├── .gitignore ├── Cargo.lock ├── Cargo.toml ├── LICENSE ├── README.md ├── REFACTORING_STATUS.md ├── agent ├── docs │ ├── ARCHITECTURE.md │ ├── REFACTORING_NUTRITION.md │ ├── SESSION_AS_SUMMARY.md │ ├── SESSION_LOGS_ARCHIVE.md │ ├── SESSION_SUMMARY_OCT10_HN_RESPONSE.md │ ├── SESSION_SUMMARY_OCT10_NIGHT.md │ ├── SESSION_SUMMARY_OCT11_AW.md │ ├── SESSION_SUMMARY_OCT11_AX.md │ ├── SESSION_SUMMARY_OCT11_AY.md │ ├── SESSION_SUMMARY_OCT11_AZ.md │ ├── SESSION_SUMMARY_OCT11_BA.md │ ├── SESSION_SUMMARY_OCT11_BB.md │ ├── SESSION_SUMMARY_OCT11_BC.md │ ├── SESSION_SUMMARY_OCT11_BD.md │ ├── SESSION_SUMMARY_OCT11_BE.md │ ├── SESSION_SUMMARY_OCT11_BF.md │ ├── SESSION_SUMMARY_OCT11_BG.md │ └── reference_implementations │ │ ├── bone_matrix.rs │ │ ├── bone_strength.rs │ │ ├── collagen.rs │ │ ├── crosslinks.rs │ │ ├── hydroxyapatite.rs │ │ └── lysyl_oxidase.rs ├── docs_archive │ ├── ARCHITECTURE.md │ ├── CAPABILITIES.md │ ├── COMPLETION_SUMMARY.md │ ├── EXAMPLES.md │ ├── FINAL_REPORT.md │ ├── FINAL_STATUS.md │ ├── IMPLEMENTATION_PLAN.md │ ├── LATEST_ADDITIONS.md │ ├── LATEST_ENHANCEMENTS.md │ ├── LATEST_UPDATES.md │ ├── PATHOLOGY_COVERAGE.md │ ├── PERSONALIZED_MEDICINE_CAPABILITIES.md │ ├── PROGRESS.md │ ├── RELATIONSHIPS.md │ ├── SESSION_2025_10_09.md │ ├── SESSION_SUMMARY.md │ └── SESSION_UPDATE.md ├── prompt.md ├── ralph.sh └── visualize.ts ├── config_examples └── adult_male_healthy.toml ├── data └── genetics │ ├── african_variants.toml │ ├── asian_variants.toml │ ├── cancer_variants.toml │ ├── european_variants.toml │ └── gene_catalog │ ├── asian_specific_genes.toml │ ├── cancer_genes.toml │ ├── cardiovascular_genes.toml │ ├── hematological_genes.toml │ ├── metabolic_genes.toml │ ├── metabolic_trait_genes.toml │ ├── neurological_genes.toml │ └── pain_disorder_genes.toml ├── docs └── SIMULATION_IMPROVEMENTS.md ├── examples ├── alcohol_pharmacokinetics.rs ├── calcium_homeostasis_feedback.rs ├── cancer_biomarker_simulation_groundtruth.rs ├── cardiac_ischemia_detector.rs ├── clinical_biomarker_analyzer.rs ├── drug_interaction_calculator.rs ├── exercise_physiology_vo2max.rs ├── glycolysis_kinetics_simulation.rs ├── gpcr_camp_signaling_cascade.rs ├── hemoglobin_allosteric_cooperativity.rs ├── hodgkin_huxley_action_potential.rs ├── insulin_glucose_feedback.rs ├── multi_compartment_pk.rs ├── neuron_spike_train.rs ├── pharmacodynamics_emax_model.rs ├── raas_blood_pressure_control.rs ├── respiratory_pathology.rs └── thyroid_hormone_feedback.rs ├── src ├── anthropometry.rs ├── biology │ ├── aging.rs │ ├── allergy.rs │ ├── biomarkers.rs │ ├── blood_typing.rs │ ├── cancer.rs │ ├── cellular │ │ ├── aging.rs │ │ ├── cell.rs │ │ ├── cell_signaling.rs │ │ ├── cell_types.rs │ │ ├── membrane.rs │ │ ├── mitochondria.rs │ │ ├── mod.rs │ │ ├── organelles.rs │ │ ├── processes.rs │ │ └── protein_synthesis.rs │ ├── circadian.rs │ ├── developmental.rs │ ├── embryology.rs │ ├── environmental.rs │ ├── epigenetic_clocks.rs │ ├── epigenetics.rs │ ├── exercise_physiology.rs │ ├── genetics │ │ ├── addiction_genetics.rs │ │ ├── african_variants.rs │ │ ├── allele.rs │ │ ├── ancestry.rs │ │ ├── asian_variants.rs │ │ ├── athletic_performance.rs │ │ ├── autoimmune.rs │ │ ├── blood_type.rs │ │ ├── cancer_data_loader.rs │ │ ├── cancer_genetics.rs │ │ ├── cardiovascular_genetics.rs │ │ ├── chromosome.rs │ │ ├── comprehensive_risk_calculator.rs │ │ ├── dermatology.rs │ │ ├── dietary_genetics.rs │ │ ├── disease_association.rs │ │ ├── disease_susceptibility.rs │ │ ├── dna.rs │ │ ├── epistasis.rs │ │ ├── european_variants.rs │ │ ├── eye_genetics.rs │ │ ├── gene.rs │ │ ├── gene_catalog.rs │ │ ├── gene_environment.rs │ │ ├── gene_variants.rs │ │ ├── genome.rs │ │ ├── genotype.rs │ │ ├── hair_genetics.rs │ │ ├── hla_typing.rs │ │ ├── lactose_tolerance.rs │ │ ├── longevity_genetics.rs │ │ ├── markers.rs │ │ ├── mental_health_genetics.rs │ │ ├── metabolic_disease.rs │ │ ├── migraine_genetics.rs │ │ ├── mitochondrial.rs │ │ ├── mod.rs │ │ ├── native_american_variants.rs │ │ ├── neurological_genetics.rs │ │ ├── ophthalmology.rs │ │ ├── pain_genetics.rs │ │ ├── pharmacogenomics.rs │ │ ├── phenotype.rs │ │ ├── population.rs │ │ ├── population_genetics.rs │ │ ├── population_traits.rs │ │ ├── respiratory_genetics.rs │ │ ├── skin_genetics.rs │ │ ├── sleep_genetics.rs │ │ ├── snp.rs │ │ ├── taste_smell.rs │ │ ├── trait_interactions.rs │ │ └── variation.rs │ ├── gut_brain_axis.rs │ ├── hematology.rs │ ├── hematopoiesis.rs │ ├── hormone_signaling.rs │ ├── immune_system.rs │ ├── immunology │ │ ├── delivery.rs │ │ ├── immune_response.rs │ │ ├── mod.rs │ │ └── vaccines.rs │ ├── lifestyle.rs │ ├── metabolism.rs │ ├── metabolism_pathways.rs │ ├── microbiome.rs │ ├── mod.rs │ ├── molecular │ │ ├── bone_matrix.md │ │ ├── bone_matrix.rs │ │ ├── hydroxyapatite.rs │ │ ├── lysyl_oxidase.rs │ │ └── mod.rs │ ├── neural │ │ ├── mod.rs │ │ ├── neurodegenerative.rs │ │ ├── neuron.rs │ │ └── neuroplasticity.rs │ ├── neurotransmitters.rs │ ├── nutrition.rs │ ├── proteomics.rs │ ├── radiation_biology.rs │ ├── rare_diseases.rs │ ├── skeletal │ │ ├── biomechanics.rs │ │ ├── bone.rs │ │ ├── bone_health.rs │ │ ├── bone_remodeling.rs │ │ ├── joint.rs │ │ ├── mod.rs │ │ └── skeleton.rs │ ├── sleep.rs │ ├── tissue │ │ ├── extracellular_matrix.rs │ │ ├── mod.rs │ │ ├── organization.rs │ │ └── tissue_types.rs │ ├── toxicology.rs │ └── wound_healing.rs ├── biometrics.rs ├── chemistry │ └── mod.rs ├── comprehensive_health.rs ├── config │ ├── baseline_params.rs │ ├── human_presets.rs │ └── mod.rs ├── development.rs ├── diagnosis │ ├── biomarkers.rs │ ├── comprehensive_assessment.rs │ ├── genetic_risk_assessment.rs │ ├── laboratory.rs │ ├── mod.rs │ ├── population_analyzer.rs │ └── screening.rs ├── exercise.rs ├── human.rs ├── lib.rs ├── metabolism │ ├── alcohol_metabolism.rs │ ├── amino_acid_metabolism.rs │ ├── comprehensive_pathways.rs │ ├── detailed_pathways.rs │ ├── detoxification.rs │ ├── energy.rs │ ├── enzyme_kinetics.rs │ ├── enzymes.rs │ ├── lipid_metabolism.rs │ ├── mod.rs │ ├── nutrients.rs │ ├── pathways.rs │ └── vitamins_minerals.rs ├── microbiome.rs ├── nutrition │ ├── evidence_base.rs │ ├── mod.rs │ ├── recommendation_engine.rs │ └── requirements.rs ├── pathology │ ├── allergy_immunology.rs │ ├── cardiovascular.rs │ ├── condition.rs │ ├── dermatology.rs │ ├── diagnosis.rs │ ├── disease.rs │ ├── gastroenterology.rs │ ├── headache.rs │ ├── infectious_disease.rs │ ├── metabolic.rs │ ├── mod.rs │ ├── neurological.rs │ ├── neuromuscular.rs │ ├── ophthalmology.rs │ ├── orthopedics.rs │ ├── otolaryngology.rs │ ├── pain.rs │ ├── psychiatry.rs │ ├── pulmonology.rs │ ├── rheumatology.rs │ ├── sports_medicine.rs │ ├── symptom.rs │ ├── toxicology.rs │ └── transplant.rs ├── personalized_medicine.rs ├── pharmacology │ ├── drug.rs │ ├── drug_interaction.rs │ ├── drug_interactions.rs │ ├── mod.rs │ ├── pain_pharmacogenomics.rs │ ├── pharmacodynamics.rs │ ├── pharmacogenomics.rs │ └── pharmacokinetics.rs ├── physics │ ├── biomechanics.rs │ ├── biomechanics_advanced.rs │ └── mod.rs ├── physiology │ ├── aging.rs │ ├── inflammation.rs │ ├── mod.rs │ ├── stress_response.rs │ ├── thermoregulation.rs │ └── time_series.rs ├── simulation.rs ├── simulation │ └── physiology_engine.rs ├── simulation_utils.rs ├── systems │ ├── auditory.rs │ ├── cardiovascular │ │ ├── arrhythmia.rs │ │ ├── blood.rs │ │ ├── blood_cells.rs │ │ ├── blood_vessel.rs │ │ ├── bone_marrow.rs │ │ ├── cardiac_conduction.rs │ │ ├── cardiac_mechanics.rs │ │ ├── circulation.rs │ │ ├── coronary_arteries.rs │ │ ├── electrophysiology.rs │ │ ├── heart.rs │ │ ├── hematology.rs │ │ ├── hematopoiesis.rs │ │ ├── hemodynamics.rs │ │ └── mod.rs │ ├── dental.rs │ ├── digestive │ │ ├── absorption.rs │ │ ├── digestion.rs │ │ ├── gi_tract.rs │ │ ├── gut_brain_axis.rs │ │ ├── liver.rs │ │ ├── mod.rs │ │ ├── motility.rs │ │ └── pancreas.rs │ ├── endocrine │ │ ├── adipokine_inflammation.rs │ │ ├── feedback.rs │ │ ├── glands.rs │ │ ├── hormone_signaling.rs │ │ ├── hormones.rs │ │ ├── metabolic_hormones.rs │ │ ├── microbiome_hpa_axis.rs │ │ └── mod.rs │ ├── gastrointestinal.rs │ ├── hematology.rs │ ├── hepatic.rs │ ├── immune │ │ ├── adaptive_immunity.rs │ │ ├── cytokines.rs │ │ ├── immune_synapse.rs │ │ ├── innate_immunity.rs │ │ ├── lymphatic.rs │ │ ├── metabolic_immune_crosstalk.rs │ │ ├── mod.rs │ │ └── white_blood_cells.rs │ ├── integumentary │ │ ├── appendages.rs │ │ ├── mod.rs │ │ ├── skin.rs │ │ └── wound_healing.rs │ ├── lymphatic │ │ ├── lymph_fluid.rs │ │ ├── lymph_nodes.rs │ │ ├── lymph_vessels.rs │ │ ├── mod.rs │ │ ├── spleen.rs │ │ └── thymus.rs │ ├── mod.rs │ ├── muscular │ │ ├── contraction.rs │ │ ├── metabolism.rs │ │ ├── mod.rs │ │ ├── muscle.rs │ │ └── performance.rs │ ├── nervous │ │ ├── action_potential.rs │ │ ├── blood_brain_barrier_neuroimmune.rs │ │ ├── brain_connectivity.rs │ │ ├── central.rs │ │ ├── circadian.rs │ │ ├── mod.rs │ │ ├── neurotransmitter_pathways.rs │ │ ├── pain_pathways.rs │ │ └── peripheral.rs │ ├── renal │ │ ├── acid_base.rs │ │ ├── filtration.rs │ │ ├── fluid_balance.rs │ │ ├── hormones.rs │ │ ├── kidney.rs │ │ ├── mod.rs │ │ └── nephron.rs │ ├── reproductive │ │ ├── female.rs │ │ ├── hormone_cycling.rs │ │ ├── male.rs │ │ └── mod.rs │ ├── respiratory │ │ ├── breathing.rs │ │ ├── gas_exchange.rs │ │ ├── lung.rs │ │ ├── mod.rs │ │ ├── oxygen_transport.rs │ │ ├── pulmonary_function.rs │ │ ├── respiratory_mechanics.rs │ │ └── ventilation.rs │ ├── sensory │ │ ├── hearing.rs │ │ ├── mechanoreception.rs │ │ ├── mod.rs │ │ ├── nociception.rs │ │ ├── proprioception.rs │ │ ├── smell.rs │ │ ├── taste.rs │ │ ├── touch.rs │ │ ├── vestibular.rs │ │ ├── vision.rs │ │ └── visual_processing.rs │ └── vision.rs └── validation │ ├── ground_truth │ ├── aldh2.rs │ ├── alzheimers.rs │ ├── auditory.rs │ ├── cardiovascular.rs │ ├── dental.rs │ ├── dermatology.rs │ ├── endocrine.rs │ ├── gastrointestinal.rs │ ├── hematology.rs │ ├── hepatic.rs │ ├── immunology.rs │ ├── metabolic.rs │ ├── mod.rs │ ├── 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