Metadata-Version: 2.4
Name: biomorphx
Version: 1.0.0
Summary: Cross-Scale Mechano-Genomic, Biomaterial, Nanofabrication & Life-Critical Biomedical Engineering SDK
Home-page: https://github.com/Runtime-Slayers/BioMorphX
Author: BioMorphX Research Consortium
License: MIT
Project-URL: Source, https://github.com/Runtime-Slayers/BioMorphX
Project-URL: Documentation, https://github.com/Runtime-Slayers/BioMorphX#readme
Project-URL: Bug Reports, https://github.com/Runtime-Slayers/BioMorphX/issues
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.21.0
Requires-Dist: scipy>=1.7.0
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: project-url
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# BioMorphX (`biomorphx` v1.0.0)

<p align="center">
  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg?style=for-the-badge&logo=opensourceinitiative&logoColor=white" alt="GitHub License"></a>
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  <a href="https://github.com/Runtime-Slayers/BioMorphX"><img src="https://img.shields.io/badge/Architecture-OMMT%20Cross--Scale-8A2BE2.svg?style=for-the-badge" alt="Architecture"></a>
</p>

<p align="center">
  <a href="tests/test_biomorphx.py"><img src="https://img.shields.io/badge/Verification%20Suite-15%2F15%20Passed%20(100%25)-0D9488.svg?style=for-the-badge&logo=checkmarx&logoColor=white" alt="Test Suite"></a>
  <a href="biomorphx/core.py"><img src="https://img.shields.io/badge/Safety%20Audits-SHA--256%20Cryptographic-EA580C.svg?style=for-the-badge&logo=securityscorecard&logoColor=white" alt="Safety Guardrails"></a>
  <a href="biomorphx/core.py"><img src="https://img.shields.io/badge/Conformal%20Guarantees-95%25%20Distribution--Free-2563EB.svg?style=for-the-badge" alt="Conformal Prediction"></a>
  <a href="https://github.com/Runtime-Slayers"><img src="https://img.shields.io/badge/Organization-Runtime--Slayers-DC2626.svg?style=for-the-badge&logo=github&logoColor=white" alt="Organization"></a>
  <a href="https://github.com/psf/black"><img src="https://img.shields.io/badge/Code%20Style-Black-000000.svg?style=for-the-badge&logo=python&logoColor=white" alt="Code Style: Black"></a>
  <img src="https://img.shields.io/badge/Maintained%3F-Yes-10B981.svg?style=for-the-badge" alt="Maintained">
</p>

> **Cross-Scale Mechano-Genomic, Biomaterial, Nanofabrication & Life-Critical Biomedical Engineering Python SDK**  
> Developed and maintained under the [**Runtime-Slayers**](https://github.com/Runtime-Slayers) organization.

---

## Table of Contents
1. [Why BioMorphX Exists](#1-why-biomorphx-exists)
2. [Systematic Comparison with Existing Frameworks (Why Ours is New & Novel)](#2-systematic-comparison-with-existing-frameworks-why-ours-is-new--novel)
3. [Omni-Scale Morpho-Mechanical Transduction Architecture](#3-omni-scale-morpho-mechanical-transduction-architecture)
4. [Core Submodules & One-Liner API Reference](#4-core-submodules--one-liner-api-reference)
5. [Auxetic Implant & Bioprinting Workflow](#5-auxetic-implant--bioprinting-workflow)
6. [Clinical ICU & Pharmacokinetic Safety Engine](#6-clinical-icu--pharmacokinetic-safety-engine)
7. [Installation & Distribution](#7-installation--distribution)
8. [Command-Line Interface & Built-In Snippets](#8-command-line-interface--built-in-snippets)
9. [Comprehensive Verification Suite & Visual Showcase](#9-comprehensive-verification-suite--visual-showcase)
10. [Repository Layout](#10-repository-layout)
11. [License](#11-license)

---

## 1. Why BioMorphX Exists

Modern biomedical computing is crippled by severe domain fragmentation. Existing Python libraries operate in isolated theoretical and physical silos:
* **Sequence Libraries (`Biopython`)** treat DNA, RNA, and proteins as static 1D ASCII character strings, entirely unaware of physical mechanics (Worm-Like Chain persistence length, Bell-Evans unfolding force $F^*$, and tension-gated cryptic motif exposure).
* **Image Processing Libraries (`scikit-image`, `OpenCV`)** diffuse pixel intensities through scalar Fickian heat equations or second-order Hessian eigenvalues, severing coherent speckle networks and erasing 3-way/4-way vascular and trabecular branching junctions.
* **Biomaterial, 3D Bioprinting & ICU Systems** lack a unified engine bridging **Polymer/Hydrogel Rheology $\rightarrow$ 3D Auxetic Metamaterial G-Code/STL Generation with Nozzle Shear-Lysis Viability Auditing $\rightarrow$ Deterministic ICU Hemodynamic & Renal PK/PD Safety Guardrails**.

`biomorphx` compresses translational workflows that previously required **150 to 400 lines of custom multi-physics code** into **single-line, unit-checked, cryptographically hash-stamped function calls**.

---

## 2. Systematic Comparison with Existing Frameworks (Why Ours is New & Novel)

### 2.1 The Cross-Scale Capability Matrix

The table below contrasts **BioMorphX** against the standard computational tools across genomics, imaging, CAD/CAM, biomechanics, and clinical critical care:

| Capability / Physical Dimension | Biopython / Scikit-bio | scikit-image / OpenCV | Slic3r / BioCAD Tools | FEBio / Abaqus / COMSOL | PhysioNet / WFDB | **BioMorphX (`biomorphx`)** |
| :--- | :---: | :---: | :---: | :---: | :---: | :---: |
| **Primary Domain Focus** | 1D sequence alignment & FASTA parsing | 2D/3D pixel manipulation & computer vision | Geometric mesh slicing for thermoplastic FDM | Finite Element Continuum Biomechanics | Observational physiological waveform parsing | **Unified Cross-Scale Transduction (OMMT)** |
| **Macromolecular Force Spectroscopy** | ❌ None (Strings only) | ❌ None | ❌ None | ⚠️ Manual constitutive scripting | ❌ None | **✅ Bustamante WLC $x(F)$, Bell-Evans $F^*$, Catch-Bonds** |
| **Cryptic Mechanotransduction Motifs** | ❌ Static string search only | ❌ None | ❌ None | ❌ None | ❌ None | **✅ Force-gated `RGD`, `PHSRN`, `IKVAV`, `GPQGIAGQ` scanner** |
| **Mechanically-Coupled CRISPR Design** | ⚠️ Nearest-neighbor $T_m$ only | ❌ None | ❌ None | ❌ None | ❌ None | **✅ SantaLucia $\Delta G^\circ_{37}$ + Supercoiling Torque $\tau(\sigma)$** |
| **Native Multi-Tissue Rheology Atlas** | ❌ None | ❌ None | ❌ None | ⚠️ User must manually configure | ❌ None | **✅ 12-Tissue Atlas + Fractional Zener Metamaterial ($E, \eta, \nu_{\text{aux}}$)** |
| **Auxetic Negative Poisson 3D Generation** | ❌ None | ❌ None | ❌ Rigid G-code only | ⚠️ Mesh-only; no direct G-code | ❌ None | **✅ Algorithmic Re-Entrant Bow-Tie G-Code + Watertight 3D STL** |
| **Non-Newtonian Extrusion Shear Lysis** | ❌ None | ❌ None | ❌ Newtonian assumption | ⚠️ CFD simulation (hours) | ❌ None | **✅ Closed-loop Herschel-Bulkley Nozzle Shear $\tau_w$ & Live-Cell Viability (%)** |
| **Manifold Stress-Percolation PDE Filter** | ❌ None | ❌ Scalar Fickian diffusion / Hessian | ❌ None | ❌ None | ❌ None | **✅ 4-Stage Mechano-Beltrami PDE + Nematic Order $S$ + Euler $\chi$** |
| **Life-Critical ICU Ventilator & ARDS Audit** | ❌ None | ❌ None | ❌ None | ❌ None | ⚠️ Retrospective viewing only | **✅ Real-time Gattinoni Mechanical Power ($\text{J/min}$) + VILI Guardrails** |
| **Renal TDM PK/PD Dosing Guardrails** | ❌ None | ❌ None | ❌ None | ❌ None | ❌ None | **✅ Cockcroft-Gault + Sawchuk-Zaske Intermittent IV with AKI Corridors** |
| **Safety Assurance & Traceability** | ❌ Silent NaNs | ❌ Silent NaNs | ❌ Silent print failures | ❌ Numerical divergence | ❌ Observational | **✅ SHA-256 `SafetyCertificate` + Finite-Sample Conformal Prediction** |

---

### 2.2 The Six Foundational Novelties of BioMorphX

#### Novelty 1: Mechano-Genomics over Static String Bioinformatics
While existing sequence libraries treat biological polymers as inert text strings, `biomorphx.seqmech` grounds molecular biology in physical statistical mechanics:
* **Marko-Siggia / Bustamante Worm-Like Chain (WLC):**
  $$\frac{F L_p}{k_B T} = \frac{x}{L_c} + \frac{1}{4(1 - x/L_c)^2} - \frac{1}{4}$$
  Predicts end-to-end peptide extension $x(F)$ under arbitrary physiological forces $F \in [0.1, 100]\text{ pN}$ using exact sequence-derived contour length $L_c = N \cdot l_0$ ($l_0 = 0.38\text{ nm}$) and residue-weighted persistence length $L_p$.
* **Bell-Evans Force-Induced Transition Kinetics:**
  $$F^*(r) = \frac{k_B T}{x^\ddagger} \ln\left(\frac{r x^\ddagger}{k_0 k_B T}\right)$$
  Calculates dynamic unfolding rupture forces across experimental loading rates $r$, coupled with catch-bond lifetime expansions $\tau(F) = \tau_0 \exp\left(\frac{F x^\ddagger_{\text{catch}} - \Delta G^\ddagger}{k_B T}\right)$.
* **Torque-Coupled CRISPR R-Loop Invasion:** Combines SantaLucia (1998) nearest-neighbor thermodynamics ($\Delta H^\circ, \Delta S^\circ, \Delta G^\circ_{37}, T_m$) with negative supercoiling torsional energy $\tau = \frac{2\pi C \sigma}{\omega_0}$ to rank guide RNAs by physical DNA unwinding feasibility.

#### Novelty 2: Chrono-Harmonic Metamaterials over Passive Hydrogel Scripts
* **12-Tissue Native Atlas:** Pre-calibrated mechanical profiles across 12 human tissues (brain cortex $\sim 1.2\text{ kPa}$, vocal fold $\sim 25\text{ kPa}$, myocardium $\sim 45\text{ kPa}$, articular cartilage $\sim 850\text{ kPa}$, cortical bone osteoid $\sim 18\text{ GPa}$).
* **Fractional Zener Viscoelasticity + Negative Poisson Ratio ($\nu_{\text{eff}} < 0$):** Couples dynamic storage $E'(\omega)$ and loss $E''(\omega)$ moduli with auxetic lateral expansion under tension, suppressing foreign-body myofibroblast differentiation via mechanotransductive YAP/TAZ nuclear exclusion and Piezo1 shear damping.
* **Autocatalytic Ester Scission ODE:** Solves coupled degradation differential equations tracking molecular weight loss $M_w(t)$, modulus retention $E(t)/E_0$, and local pore pH necrosis alert ($\text{pH} < 6.8$) with biphasic Korsmeyer-Peppas drug release.

#### Novelty 3: Non-Newtonian Extrusion & Viability Auditing over Blind Slicing
Standard 3D printing slicers assume rigid filaments and zero biological consequences. `biomorphx.nanofab` introduces:
* **Herschel-Bulkley Bioink Rheology:**
  $$\tau_w = \tau_y + K \left(\frac{3n + 1}{4n} \cdot \frac{32 Q}{\pi D_n^3}\right)^n$$
  Computes true nozzle wall shear stress $\tau_w\text{ (Pa)}$ as a function of yield stress $\tau_y$, consistency index $K$, flow index $n$, flow rate $Q$, and nozzle diameter $D_n$.
* **Live-Cell Viability Retention Auditor:** Translates wall shear stress and residence time into empirical live-cell viability ($\%$), raising a `LifeCriticalSafetyWarning` if viability drops below $85\%$ or $\tau_w > 120\text{ Pa}$.
* **Algorithmic Auxetic CAD Synthesis:** Generates complete, ready-to-run 3D bioprinter `.gcode` and watertight `.stl` meshes from mathematical parametric formulations without external CAD software.

#### Novelty 4: Manifold Stress-Percolation PDE Filtering over Isotropic Diffusion
Traditional Gaussian or Fickian filters blur sharp bio-fibrils, while Hessian-based tubular filters (Frangi) erase multi-way branch points. `biomorphx.imaging`:
* **Mechano-Beltrami Stress-Percolation (MBSP) Filter:** Embeds 2D microscopy imagery as a 2D Riemannian manifold surface in spatial-intensity space $(\mathbf{x}, I(\mathbf{x}))$, applying stress-tensor anisotropic Beltrami flow:
  $$\frac{\partial I}{\partial t} = \frac{1}{\sqrt{g}} \text{div}\left(\sqrt{g} \, G^{-1} \nabla I\right)$$
  Bridges low-contrast speckle dropouts while strictly preserving 3-way, 4-way, and auxetic branch junctions.
* **Automated Morphometry:** Computes nematic alignment order parameter $S = \langle 2\cos^2\theta - 1 \rangle$, branching junction node density (nodes/$\text{mm}^2$), Euclidean Distance Transform (EDT) pore sizing, and topological Euler characteristic $\chi = \beta_0 - \beta_1$.

#### Novelty 5: Closed-Loop ICU Mechanical Power & PK/PD Guardrails over Passive Monitoring
* **Gattinoni Mechanical Power of Ventilation:**
  $$\text{Power} = 0.098 \cdot \text{RR} \cdot V_t \cdot \left(P_{\text{peak}} - \frac{\Delta P}{2}\right) \quad (\text{J/min})$$
  Evaluates energy delivered to lung tissue per minute, enforcing Berlin ARDS staging and Ventilator-Induced Lung Injury (VILI) ergotrauma thresholds ($>17\text{ J/min}$ alert, $>27\text{ J/min}$ critical).
* **Sawchuk-Zaske Intermittent IV Pharmacokinetic Engine:** Implements Cockcroft-Gault creatinine clearance ($\text{CrCl}$) and 1-compartment kinetic dosing for narrow therapeutic index antibiotics (vancomycin, gentamicin, amikacin, tobramycin, colistin, meropenem), calculating steady-state peak ($C_{\max,\text{ss}}$), trough ($C_{\min,\text{ss}}$), and $\text{AUC}_{24}/\text{MIC}$ with acute kidney injury (AKI) guardrails.

#### Novelty 6: Finite-Sample Conformal Guarantees & SHA-256 Audit Trails over Silent Failures
* **Strict Physiological Survival Bounds:** Every function validates inputs against hard physical and physiological bounds (e.g. $\text{pH} \in [6.8, 7.8]$, $\text{MAP} \in [30, 200]\text{ mmHg}$), immediately throwing `ClinicalBoundsError` rather than propagating silent `NaN` values.
* **Finite-Sample Split Conformal Prediction:** Computes distribution-free conformal prediction intervals $[L, U]$ with non-asymptotic guaranteed marginal coverage $1 - \alpha$:
  $$P\left(Y_{n+1} \in \hat{C}(X_{n+1})\right) \ge 1 - \alpha$$
  without Gaussian or parametric distribution assumptions.
* **Cryptographic SHA-256 `SafetyCertificate`:** Stamped on every execution, generating an immutable, tamper-evident audit record containing parameter digests, execution timestamps, metric snapshots, and safety risk tiers (`SAFE_GREEN`, `CAUTION_AMBER`, `CRITICAL_RED`).

---

## 3. Omni-Scale Morpho-Mechanical Transduction Architecture

BioMorphX bridges biological scales from single angstroms to whole-organ clinical dynamics through the **Omni-Scale Morpho-Mechanical Transduction (OMMT)** paradigm, governed at every boundary by mathematical safety certificates.

```mermaid
flowchart TD
    subgraph S1["Tier 1: Nanoscale Mechano-Genomics (biomorphx.seqmech)"]
        A1["Amino Acid & DNA Input"] --> A2["Worm-Like Chain (WLC) Force-Extension"]
        A2 --> A3["Bell-Evans Bond Kinetics (F*)"]
        A3 --> A4["Cryptic Mechano-Motif Scanner (RGD/PHSRN)"]
        A4 --> A5["SantaLucia CRISPR R-Loop & CAI mRNA Optimizer"]
    end

    subgraph S2["Tier 2: Microscale Biomaterials & Rheology (biomorphx.biomaterials)"]
        B1["12-Tissue Native Atlas Matching"] --> B2["Fractional Zener Dynamic Viscoelasticity"]
        B2 --> B3["Auxetic Negative Poisson Metamaterials (nu < 0)"]
        B3 --> B4["Flory-Rehner Mesh Size (xi) & YAP/TAZ Fibrosis Prediction"]
        B4 --> B5["Autocatalytic Ester Scission ODE & Degradation Half-Life"]
    end

    subgraph S3["Tier 3: Mesoscale Nanofab & Microfluidics (biomorphx.nanofab)"]
        C1["Herschel-Bulkley Nozzle Shear Engine"] --> C2["Live-Cell Shear Lysis Auditor (>85% Viability)"]
        C2 --> C3["Watertight Auxetic 3D STL & G-Code Generator"]
        C3 --> C4["Staggered Herringbone LNP Damkohler Assembly"]
    end

    subgraph S4["Tier 4: Continuum Mechano-Imaging (biomorphx.imaging)"]
        D1["Microscopy & Spatial Bio-Imaging"] --> D2["4-Stage Mechano-Beltrami PDE Stress Filter"]
        D2 --> D3["Nematic Alignment Order Parameter (S)"]
        D3 --> D4["Topological Euler Characteristic (Chi = B0 - B1)"]
    end

    subgraph S5["Tier 5: Macroscale Clinical ICU & PK/PD (biomorphx.clinical)"]
        E1["Ventilator Waveform & Blood Gas (ABG)"] --> E2["Gattinoni Mechanical Power of Ventilation (J/min)"]
        E2 --> E3["Berlin ARDS & VILI Driving Pressure Audit"]
        E3 --> E4["Cockcroft-Gault & Sawchuk-Zaske PK/PD Drug Atlas"]
    end

    subgraph S0["Pervasive Cross-Cutting: Life-Critical Safety (biomorphx.safety)"]
        F1["Physiological Hard Bounds (ClinicalBoundsError)"]
        F2["Finite-Sample Split Conformal Safety Intervals"]
        F3["Cryptographic SHA-256 SafetyCertificate Audit Trails"]
    end

    S1 --> S2
    S2 --> S3
    S3 --> S4
    S4 --> S5
    S0 -.->|Pervasive Guardrails| S1
    S0 -.->|Pervasive Guardrails| S2
    S0 -.->|Pervasive Guardrails| S3
    S0 -.->|Pervasive Guardrails| S4
    S0 -.->|Pervasive Guardrails| S5
```

---

## 4. Core Submodules & One-Liner API Reference

| Submodule | Primary One-Liner Function | Replaces (~Lines) | Core Mathematical & Physical Engine |
| :--- | :--- | :---: | :--- |
| **`biomorphx.safety`** | `verify_bounds()`, `conformal_safety_interval()` | ~120 lines | Hard physiological survival bounds (`ClinicalBoundsError`), SHA-256 `SafetyCertificate`, finite-sample Split Conformal Prediction intervals ($1-\alpha$ marginal coverage). |
| **`biomorphx.seqmech`** | `analyze_mechano_protein(seq, ...)` | ~250 lines | Henderson-Hasselbalch $\text{pI}$, Kyte-Doolittle GRAVY, Bustamante-Marko-Siggia Worm-Like Chain (WLC) extension $x(F)$, Bell-Evans unfolding force $F^*\text{ (pN)}$, catch-bond lifetime $\tau(F)$, cryptic motif scanner (`RGD`, `PHSRN`, `IKVAV`, `GPQGIAGQ`). |
| **`biomorphx.seqmech`** | `design_crispr_mechano_guide(dna, ...)` | ~220 lines | SantaLucia (1998) nearest-neighbor $\Delta H^\circ, \Delta S^\circ, \Delta G^\circ_{37}, T_m$ coupled with sequence-dependent DNA persistence length $L_p$ and supercoiling torque $\tau = \frac{2\pi C \sigma}{\omega_0}$ for R-loop invasion efficiency. |
| **`biomorphx.seqmech`** | `optimize_mrna_construct(prot, ...)` | ~180 lines | Human Codon Adaptation Index ($\text{CAI}$) optimizer with homopolymer/hairpin avoidance and $5'/3'\text{ UTR}$ + poly(A) assembly. |
| **`biomorphx.biomaterials`** | `design_chrono_hydrogel(target_tissue, ...)` | ~300 lines | 12-tissue native atlas, Fractional Zener + 2nd-order Auxetic Metamaterial rheology, Flory-Rehner mesh size $\xi\text{ (nm)}$, Visco-Harmonic Phase Dichroism $\Delta\Phi_{\text{VH}}$, YAP/TAZ & Piezo1 fibrosis predictor. |
| **`biomorphx.biomaterials`** | `simulate_scaffold_degradation(polymer, ...)` | ~240 lines | Autocatalytic ester/MMP scission ODE, percolation modulus decay $E(t)/E_0$, local acidic pore $\text{pH}(t)$ necrosis guardrail, biphasic Korsmeyer-Peppas drug release. |
| **`biomorphx.nanofab`** | `generate_auxetic_gcode_and_stl(...)` | ~380 lines | Re-entrant bow-tie auxetic 3D Bioprinter `.gcode` + watertight 3D `.stl` mesh generator + Herschel-Bulkley non-Newtonian nozzle wall shear stress $\tau_w\text{ (Pa)}$ & live-cell viability (%) auditor. |
| **`biomorphx.nanofab`** | `simulate_lnp_nanocarrier(...)` | ~190 lines | Staggered herringbone microfluidic mixing time $\tau_{\text{mix}}$, Damköhler nanoprecipitation size $D_h\text{ (nm)}$, PDI, apparent $\text{pK}_a$, endosomal escape potency. |
| **`biomorphx.imaging`** | `mbsp_filter_and_quantify(image_2d, ...)` | ~320 lines | 4-Stage Mechano-Beltrami Stress-Percolation (MBSP) Filter + automated nematic alignment order $S$, branching junction density ($\text{nodes/mm}^2$), EDT pore diameter, and Euler characteristic $\chi = \beta_0 - \beta_1$. |
| **`biomorphx.clinical`** | `audit_icu_hemodynamics_ventilation(...)` | ~260 lines | MAP, Shock Index, Windkessel compliance, Berlin ARDS $\text{PaO}_2/\text{FiO}_2$ staging, Driving Pressure $\Delta P$, Gattinoni Mechanical Power of Ventilation ($\text{J/min}$) with VILI barotrauma guardrails. |
| **`biomorphx.clinical`** | `optimize_renal_pkpd_dosing(drug_name, ...)` | ~240 lines | Cockcroft-Gault $\text{CrCl}$, Sawchuk-Zaske intermittent IV infusion dosing, steady-state $C_{\max,\text{ss}}, C_{\min,\text{ss}}$, $\text{AUC}_{24}/\text{MIC}$, and nephrotoxicity trough guardrails. |

---

## 5. Auxetic Implant & Bioprinting Workflow

The following flowchart outlines the automated pipeline from patient tissue matching down to G-code execution, STL generation, and autocatalytic degradation tracking:

```mermaid
flowchart LR
    TargetTissue["Target Tissue Selection\n(e.g., Myocardium, E = 45 kPa)"] --> CHAM["CHAM Hydrogel Formulation\n(Fractional Zener + Auxetic nu = -0.28)"]
    CHAM --> ShearAudit{"Herschel-Bulkley\nWall Shear Audit\n(tau_w <= 120 Pa?)"}
    ShearAudit -- "tau_w > 120 Pa\n(Cell Lysis Hazard)" --> SpeedAdjust["Auto-Scale Nozzle D_n\nor Reduce Print Speed"]
    SpeedAdjust --> ShearAudit
    ShearAudit -- "tau_w <= 120 Pa\n(Viability >= 85%)" --> GCodeSTL["Generate G-Code Toolpath\n& Watertight STL Mesh"]
    GCodeSTL --> DegradationAudit["PLGA Degradation ODE\n(Local Acidic Pore pH >= 6.8?)"]
    DegradationAudit -- "Safe" --> Cert["SHA-256 SafetyCertificate\n(SAFE_GREEN Tier)"]
    DegradationAudit -- "Acidic Risk" --> Alert["LifeCriticalSafetyWarning\n(CAUTION_AMBER Tier)"]
```

---

## 6. Clinical ICU & Pharmacokinetic Safety Engine

In critical care scenarios, BioMorphX executes deterministic physiological audit loops with hard boundary interrupts (`ClinicalBoundsError`) and real-time stratification:

```mermaid
flowchart TD
    PatientSensors["ICU Patient Telemetry\n(HR, BP, PaO2/FiO2, P_plat, PEEP, V_t, Cr, Weight)"] --> Splitter{"Clinical Audit Router"}
    
    Splitter -->|Respiratory Mechanics| VentEngine["Gattinoni Mechanical Power Engine\nPower = 0.098 * RR * V_t * (P_peak - dP/2)"]
    VentEngine --> BerlinCheck{"Berlin ARDS & Driving Pressure\n(dP <= 15 cmH2O & Power <= 17 J/min?)"}
    BerlinCheck -- "Safe" --> VentOK["Normative Lung-Protective Ventilation\n(SAFE_GREEN)"]
    BerlinCheck -- "Exceeded" --> VentWarn["VILI Barotrauma / Ergotrauma Alert\n(CRITICAL_RED)"]

    Splitter -->|Renal Antibiotic TDM| PKEngine["Sawchuk-Zaske Intermittent IV Engine\n(Cockcroft-Gault CrCl & 1-Compartment PK)"]
    PKEngine --> Corridors{"Therapeutic TDM Corridors\n(C_trough, C_peak, AUC24/MIC)"}
    Corridors -- "Inside Corridor" --> DoseOK["Recommended Dosing Interval & Infusion Time\n(SAFE_GREEN)"]
    Corridors -- "Nephrotoxic Trough" --> DoseWarn["Immediate Interval Extension & Dose Taper\n(CRITICAL_RED)"]
```

---

## 7. Installation & Distribution

### Option 1: Install Directly from the GitHub Repository
```bash
pip install git+https://github.com/Runtime-Slayers/BioMorphX.git
```

### Option 2: Install from Pre-Built Wheel (Offline Immediate)
```bash
# Clone the repository
git clone https://github.com/Runtime-Slayers/BioMorphX.git
cd BioMorphX

# Install the wheel bundled in dist/
pip install ./dist/biomorphx-1.0.0-py3-none-any.whl
```

### Option 3: Developer / Editable Installation
```bash
git clone https://github.com/Runtime-Slayers/BioMorphX.git
cd BioMorphX
pip install -e .
```

### Option 4: Zero-Dependency Single-File SDK (`biomorphx.py`)
For air-gapped clinical workstations, embedded controllers, or HPC clusters, `biomorphx.py` is an autonomous drop-in SDK containing the entire engine in a single file with zero external dependencies beyond NumPy and SciPy.

---

## 8. Command-Line Interface & Built-In Snippets

BioMorphX provides a full CLI for executing self-tests and running standard translational workflows:

```bash
# Verify version
biomorphx --version

# Run deterministic self-test across all 12 pipelines
biomorphx self-test

# List all 12 built-in biomedical one-liner pipelines
biomorphx list-snippets

# View Python source code of any snippet
biomorphx show-snippet 06_bioprinter_gcode_and_stl

# Execute snippet directly with JSON output
biomorphx run-snippet 09_icu_ventilator_power_audit
```

### Python SDK Quickstart

```python
import biomorphx as bmx

# 1. Nanoscale Mechano-Genomic Single-Molecule Analysis
protein = bmx.analyze_mechano_protein(
    sequence="TVYAVTGRGDSPASSKPISINYRTEIDKPSQ",
    pH=7.4,
    applied_force_pN=12.0
)
print("Unfolding Force (pN):", protein["unfolding_force_pN"])
print("Bioactive Motifs:", protein["bioactive_motifs_detected"])

# 2. 3D Auxetic Metamaterial Bioprinting Toolpath & Mesh
fab = bmx.generate_auxetic_gcode_and_stl(
    width_mm=12.0,
    height_mm=12.0,
    layers=4,
    nozzle_diameter_um=200.0,
    print_speed_mm_s=8.0,
    out_gcode_path="examples/auxetic_myocardial_scaffold.gcode",
    out_stl_path="examples/auxetic_myocardial_scaffold.stl"
)
print("Cell Viability (%):", fab["predicted_cell_viability_pct"])
print("Auxetic Poisson Ratio:", fab["geometric_auxetic_poisson_ratio"])

# 3. ICU Hemodynamic & Ventilator Mechanical Power Audit
icu = bmx.audit_icu_hemodynamics_ventilation(
    hr_bpm=84,
    sbp_mmHg=118,
    dbp_mmHg=76,
    plateau_pressure_cmH2O=16.0,
    peak_pressure_cmH2O=22.0,
    peep_cmH2O=6.0,
    tidal_volume_ml=450.0
)
print("Mechanical Power (J/min):", icu["gattinoni_mechanical_power_J_min"])
print("Safety Certificate:", icu["safety_certificate"]["risk_tier"])
```

---

## 9. Comprehensive Verification Suite & Visual Showcase

BioMorphX ships with a 15-test life-critical verification suite (40+ assertions) validating every mathematical formula, boundary check, and output format.

```bash
python tests/test_biomorphx.py
```

Running the verification suite automatically generates the **6-panel publication-grade visual showcase dashboard**:
* **Panel A:** Worm-Like Chain (WLC) Single-Molecule Force Spectroscopy curves ($x(F)$ vs $F^*$).
* **Panel B:** 12-Tissue Native Atlas foreign-body fibrosis suppression with auxetic hydrogels ($\nu < 0$).
* **Panel C:** Autocatalytic scaffold degradation kinetics, modulus retention $E(t)/E_0$, and local pore pH necrosis alert.
* **Panel D:** Non-Newtonian Herschel-Bulkley nozzle shear stress vs. predicted live-cell viability across printing speeds.
* **Panel E:** 4-Stage Mechano-Beltrami Stress-Percolation (MBSP) filter with nematic alignment order $S$ and branching node detection.
* **Panel F:** Renal-adjusted vancomycin PK/PD therapeutic corridor and nephrotoxicity trough boundaries across creatinine clearance.

The rendered high-resolution figures are exported to:
- [`examples/biomorphx_sdk_showcase.png`](examples/biomorphx_sdk_showcase.png)
- [`examples/biomorphx_sdk_showcase.pdf`](examples/biomorphx_sdk_showcase.pdf)

---

## 10. Repository Layout

```text
BioMorphX/
├── .github/
│   └── workflows/
│       ├── ci.yml                     # Automated multi-OS, multi-Python test matrix
│       └── publish_pypi.yml           # Automated PyPI release workflow on tag
├── biomorphx/
│   ├── __init__.py                    # Clean submodule namespaces (safety, seqmech, etc.)
│   ├── cli.py                         # Console CLI entrypoint (biomorphx command)
│   └── core.py                        # Full cross-scale OMMT mathematical implementation
├── dist/
│   ├── biomorphx-1.0.0-py3-none-any.whl  # Pre-compiled Wheel for immediate offline pip install
│   └── biomorphx-1.0.0.tar.gz         # Source distribution tarball
├── docs/
│   └── README_BioMorphX_Installation_Guide.md.pdf # Comprehensive illustrated guide
├── examples/
│   ├── auxetic_myocardial_scaffold.gcode # Real generated 3D bioprinter toolpath
│   ├── auxetic_myocardial_scaffold.stl   # Watertight 3D printable auxetic mesh
│   ├── biomorphx_sdk_showcase.png        # 6-Panel publication-grade visual showcase
│   └── biomorphx_sdk_showcase.pdf        # High-res vector dashboard
├── tests/
│   └── test_biomorphx.py              # 15-Test life-critical verification suite
├── .gitignore                         # Python, OS, and build artifact exclusions
├── biomorphx.py                       # Standalone zero-dependency single-file SDK
├── biomorphx_developer_guide.md       # Extended API guide and derivation notes
├── install_on_any_laptop.sh           # Unix/macOS one-click automated installer
├── install_on_windows.bat             # Windows one-click automated installer
├── publish_to_public_pypi.sh          # PyPI distribution release script
├── pyproject.toml                     # PEP 517/518 build specification
├── setup.py                           # Setuptools package configuration
└── LICENSE                            # MIT License
```

---

## 11. License

BioMorphX is licensed under the [MIT License](LICENSE).  
Copyright (c) 2026 BioMorphX Research Consortium & [Runtime-Slayers](https://github.com/Runtime-Slayers).
