cardiovascular    # System-specific tests

Documentation

• Full Rust docs: cargo doc --open
• Architecture: agent/docs_archive/ARCHITECTURE.md
• Previous sessions: agent/docs_archive/

Contributing

Contributions welcome! Focus areas:

• Expanding genetic databases
• Additional disease models
• Validation against clinical data
• Performance optimization
• Documentation improvements

License

MIT License - see LICENSE file

Acknowledgments

Built with references to medical literature (Guyton & Hall, Ganong's, peer-reviewed research). Validation status varies: some modules have ground-truth implementations (see examples/*_groundtruth.rs), while others are scaffolds awaiting proper validation.

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Version: 0.1.0 Last Updated: October 13, 2025