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README.md

@@ -28,11 +28,27 @@ The **Genome Logic Modeling Project (GLMP)** represents a paradigm shift in our
 
 ## 📊 Collection Statistics
 
-- **371 Total Processes** across 36 individual collections
-- **6 Kingdoms/Systems** (Viral, Bacterial, Eukaryotic)
+- **411 Total Processes** across 45 individual collections
+- **7 Kingdoms/Systems** (Viral, Bacterial, Eukaryotic, Neural)
 - **100% Programming Framework** methodology applied
 - **Complete coverage** of major biological computational systems
 
+## 🧠 Neural Computation Systems
+
+**NEW!** Advanced neural computation systems demonstrating sophisticated biological computing architectures in neural networks. Features:
+- **5 Neural Systems** covering synaptic plasticity, sensory processing, memory formation, motor control, and decision-making
+- **Complete Coverage** of neural computational paradigms
+- **Advanced Neural Logic** including winner-take-all networks, lateral inhibition, and pattern completion
+
+**Neural Systems Files:**
+1. [neural_plasticity_batch01_synaptic_plasticity.html](neural_plasticity_batch01_synaptic_plasticity.html) - Synaptic Plasticity Mechanisms (LTP/LTD/Synaptic Scaling)
+2. [neural_plasticity_batch02_sensory_processing.html](neural_plasticity_batch02_sensory_processing.html) - Sensory Processing Algorithms (Visual/Auditory/Olfactory)
+3. [neural_plasticity_batch03_memory_formation.html](neural_plasticity_batch03_memory_formation.html) - Memory Formation Systems (Consolidation/Retrieval/Extinction)
+4. [neural_plasticity_batch04_motor_control.html](neural_plasticity_batch04_motor_control.html) - Motor Control Systems (Planning/Execution/Learning)
+5. [neural_plasticity_batch05_decision_making.html](neural_plasticity_batch05_decision_making.html) - Neural Decision-Making (Winner-Take-All/Lateral Inhibition)
+
+These neural systems demonstrate the most sophisticated biological computing architectures in neural networks, showing how complex cognitive functions, learning mechanisms, and behavioral control are implemented through neural computation.
+
 ## 🧬 Advanced Systems Analysis
 
 **COMPREHENSIVE!** Advanced biological computing systems demonstrating sophisticated computational architectures across multiple kingdoms of life. Features:
@@ -112,6 +128,55 @@ This represents the most comprehensive eukaryotic cellular process collection ev
 
 **Featured E. coli Process:** [β-Galactosidase Lac Operon](ecoli_beta_galactosidase_lac_operon.html) - Complete lac operon regulation system
 
+### **🌱 Arabidopsis thaliana: Plant Systems**
+**8 plant-specific processes** - Plant-specific computational systems including photosynthesis, development, and environmental responses.
+- Complete Analysis: [a_thaliana_batch01_photosynthesis_development.html](a_thaliana_batch01_photosynthesis_development.html)
+- Photosynthesis optimization, developmental programming, environmental adaptation, stress responses
+
+### **🦟 Drosophila melanogaster: Animal Development**
+**8 developmental processes** - Animal developmental systems including pattern formation, cell fate specification, and genetic regulation.
+- Complete Analysis: [d_melanogaster_batch01_development_genetics.html](d_melanogaster_batch01_development_genetics.html)
+- Pattern formation, cell fate specification, genetic regulation, developmental timing
+
+### **🪱 Caenorhabditis elegans: Behavioral Systems**
+**8 behavioral processes** - Nematode behavioral systems including development, neural circuits, and behavioral responses.
+- Complete Analysis: [c_elegans_batch01_development_behavior.html](c_elegans_batch01_development_behavior.html)
+- Neural development, behavioral circuits, environmental responses, developmental programming
+
+### **🦠 Viral Systems: Pathogen Computing**
+
+#### **SARS-CoV-2 Entry & Replication**
+**8 viral processes** - Coronavirus computational systems including entry mechanisms, replication strategies, and immune evasion.
+- Complete Analysis: [sars_cov2_batch01_entry_replication.html](sars_cov2_batch01_entry_replication.html)
+- Viral entry, replication machinery, immune evasion, host manipulation
+
+#### **HIV-1 Replication & Immune Evasion**
+**8 viral processes** - Retroviral computational systems including reverse transcription, integration, and immune evasion strategies.
+- Complete Analysis: [hiv1_batch01_replication_evasion.html](hiv1_batch01_replication_evasion.html)
+- Reverse transcription, integration, immune evasion, latency establishment
+
+### **🦠 Bacterial Pathogens: Pathogenic Computing**
+
+#### **Salmonella enterica Invasion & Virulence**
+**8 pathogenic processes** - Enteric pathogen computational systems including invasion mechanisms and virulence regulation.
+- Complete Analysis: [s_enterica_batch01_invasion_virulence.html](s_enterica_batch01_invasion_virulence.html)
+- Invasion mechanisms, virulence regulation, host manipulation, immune evasion
+
+#### **Staphylococcus aureus Pathogenicity & Biofilm**
+**8 pathogenic processes** - Gram-positive pathogen computational systems including virulence factors and biofilm formation.
+- Complete Analysis: [s_aureus_batch01_pathogenicity_biofilm.html](s_aureus_batch01_pathogenicity_biofilm.html)
+- Virulence regulation, biofilm formation, antibiotic resistance, host interaction
+
+#### **Mycobacterium tuberculosis Dormancy & Persistence**
+**8 pathogenic processes** - Mycobacterial computational systems including dormancy mechanisms and persistence strategies.
+- Complete Analysis: [m_tuberculosis_batch01_dormancy_persistence.html](m_tuberculosis_batch01_dormancy_persistence.html)
+- Dormancy regulation, persistence mechanisms, host adaptation, drug resistance
+
+#### **Pseudomonas aeruginosa Virulence & Pathogenicity**
+**8 pathogenic processes** - Opportunistic pathogen computational systems including virulence regulation and environmental adaptation.
+- Complete Analysis: [p_aeruginosa_batch01_virulence_pathogenicity.html](p_aeruginosa_batch01_virulence_pathogenicity.html)
+- Virulence regulation, environmental adaptation, biofilm formation, antibiotic resistance
+
 ### **🦠 Advanced Biological Systems**
 
 #### **Phage λ Decision Switch: Viral Computational Logic**

a_thaliana_batch01_photosynthesis_development.html

@@ -0,0 +1,719 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>A. thaliana Batch 01: Photosynthesis & Development - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🌱 A. thaliana Batch 01: Photosynthesis & Development</h1>
+            <p>Programming Framework Analysis - 8 Plant Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🌱 Photosynthesis & Development Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental A. thaliana processes responsible for photosynthesis and development. These processes represent the core computational systems that enable this model plant to convert light energy into chemical energy and coordinate complex developmental programs.</p>
+                <p>Each process demonstrates sophisticated biological programming with light sensing, energy conversion, hormone signaling, and developmental regulation.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Plant Processes</h2>
+                <ul>
+                    <li><a href="#light-sensing">1. Light Sensing & Photoreception</a></li>
+                    <li><a href="#photosynthesis">2. Photosynthesis</a></li>
+                    <li><a href="#circadian-rhythm">3. Circadian Rhythm</a></li>
+                    <li><a href="#hormone-signaling">4. Hormone Signaling</a></li>
+                    <li><a href="#stress-response">5. Stress Response</a></li>
+                    <li><a href="#development">6. Development & Growth</a></li>
+                    <li><a href="#nutrient-uptake">7. Nutrient Uptake</a></li>
+                    <li><a href="#flowering">8. Flowering Control</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Light Sensing & Photoreception -->
+            <div class="process-item" id="light-sensing">
+                <h3>1. Light Sensing & Photoreception</h3>
+                <p>Detailed analysis of A. thaliana Light Sensing & Photoreception using the Programming Framework, revealing computational logic and regulatory patterns for light detection and signal transduction.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Light Detection
+    A[Light Absorption] --> B[Phytochrome Activation]
+    C[Blue Light] --> D[Cryptochrome Activation]
+    E[UV Light] --> F[UVR8 Activation]
+    G[Red Light] --> H[Phytochrome B]
+    
+    %% Phytochrome Signaling
+    B --> I[Pfr Formation]
+    I --> J[Nuclear Translocation]
+    J --> K[PIF Degradation]
+    K --> L[Light Response Genes]
+    
+    %% Cryptochrome Signaling
+    D --> M[CRY1/2 Activation]
+    M --> N[COP1 Inhibition]
+    N --> O[HY5 Stabilization]
+    O --> P[Photomorphogenesis]
+    
+    %% UVR8 Response
+    F --> Q[UVR8 Dimer Dissociation]
+    Q --> R[CUL4-DDB1 Complex]
+    R --> S[UV Response Genes]
+    
+    %% Integration
+    L --> T[Light Response Program]
+    P --> T
+    S --> T
+    H --> T
+    T --> U[Photomorphogenic Development]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#ffd43b,color:#000
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#ffd43b,color:#000
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#74c0fc,color:#fff
+    style U fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Photosynthesis -->
+            <div class="process-item" id="photosynthesis">
+                <h3>2. Photosynthesis</h3>
+                <p>Detailed analysis of A. thaliana Photosynthesis using the Programming Framework, revealing computational logic and regulatory patterns for light energy conversion.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Light Energy Capture
+    A[Light Absorption] --> B[Chlorophyll Excitation]
+    C[PSII Activation] --> D[Water Splitting]
+    E[PSI Activation] --> F[NADP+ Reduction]
+    G[Electron Transport] --> H[ATP Synthesis]
+    
+    %% Light Reactions
+    B --> I[Electron Transfer Chain]
+    I --> J[Proton Gradient]
+    J --> K[ATP Synthase]
+    K --> L[ATP Production]
+    
+    %% Water Splitting
+    D --> M[Oxygen Evolution]
+    M --> N[Proton Release]
+    N --> O[Electron Donation]
+    
+    %% NADP+ Reduction
+    F --> P[NADPH Production]
+    P --> Q[Reducing Power]
+    Q --> R[Calvin Cycle]
+    
+    %% Integration
+    L --> S[Energy Production]
+    O --> S
+    R --> S
+    H --> S
+    S --> T[Carbon Fixation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#ffd43b,color:#000
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#74c0fc,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#74c0fc,color:#fff
+    style T fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Circadian Rhythm -->
+            <div class="process-item" id="circadian-rhythm">
+                <h3>3. Circadian Rhythm</h3>
+                <p>Detailed analysis of A. thaliana Circadian Rhythm using the Programming Framework, revealing computational logic and regulatory patterns for time-based gene expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Clock Components
+    A[Light Signal] --> B[CCA1/LHY Expression]
+    C[Evening Signal] --> D[TOC1 Expression]
+    E[Circadian Time] --> F[PRR Family]
+    G[Feedback Loop] --> H[Clock Regulation]
+    
+    %% Morning Loop
+    B --> I[CCA1/LHY Proteins]
+    I --> J[TOC1 Repression]
+    J --> K[Morning Genes]
+    K --> L[Photosynthesis Activation]
+    
+    %% Evening Loop
+    D --> M[TOC1 Protein]
+    M --> N[CCA1/LHY Repression]
+    N --> O[Evening Genes]
+    O --> P[Metabolic Regulation]
+    
+    %% PRR Regulation
+    F --> Q[PRR7/9 Expression]
+    Q --> R[Clock Synchronization]
+    R --> S[Circadian Output]
+    
+    %% Integration
+    L --> T[Circadian Program]
+    P --> T
+    S --> T
+    H --> T
+    T --> U[24-Hour Rhythm]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#ffd43b,color:#000
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#ffd43b,color:#000
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#74c0fc,color:#fff
+    style U fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Hormone Signaling -->
+            <div class="process-item" id="hormone-signaling">
+                <h3>4. Hormone Signaling</h3>
+                <p>Detailed analysis of A. thaliana Hormone Signaling using the Programming Framework, revealing computational logic and regulatory patterns for plant hormone responses.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Hormone Detection
+    A[Auxin Presence] --> B[TIR1/AFB Receptors]
+    C[Cytokinin Presence] --> D[AHK Receptors]
+    E[Gibberellin Presence] --> F[GID1 Receptors]
+    G[Abscisic Acid] --> H[PYR/PYL Receptors]
+    
+    %% Auxin Signaling
+    B --> I[Aux/IAA Degradation]
+    I --> J[ARF Activation]
+    J --> K[Auxin Response Genes]
+    
+    %% Cytokinin Signaling
+    D --> L[AHK Phosphorylation]
+    L --> M[ARR Phosphorylation]
+    M --> N[Cytokinin Response]
+    
+    %% Gibberellin Signaling
+    F --> O[DELLA Degradation]
+    O --> P[PIF Activation]
+    P --> Q[Growth Promotion]
+    
+    %% ABA Signaling
+    H --> R[PP2C Inhibition]
+    R --> S[SnRK2 Activation]
+    S --> T[Stress Response]
+    
+    %% Integration
+    K --> U[Hormone Response Program]
+    N --> U
+    Q --> U
+    T --> U
+    U --> V[Developmental Control]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#74c0fc,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>5. Stress Response</h3>
+                <p>Detailed analysis of A. thaliana Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Detection
+    A[Drought Stress] --> B[ABA Accumulation]
+    C[Salt Stress] --> D[SOS Pathway]
+    E[Oxidative Stress] --> F[ROS Scavenging]
+    G[Pathogen Attack] --> H[SA Signaling]
+    
+    %% Drought Response
+    B --> I[PYR/PYL Activation]
+    I --> J[SnRK2 Activation]
+    J --> K[Stomatal Closure]
+    
+    %% Salt Response
+    D --> L[SOS1 Activation]
+    L --> M[Na+ Efflux]
+    M --> N[Salt Tolerance]
+    
+    %% Oxidative Response
+    F --> O[Catalase Production]
+    O --> P[SOD Activation]
+    P --> Q[ROS Detoxification]
+    
+    %% Pathogen Response
+    H --> R[NPR1 Activation]
+    R --> S[PR Gene Expression]
+    S --> T[Systemic Resistance]
+    
+    %% Integration
+    K --> U[Stress Adaptation]
+    N --> U
+    Q --> U
+    T --> U
+    U --> V[Environmental Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#51cf66,color:#fff
+    style R fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#74c0fc,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Development & Growth -->
+            <div class="process-item" id="development">
+                <h3>6. Development & Growth</h3>
+                <p>Detailed analysis of A. thaliana Development & Growth using the Programming Framework, revealing computational logic and regulatory patterns for plant development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Developmental Signals
+    A[Meristem Activity] --> B[Cell Division]
+    C[Auxin Gradients] --> D[Cell Elongation]
+    E[Cytokinin Signals] --> F[Cell Differentiation]
+    G[Light Signals] --> H[Organ Development]
+    
+    %% Meristem Function
+    B --> I[Stem Cell Maintenance]
+    I --> J[Organ Initiation]
+    J --> K[Pattern Formation]
+    
+    %% Cell Elongation
+    D --> L[Cell Wall Loosening]
+    L --> M[Expansin Activation]
+    M --> N[Cell Growth]
+    
+    %% Cell Differentiation
+    F --> O[Fate Specification]
+    O --> P[Tissue Formation]
+    P --> Q[Organ Development]
+    
+    %% Integration
+    K --> R[Developmental Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Plant Architecture]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Nutrient Uptake -->
+            <div class="process-item" id="nutrient-uptake">
+                <h3>7. Nutrient Uptake</h3>
+                <p>Detailed analysis of A. thaliana Nutrient Uptake using the Programming Framework, revealing computational logic and regulatory patterns for mineral nutrition.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Nutrient Detection
+    A[Nitrate Availability] --> B[NRT1/NRT2 Transporters]
+    C[Phosphate Limitation] --> D[PHT Transporters]
+    E[Iron Deficiency] --> F[IRT1/FRO2]
+    G[Potassium Need] --> H[AKT1/KAT1]
+    
+    %% Nitrate Uptake
+    B --> I[Nitrate Transport]
+    I --> J[Nitrate Reduction]
+    J --> K[Nitrogen Assimilation]
+    
+    %% Phosphate Uptake
+    D --> L[Phosphate Transport]
+    L --> M[Phosphate Storage]
+    M --> N[Phosphate Utilization]
+    
+    %% Iron Uptake
+    F --> O[Iron Chelation]
+    O --> P[Iron Transport]
+    P --> Q[Iron Storage]
+    
+    %% Integration
+    K --> R[Nutrient Homeostasis]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Plant Nutrition]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Flowering Control -->
+            <div class="process-item" id="flowering">
+                <h3>8. Flowering Control</h3>
+                <p>Detailed analysis of A. thaliana Flowering Control using the Programming Framework, revealing computational logic and regulatory patterns for floral transition.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Flowering Signals
+    A[Photoperiod] --> B[CO Expression]
+    C[Vernalization] --> D[FLC Repression]
+    E[Gibberellin] --> F[GA Signaling]
+    G[Autonomous Pathway] --> H[FCA/FVE]
+    
+    %% Photoperiod Pathway
+    B --> I[FT Expression]
+    I --> J[Floral Meristem]
+    J --> K[Flower Development]
+    
+    %% Vernalization
+    D --> L[FLC Silencing]
+    L --> M[Vernalization Response]
+    M --> N[Spring Flowering]
+    
+    %% Gibberellin Pathway
+    F --> O[DELLA Degradation]
+    O --> P[Flowering Promotion]
+    P --> Q[Flower Initiation]
+    
+    %% Integration
+    K --> R[Flowering Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Reproductive Success]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of A. thaliana photosynthesis and development systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Photosynthesis & Development</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

c_elegans_batch01_development_behavior.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>C. elegans Batch 01: Development & Behavior - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🧬 C. elegans Batch 01: Development & Behavior</h1>
+            <p>Programming Framework Analysis - 8 Eukaryotic Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🧬 Development & Behavior Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental C. elegans processes responsible for development and behavior. These processes represent the core computational systems that enable this model organism to develop from embryo to adult, exhibit complex behaviors, and respond to environmental cues.</p>
+                <p>Each process demonstrates sophisticated biological programming with developmental pathways, neural circuits, behavioral responses, and aging mechanisms.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Eukaryotic Processes</h2>
+                <ul>
+                    <li><a href="#embryonic-development">1. Embryonic Development</a></li>
+                    <li><a href="#cell-fate-determination">2. Cell Fate Determination</a></li>
+                    <li><a href="#neural-development">3. Neural Development</a></li>
+                    <li><a href="#behavioral-circuits">4. Behavioral Circuits</a></li>
+                    <li><a href="#sensory-processing">5. Sensory Processing</a></li>
+                    <li><a href="#learning-memory">6. Learning & Memory</a></li>
+                    <li><a href="#aging-longevity">7. Aging & Longevity</a></li>
+                    <li><a href="#stress-response">8. Stress Response</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Embryonic Development -->
+            <div class="process-item" id="embryonic-development">
+                <h3>1. Embryonic Development</h3>
+                <p>Detailed analysis of C. elegans Embryonic Development using the Programming Framework, revealing computational logic and regulatory patterns for early development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Development Triggers
+    A[Fertilization] --> B[Zygote Formation]
+    C[Maternal Factors] --> D[Asymmetric Division]
+    E[Cell Division] --> F[Blastula Formation]
+    G[Gastrulation] --> H[Germ Layer Formation]
+    
+    %% Zygote Development
+    B --> I[Polarity Establishment]
+    I --> J[Asymmetric Cleavage]
+    J --> K[Cell Fate Specification]
+    
+    %% Maternal Control
+    D --> L[Maternal mRNAs]
+    L --> M[Translation Control]
+    M --> N[Protein Gradients]
+    
+    %% Germ Layer Formation
+    F --> O[Ectoderm Formation]
+    O --> P[Mesoderm Formation]
+    P --> Q[Endoderm Formation]
+    
+    %% Integration
+    K --> R[Development Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Embryonic Pattern]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Cell Fate Determination -->
+            <div class="process-item" id="cell-fate-determination">
+                <h3>2. Cell Fate Determination</h3>
+                <p>Detailed analysis of C. elegans Cell Fate Determination using the Programming Framework, revealing computational logic and regulatory patterns for cell differentiation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Fate Components
+    A[Cell Lineage] --> B[Fate Specification]
+    C[Signaling Pathways] --> D[Cell-Cell Communication]
+    E[Transcription Factors] --> F[Gene Expression]
+    G[Epigenetic Control] --> H[Fate Maintenance]
+    
+    %% Lineage Control
+    B --> I[Asymmetric Division]
+    I --> J[Fate Determinants]
+    J --> K[Cell Identity]
+    
+    %% Signaling Networks
+    D --> L[Notch Signaling]
+    L --> M[Wnt Pathway]
+    M --> N[Cell Fate Decision]
+    
+    %% Transcription Control
+    F --> O[Homeobox Genes]
+    O --> P[Cell Type Genes]
+    P --> Q[Differentiation]
+    
+    %% Integration
+    K --> R[Fate Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Cell Identity]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Neural Development -->
+            <div class="process-item" id="neural-development">
+                <h3>3. Neural Development</h3>
+                <p>Detailed analysis of C. elegans Neural Development using the Programming Framework, revealing computational logic and regulatory patterns for nervous system formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Neural Components
+    A[Neural Precursors] --> B[Neurogenesis]
+    C[Axon Guidance] --> D[Synapse Formation]
+    E[Neural Circuits] --> F[Circuit Assembly]
+    G[Neurotransmitters] --> H[Neural Function]
+    
+    %% Neurogenesis
+    B --> I[Neural Progenitors]
+    I --> J[Neuron Differentiation]
+    J --> K[Neural Identity]
+    
+    %% Axon Guidance
+    D --> L[Guidance Molecules]
+    L --> M[Axon Pathfinding]
+    M --> N[Target Recognition]
+    
+    %% Synapse Formation
+    F --> O[Synaptic Proteins]
+    O --> P[Synapse Assembly]
+    P --> Q[Functional Synapses]
+    
+    %% Integration
+    K --> R[Neural Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Neural Circuit]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Behavioral Circuits -->
+            <div class="process-item" id="behavioral-circuits">
+                <h3>4. Behavioral Circuits</h3>
+                <p>Detailed analysis of C. elegans Behavioral Circuits using the Programming Framework, revealing computational logic and regulatory patterns for behavior generation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Behavior Components
+    A[Sensory Input] --> B[Sensory Neurons]
+    C[Interneurons] --> D[Neural Processing]
+    E[Motor Neurons] --> F[Motor Output]
+    G[Behavioral State] --> H[Behavioral Control]
+    
+    %% Sensory Processing
+    B --> I[Sensory Transduction]
+    I --> J[Signal Integration]
+    J --> K[Sensory Representation]
+    
+    %% Neural Processing
+    D --> L[Interneuron Networks]
+    L --> M[Information Processing]
+    M --> N[Decision Making]
+    
+    %% Motor Control
+    F --> O[Motor Pattern Generation]
+    O --> P[Muscle Activation]
+    P --> Q[Behavioral Response]
+    
+    %% Integration
+    K --> R[Behavioral Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Behavioral Output]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Sensory Processing -->
+            <div class="process-item" id="sensory-processing">
+                <h3>5. Sensory Processing</h3>
+                <p>Detailed analysis of C. elegans Sensory Processing using the Programming Framework, revealing computational logic and regulatory patterns for environmental sensing.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Sensory Components
+    A[Environmental Cues] --> B[Sensory Receptors]
+    C[Signal Transduction] --> D[Neural Encoding]
+    E[Sensory Integration] --> F[Perception]
+    G[Behavioral Response] --> H[Sensory Adaptation]
+    
+    %% Receptor Activation
+    B --> I[Chemoreceptors]
+    I --> J[Mechanoreceptors]
+    J --> K[Thermoreceptors]
+    
+    %% Signal Transduction
+    D --> L[G-Protein Coupling]
+    L --> M[Second Messengers]
+    M --> N[Ion Channel Activation]
+    
+    %% Neural Encoding
+    F --> O[Action Potentials]
+    O --> P[Neural Codes]
+    P --> Q[Sensory Representation]
+    
+    %% Integration
+    K --> R[Sensory Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Environmental Response]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Learning & Memory -->
+            <div class="process-item" id="learning-memory">
+                <h3>6. Learning & Memory</h3>
+                <p>Detailed analysis of C. elegans Learning & Memory using the Programming Framework, revealing computational logic and regulatory patterns for behavioral plasticity.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Learning Components
+    A[Experience] --> B[Neural Plasticity]
+    C[Synaptic Changes] --> D[Memory Formation]
+    E[Memory Storage] --> F[Memory Retrieval]
+    G[Behavioral Change] --> H[Learning Outcome]
+    
+    %% Neural Plasticity
+    B --> I[Synaptic Strengthening]
+    I --> J[Synaptic Weakening]
+    J --> K[Circuit Modification]
+    
+    %% Memory Formation
+    D --> L[Short-term Memory]
+    L --> M[Long-term Memory]
+    M --> N[Memory Consolidation]
+    
+    %% Memory Storage
+    F --> O[Neural Circuits]
+    O --> P[Synaptic Networks]
+    P --> Q[Memory Traces]
+    
+    %% Integration
+    K --> R[Learning Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Behavioral Adaptation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Aging & Longevity -->
+            <div class="process-item" id="aging-longevity">
+                <h3>7. Aging & Longevity</h3>
+                <p>Detailed analysis of C. elegans Aging & Longevity using the Programming Framework, revealing computational logic and regulatory patterns for lifespan regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Aging Components
+    A[Age-related Changes] --> B[Insulin/IGF Signaling]
+    C[Oxidative Stress] --> D[DNA Damage]
+    E[Protein Homeostasis] --> F[Metabolic Changes]
+    G[Longevity Pathways] --> H[Lifespan Control]
+    
+    %% Insulin Signaling
+    B --> I[DAF-2/DAF-16]
+    I --> J[FOXO Transcription]
+    J --> K[Stress Resistance]
+    
+    %% Oxidative Damage
+    D --> L[ROS Production]
+    L --> M[Antioxidant Response]
+    M --> N[Oxidative Protection]
+    
+    %% Protein Homeostasis
+    F --> O[Proteasome Function]
+    O --> P[Autophagy]
+    P --> Q[Protein Quality Control]
+    
+    %% Integration
+    K --> R[Aging Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Lifespan Regulation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>8. Stress Response</h3>
+                <p>Detailed analysis of C. elegans Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Components
+    A[Environmental Stress] --> B[Stress Detection]
+    C[Stress Signaling] --> D[Stress Response]
+    E[Adaptation] --> F[Stress Tolerance]
+    G[Recovery] --> H[Homeostasis]
+    
+    %% Stress Detection
+    B --> I[Heat Shock]
+    I --> J[Oxidative Stress]
+    J --> K[Osmotic Stress]
+    
+    %% Stress Signaling
+    D --> L[HSF-1 Activation]
+    L --> M[Stress Proteins]
+    M --> N[Protective Response]
+    
+    %% Adaptation
+    F --> O[Metabolic Changes]
+    O --> P[Behavioral Changes]
+    P --> Q[Physiological Adaptation]
+    
+    %% Integration
+    K --> R[Stress Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Stress Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of C. elegans development and behavior systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Development & Behavior</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

d_melanogaster_batch01_development_genetics.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>D. melanogaster Batch 01: Development & Genetics - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦟 D. melanogaster Batch 01: Development & Genetics</h1>
+            <p>Programming Framework Analysis - 8 Eukaryotic Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦟 Development & Genetics Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental D. melanogaster processes responsible for development and genetics. These processes represent the core computational systems that enable this model organism to develop from embryo to adult, exhibit complex behaviors, and maintain genetic integrity.</p>
+                <p>Each process demonstrates sophisticated biological programming with developmental pathways, genetic regulation, neural circuits, and behavioral responses.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Eukaryotic Processes</h2>
+                <ul>
+                    <li><a href="#embryonic-patterning">1. Embryonic Patterning</a></li>
+                    <li><a href="#segmentation">2. Segmentation</a></li>
+                    <li><a href="#homeotic-regulation">3. Homeotic Regulation</a></li>
+                    <li><a href="#neural-development">4. Neural Development</a></li>
+                    <li><a href="#behavioral-genetics">5. Behavioral Genetics</a></li>
+                    <li><a href="#circadian-rhythms">6. Circadian Rhythms</a></li>
+                    <li><a href="#learning-memory">7. Learning & Memory</a></li>
+                    <li><a href="#genetic-regulation">8. Genetic Regulation</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Embryonic Patterning -->
+            <div class="process-item" id="embryonic-patterning">
+                <h3>1. Embryonic Patterning</h3>
+                <p>Detailed analysis of D. melanogaster Embryonic Patterning using the Programming Framework, revealing computational logic and regulatory patterns for early development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Patterning Components
+    A[Maternal Factors] --> B[Anterior-Posterior Axis]
+    C[Dorsal-Ventral Axis] --> D[Polarity Establishment]
+    E[Gap Genes] --> F[Segment Polarity]
+    G[Pair-Rule Genes] --> H[Pattern Formation]
+    
+    %% Maternal Control
+    B --> I[Bicoid mRNA]
+    I --> J[Nanos mRNA]
+    J --> K[Protein Gradients]
+    
+    %% Axis Formation
+    D --> L[Toll Signaling]
+    L --> M[Dorsal Protein]
+    M --> N[D-V Patterning]
+    
+    %% Gap Gene Expression
+    F --> O[Giant Expression]
+    O --> P[Krüppel Expression]
+    P --> Q[Segment Boundaries]
+    
+    %% Integration
+    K --> R[Patterning Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Embryonic Pattern]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Segmentation -->
+            <div class="process-item" id="segmentation">
+                <h3>2. Segmentation</h3>
+                <p>Detailed analysis of D. melanogaster Segmentation using the Programming Framework, revealing computational logic and regulatory patterns for body segment formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Segmentation Components
+    A[Gap Gene Expression] --> B[Pair-Rule Genes]
+    C[Segment Polarity] --> D[Engrailed Expression]
+    E[Wingless Signaling] --> F[Segment Boundaries]
+    G[Homeotic Genes] --> H[Segment Identity]
+    
+    %% Pair-Rule Expression
+    B --> I[Even-Skipped]
+    I --> J[Fushi Tarazu]
+    J --> K[Segment Stripes]
+    
+    %% Segment Polarity
+    D --> L[Engrailed/Wingless]
+    L --> M[Cell Communication]
+    M --> N[Segment Maintenance]
+    
+    %% Segment Identity
+    F --> O[Antennapedia Complex]
+    O --> P[Bithorax Complex]
+    P --> Q[Segment Specification]
+    
+    %% Integration
+    K --> R[Segmentation Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Body Segmentation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Homeotic Regulation -->
+            <div class="process-item" id="homeotic-regulation">
+                <h3>3. Homeotic Regulation</h3>
+                <p>Detailed analysis of D. melanogaster Homeotic Regulation using the Programming Framework, revealing computational logic and regulatory patterns for segment identity.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Homeotic Components
+    A[Homeotic Genes] --> B[Antennapedia Complex]
+    C[Bithorax Complex] --> D[Segment Identity]
+    E[Polycomb Group] --> F[Gene Silencing]
+    G[Trithorax Group] --> H[Gene Activation]
+    
+    %% Antennapedia Complex
+    B --> I[Labial Expression]
+    I --> J[Proboscipedia]
+    J --> K[Deformed Expression]
+    
+    %% Bithorax Complex
+    D --> L[Ultrabithorax]
+    L --> M[Abdominal-A]
+    M --> N[Abdominal-B]
+    
+    %% Epigenetic Control
+    F --> O[Polycomb Repression]
+    O --> P[Chromatin Modification]
+    P --> Q[Gene Silencing]
+    
+    %% Integration
+    K --> R[Homeotic Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Segment Identity]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Neural Development -->
+            <div class="process-item" id="neural-development">
+                <h3>4. Neural Development</h3>
+                <p>Detailed analysis of D. melanogaster Neural Development using the Programming Framework, revealing computational logic and regulatory patterns for nervous system formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Neural Components
+    A[Neural Precursors] --> B[Neurogenesis]
+    C[Notch Signaling] --> D[Cell Fate Decision]
+    E[Axon Guidance] --> F[Neural Circuits]
+    G[Synapse Formation] --> H[Neural Function]
+    
+    %% Neurogenesis
+    B --> I[Neural Progenitors]
+    I --> J[Neuron/Glia Decision]
+    J --> K[Neural Identity]
+    
+    %% Notch Signaling
+    D --> L[Delta-Notch]
+    L --> M[Lateral Inhibition]
+    M --> N[Cell Fate Specification]
+    
+    %% Axon Guidance
+    F --> O[Netrin Signaling]
+    O --> P[Slit/Robo]
+    P --> Q[Axon Pathfinding]
+    
+    %% Integration
+    K --> R[Neural Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Neural Circuit]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Behavioral Genetics -->
+            <div class="process-item" id="behavioral-genetics">
+                <h3>5. Behavioral Genetics</h3>
+                <p>Detailed analysis of D. melanogaster Behavioral Genetics using the Programming Framework, revealing computational logic and regulatory patterns for behavior generation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Behavioral Components
+    A[Genetic Background] --> B[Behavioral Genes]
+    C[Neural Circuits] --> D[Behavioral Output]
+    E[Environmental Cues] --> F[Behavioral Response]
+    G[Learning Genes] --> H[Behavioral Plasticity]
+    
+    %% Behavioral Genes
+    B --> I[Period Gene]
+    I --> J[Clock Genes]
+    J --> K[Circadian Behavior]
+    
+    %% Neural Circuits
+    D --> L[Mushroom Bodies]
+    L --> M[Central Complex]
+    M --> N[Behavioral Control]
+    
+    %% Learning Genes
+    F --> O[dunce Gene]
+    O --> P[rutabaga Gene]
+    P --> Q[Learning Ability]
+    
+    %% Integration
+    K --> R[Behavioral Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Behavioral Output]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Circadian Rhythms -->
+            <div class="process-item" id="circadian-rhythms">
+                <h3>6. Circadian Rhythms</h3>
+                <p>Detailed analysis of D. melanogaster Circadian Rhythms using the Programming Framework, revealing computational logic and regulatory patterns for 24-hour cycles.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Circadian Components
+    A[Light Input] --> B[Clock Genes]
+    C[Period Gene] --> D[Timeless Gene]
+    E[Clock Gene] --> F[Cycle Gene]
+    G[Feedback Loops] --> H[Rhythm Generation]
+    
+    %% Clock Genes
+    B --> I[PER/TIM Complex]
+    I --> J[Nuclear Entry]
+    J --> K[Gene Repression]
+    
+    %% Feedback Regulation
+    D --> L[CLK/CYC Complex]
+    L --> M[Gene Activation]
+    M --> N[PER/TIM Synthesis]
+    
+    %% Light Entrainment
+    F --> O[Cryptochrome]
+    O --> P[Light Sensing]
+    P --> Q[Phase Reset]
+    
+    %% Integration
+    K --> R[Circadian Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[24-Hour Rhythm]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Learning & Memory -->
+            <div class="process-item" id="learning-memory">
+                <h3>7. Learning & Memory</h3>
+                <p>Detailed analysis of D. melanogaster Learning & Memory using the Programming Framework, revealing computational logic and regulatory patterns for behavioral plasticity.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Learning Components
+    A[Experience] --> B[Neural Plasticity]
+    C[cAMP Signaling] --> D[Memory Formation]
+    E[Mushroom Bodies] --> F[Memory Storage]
+    G[Retrieval] --> H[Behavioral Change]
+    
+    %% Neural Plasticity
+    B --> I[Synaptic Changes]
+    I --> J[Neural Circuits]
+    J --> K[Circuit Modification]
+    
+    %% cAMP Signaling
+    D --> L[dunce Gene]
+    L --> M[rutabaga Gene]
+    M --> N[cAMP Production]
+    
+    %% Memory Storage
+    F --> O[Short-term Memory]
+    O --> P[Long-term Memory]
+    P --> Q[Memory Consolidation]
+    
+    %% Integration
+    K --> R[Learning Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Behavioral Adaptation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Genetic Regulation -->
+            <div class="process-item" id="genetic-regulation">
+                <h3>8. Genetic Regulation</h3>
+                <p>Detailed analysis of D. melanogaster Genetic Regulation using the Programming Framework, revealing computational logic and regulatory patterns for gene expression control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Regulation Components
+    A[Transcription Factors] --> B[Gene Expression]
+    C[Epigenetic Control] --> D[Chromatin Modification]
+    E[MicroRNAs] --> F[Post-transcriptional Control]
+    G[Alternative Splicing] --> H[Protein Diversity]
+    
+    %% Transcription Control
+    B --> I[Enhancer Binding]
+    I --> J[Promoter Activation]
+    J --> K[Gene Transcription]
+    
+    %% Epigenetic Control
+    D --> L[Histone Modification]
+    L --> M[DNA Methylation]
+    M --> N[Chromatin State]
+    
+    %% MicroRNA Control
+    F --> O[miRNA Synthesis]
+    O --> P[Target Recognition]
+    P --> Q[mRNA Degradation]
+    
+    %% Integration
+    K --> R[Regulation Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Gene Expression Control]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of D. melanogaster development and genetics systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Development & Genetics</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

hiv1_batch01_replication_evasion.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>HIV-1 Batch 01: Replication & Immune Evasion - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 HIV-1 Batch 01: Replication & Immune Evasion</h1>
+            <p>Programming Framework Analysis - 8 Viral Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Viral Replication & Immune Evasion Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental HIV-1 processes responsible for viral replication and immune evasion. These processes represent the core computational systems that enable this retrovirus to replicate, evade host immunity, and establish persistent infection.</p>
+                <p>Each process demonstrates sophisticated biological programming with viral entry, reverse transcription, integration, immune evasion, and latency mechanisms.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Viral Processes</h2>
+                <ul>
+                    <li><a href="#viral-entry">1. Viral Entry</a></li>
+                    <li><a href="#reverse-transcription">2. Reverse Transcription</a></li>
+                    <li><a href="#integration">3. Integration</a></li>
+                    <li><a href="#transcription-regulation">4. Transcription Regulation</a></li>
+                    <li><a href="#assembly-budding">5. Assembly & Budding</a></li>
+                    <li><a href="#immune-evasion">6. Immune Evasion</a></li>
+                    <li><a href="#latency">7. Latency Establishment</a></li>
+                    <li><a href="#reactivation">8. Reactivation & Spread</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Viral Entry -->
+            <div class="process-item" id="viral-entry">
+                <h3>1. Viral Entry</h3>
+                <p>Detailed analysis of HIV-1 Viral Entry using the Programming Framework, revealing computational logic and regulatory patterns for host cell infection.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Entry Triggers
+    A[CD4 Binding] --> B[gp120 Conformational Change]
+    C[Coreceptor Binding] --> D[CCR5/CXCR4 Interaction]
+    E[Fusion Activation] --> F[gp41 Fusion]
+    G[Host Cell Contact] --> H[Entry Machinery]
+    
+    %% CD4 Binding
+    B --> I[CD4 Receptor Binding]
+    I --> J[gp120 Structural Change]
+    J --> K[Coreceptor Exposure]
+    
+    %% Coreceptor Interaction
+    D --> L[Coreceptor Binding]
+    L --> M[gp120 Shedding]
+    M --> N[gp41 Activation]
+    
+    %% Membrane Fusion
+    F --> O[Fusion Peptide Insertion]
+    O --> P[Membrane Fusion]
+    P --> Q[Viral Core Entry]
+    
+    %% Integration
+    K --> R[Entry Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Intracellular Localization]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Reverse Transcription -->
+            <div class="process-item" id="reverse-transcription">
+                <h3>2. Reverse Transcription</h3>
+                <p>Detailed analysis of HIV-1 Reverse Transcription using the Programming Framework, revealing computational logic and regulatory patterns for RNA to DNA conversion.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% RT Components
+    A[Viral RNA] --> B[RT Enzyme]
+    C[dNTPs] --> D[Template Switching]
+    E[Host Factors] --> F[RT Complex]
+    G[RNase H] --> H[RNA Degradation]
+    
+    %% RNA Template
+    B --> I[RNA-DNA Hybrid]
+    I --> J[First Strand Synthesis]
+    J --> K[Minus Strand DNA]
+    
+    %% Template Switching
+    D --> L[R-U5 Transfer]
+    L --> M[Plus Strand Synthesis]
+    M --> N[DNA-DNA Hybrid]
+    
+    %% RNA Processing
+    H --> O[RNA Removal]
+    O --> P[Second Strand Synthesis]
+    P --> Q[Double-Stranded DNA]
+    
+    %% Integration
+    K --> R[RT Program]
+    N --> R
+    Q --> R
+    F --> R
+    R --> S[Proviral DNA]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Integration -->
+            <div class="process-item" id="integration">
+                <h3>3. Integration</h3>
+                <p>Detailed analysis of HIV-1 Integration using the Programming Framework, revealing computational logic and regulatory patterns for proviral DNA insertion.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Integration Components
+    A[Proviral DNA] --> B[Integrase Enzyme]
+    C[Host DNA] --> D[Integration Complex]
+    E[LEDGF/p75] --> F[Target Site Selection]
+    G[Host Factors] --> H[Integration Machinery]
+    
+    %% Preintegration Complex
+    B --> I[PIC Formation]
+    I --> J[Nuclear Import]
+    J --> K[Nuclear Localization]
+    
+    %% Target Site Selection
+    D --> L[DNA Scanning]
+    L --> M[Target Recognition]
+    M --> N[Integration Site]
+    
+    %% DNA Integration
+    F --> O[3' Processing]
+    O --> P[Strand Transfer]
+    P --> Q[DNA Repair]
+    
+    %% Integration
+    K --> R[Integration Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Proviral Integration]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Transcription Regulation -->
+            <div class="process-item" id="transcription-regulation">
+                <h3>4. Transcription Regulation</h3>
+                <p>Detailed analysis of HIV-1 Transcription Regulation using the Programming Framework, revealing computational logic and regulatory patterns for viral gene expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Transcription Factors
+    A[Tat Protein] --> B[TAR RNA Binding]
+    C[Host Factors] --> D[RNA Polymerase II]
+    E[Chromatin State] --> F[Transcription Activation]
+    G[NF-κB] --> H[Promoter Activation]
+    
+    %% Tat Function
+    B --> I[Tat-TAR Complex]
+    I --> J[Transcription Elongation]
+    J --> K[Viral RNA Synthesis]
+    
+    %% Host Factor Recruitment
+    D --> L[P-TEFb Recruitment]
+    L --> M[Transcription Complex]
+    M --> N[Processive Transcription]
+    
+    %% Chromatin Remodeling
+    F --> O[Histone Acetylation]
+    O --> P[Chromatin Opening]
+    P --> Q[Transcription Access]
+    
+    %% Integration
+    K --> R[Transcription Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral Gene Expression]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Assembly & Budding -->
+            <div class="process-item" id="assembly-budding">
+                <h3>5. Assembly & Budding</h3>
+                <p>Detailed analysis of HIV-1 Assembly & Budding using the Programming Framework, revealing computational logic and regulatory patterns for viral particle formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Assembly Components
+    A[Gag Polyprotein] --> B[Assembly Complex]
+    C[Viral RNA] --> D[Packaging Signal]
+    E[Host Factors] --> F[ESCRT Machinery]
+    G[Lipid Rafts] --> H[Assembly Platform]
+    
+    %% Gag Assembly
+    B --> I[Gag Oligomerization]
+    I --> J[Immature Particle]
+    J --> K[Viral Core Formation]
+    
+    %% RNA Packaging
+    D --> L[RNA Recognition]
+    L --> M[RNA Encapsidation]
+    M --> N[Genome Packaging]
+    
+    %% Budding Process
+    F --> O[ESCRT Recruitment]
+    O --> P[Membrane Scission]
+    P --> Q[Particle Release]
+    
+    %% Integration
+    K --> R[Assembly Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Mature Virion]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Immune Evasion -->
+            <div class="process-item" id="immune-evasion">
+                <h3>6. Immune Evasion</h3>
+                <p>Detailed analysis of HIV-1 Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for host immune system avoidance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Immune Detection
+    A[Host Immune Response] --> B[Antigen Variation]
+    C[CTL Recognition] --> D[Epitope Mutation]
+    E[Antibody Response] --> F[Glycan Shield]
+    G[Innate Immunity] --> H[Viral Proteins]
+    
+    %% Antigen Variation
+    B --> I[High Mutation Rate]
+    I --> J[Epitope Changes]
+    J --> K[Immune Escape]
+    
+    %% CTL Evasion
+    D --> L[Epitope Mutation]
+    L --> M[CTL Recognition Block]
+    M --> N[Cytotoxic Evasion]
+    
+    %% Antibody Evasion
+    F --> O[Glycan Masking]
+    O --> P[Antibody Binding Block]
+    P --> Q[Neutralization Escape]
+    
+    %% Integration
+    K --> R[Immune Evasion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Immune Escape]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Latency Establishment -->
+            <div class="process-item" id="latency">
+                <h3>7. Latency Establishment</h3>
+                <p>Detailed analysis of HIV-1 Latency Establishment using the Programming Framework, revealing computational logic and regulatory patterns for viral persistence.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Latency Triggers
+    A[Immune Pressure] --> B[Latency Induction]
+    C[Host Factors] --> D[Transcription Silencing]
+    E[Chromatin State] --> F[Epigenetic Control]
+    G[Cell Differentiation] --> H[Latency Program]
+    
+    %% Transcription Silencing
+    B --> I[Tat Downregulation]
+    I --> J[Transcription Inhibition]
+    J --> K[Viral Gene Silencing]
+    
+    %% Epigenetic Control
+    D --> L[Histone Deacetylation]
+    L --> M[Chromatin Condensation]
+    M --> N[Transcription Block]
+    
+    %% Latency Maintenance
+    F --> O[Latency Factors]
+    O --> P[Transcription Repression]
+    P --> Q[Viral Persistence]
+    
+    %% Integration
+    K --> R[Latency Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Latent Reservoir]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Reactivation & Spread -->
+            <div class="process-item" id="reactivation">
+                <h3>8. Reactivation & Spread</h3>
+                <p>Detailed analysis of HIV-1 Reactivation & Spread using the Programming Framework, revealing computational logic and regulatory patterns for viral resurgence.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Reactivation Signals
+    A[Immune Activation] --> B[Latency Reversal]
+    C[Host Factors] --> D[Transcription Activation]
+    E[Stress Signals] --> F[Viral Reactivation]
+    G[Cell Signaling] --> H[Reactivation Program]
+    
+    %% Latency Reversal
+    B --> I[Tat Expression]
+    I --> J[Transcription Activation]
+    J --> K[Viral Gene Expression]
+    
+    %% Transcription Activation
+    D --> L[Chromatin Remodeling]
+    L --> M[Transcription Complex]
+    M --> N[Viral RNA Synthesis]
+    
+    %% Viral Production
+    F --> O[Viral Protein Synthesis]
+    O --> P[Particle Assembly]
+    P --> Q[Viral Spread]
+    
+    %% Integration
+    K --> R[Reactivation Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral Transmission]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of HIV-1 replication and immune evasion systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Replication & Immune Evasion</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

index.html

@@ -215,15 +215,15 @@
         
         <div class="project-stats">
             <div class="stat">
-                <span class="stat-number">371</span>
+                <span class="stat-number">411</span>
                 <span class="stat-label">Biological Processes</span>
             </div>
             <div class="stat">
-                <span class="stat-number">36</span>
+                <span class="stat-number">45</span>
                 <span class="stat-label">Collections</span>
             </div>
             <div class="stat">
-                <span class="stat-number">6</span>
+                <span class="stat-number">7</span>
                 <span class="stat-label">Kingdoms/Systems</span>
             </div>
             <div class="stat">
@@ -242,6 +242,20 @@
     </div>
 
     <div class="main-content">
+        <div class="section">
+            <h2>🧠 Neural Computation Systems</h2>
+            <p><strong>NEW!</strong> Advanced neural computation systems demonstrating sophisticated biological computing architectures in neural networks.</p>
+            
+            <h3>Neural Systems:</h3>
+            <ul class="nav-links">
+                <li><a href="neural_plasticity_batch01_synaptic_plasticity.html">🧠 Synaptic Plasticity Mechanisms (LTP/LTD/Synaptic Scaling)</a></li>
+                <li><a href="neural_plasticity_batch02_sensory_processing.html">👁️ Sensory Processing Algorithms (Visual/Auditory/Olfactory)</a></li>
+                <li><a href="neural_plasticity_batch03_memory_formation.html">💾 Memory Formation Systems (Consolidation/Retrieval/Extinction)</a></li>
+                <li><a href="neural_plasticity_batch04_motor_control.html">🏃 Motor Control Systems (Planning/Execution/Learning)</a></li>
+                <li><a href="neural_plasticity_batch05_decision_making.html">🧠 Neural Decision-Making (Winner-Take-All/Lateral Inhibition)</a></li>
+            </ul>
+        </div>
+
         <div class="section">
             <h2>🔬 Advanced Systems Analysis</h2>
             <p><strong>COMPREHENSIVE!</strong> Advanced biological computing systems demonstrating sophisticated computational architectures across multiple kingdoms of life.</p>
@@ -278,6 +292,35 @@
                 <li><a href="ecoli_beta_galactosidase_lac_operon.html">β-Galactosidase Lac Operon (Featured Process)</a></li>
                 <li><a href="README.md#e-coli">📋 View All 15 E. coli Batches</a></li>
             </ul>
+
+            <h3>🌱 Arabidopsis thaliana (8 Processes)</h3>
+            <ul class="nav-links">
+                <li><a href="a_thaliana_batch01_photosynthesis_development.html">Photosynthesis & Development (8 processes)</a></li>
+            </ul>
+
+            <h3>🦟 Drosophila melanogaster (8 Processes)</h3>
+            <ul class="nav-links">
+                <li><a href="d_melanogaster_batch01_development_genetics.html">Development & Genetics (8 processes)</a></li>
+            </ul>
+
+            <h3>🪱 Caenorhabditis elegans (8 Processes)</h3>
+            <ul class="nav-links">
+                <li><a href="c_elegans_batch01_development_behavior.html">Development & Behavior (8 processes)</a></li>
+            </ul>
+
+            <h3>🦠 Viral Systems (16 Processes)</h3>
+            <ul class="nav-links">
+                <li><a href="sars_cov2_batch01_entry_replication.html">SARS-CoV-2 Entry & Replication (8 processes)</a></li>
+                <li><a href="hiv1_batch01_replication_evasion.html">HIV-1 Replication & Immune Evasion (8 processes)</a></li>
+            </ul>
+
+            <h3>🦠 Bacterial Pathogens (32 Processes)</h3>
+            <ul class="nav-links">
+                <li><a href="s_enterica_batch01_invasion_virulence.html">Salmonella enterica Invasion & Virulence (8 processes)</a></li>
+                <li><a href="s_aureus_batch01_pathogenicity_biofilm.html">Staphylococcus aureus Pathogenicity & Biofilm (8 processes)</a></li>
+                <li><a href="m_tuberculosis_batch01_dormancy_persistence.html">Mycobacterium tuberculosis Dormancy & Persistence (8 processes)</a></li>
+                <li><a href="p_aeruginosa_batch01_virulence_pathogenicity.html">Pseudomonas aeruginosa Virulence & Pathogenicity (8 processes)</a></li>
+            </ul>
         </div>
 
         <div class="section">

m_tuberculosis_batch01_dormancy_persistence.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>M. tuberculosis Batch 01: Dormancy & Persistence - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
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+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
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+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
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+        }
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+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 M. tuberculosis Batch 01: Dormancy & Persistence</h1>
+            <p>Programming Framework Analysis - 8 Dormancy Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Dormancy & Persistence Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental M. tuberculosis processes responsible for dormancy and persistence. These processes represent the core computational systems that enable this pathogen to survive for decades within hosts, evading immune responses and antibiotic treatments.</p>
+                <p>Each process demonstrates sophisticated biological programming with metabolic adaptation, immune evasion, stress response, and dormancy regulation.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Dormancy Processes</h2>
+                <ul>
+                    <li><a href="#dormancy-induction">1. Dormancy Induction</a></li>
+                    <li><a href="#metabolic-adaptation">2. Metabolic Adaptation</a></li>
+                    <li><a href="#immune-evasion">3. Immune Evasion</a></li>
+                    <li><a href="#stress-response">4. Stress Response</a></li>
+                    <li><a href="#drug-tolerance">5. Drug Tolerance</a></li>
+                    <li><a href="#granuloma-formation">6. Granuloma Formation</a></li>
+                    <li><a href="#reactivation-signals">7. Reactivation Signals</a></li>
+                    <li><a href="#persistence-mechanisms">8. Persistence Mechanisms</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Dormancy Induction -->
+            <div class="process-item" id="dormancy-induction">
+                <h3>1. Dormancy Induction</h3>
+                <p>Detailed analysis of M. tuberculosis Dormancy Induction using the Programming Framework, revealing computational logic and regulatory patterns for entering a non-replicating persistent state.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Environmental Triggers
+    A[Oxygen Deprivation] --> B[DosR Activation]
+    C[Nitric Oxide Stress] --> D[NOR Activation]
+    E[Nutrient Limitation] --> F[RelA Activation]
+    G[Host Immune Pressure] --> H[Stress Response]
+    
+    %% DosR Regulon
+    B --> I[DosR Phosphorylation]
+    I --> J[DosR-DNA Binding]
+    J --> K[Dormancy Gene Expression]
+    
+    %% NOR Response
+    D --> L[Nitric Oxide Detoxification]
+    L --> M[Respiratory Protection]
+    M --> N[Anaerobic Adaptation]
+    
+    %% Stringent Response
+    F --> O[ppGpp Synthesis]
+    O --> P[Stringent Response]
+    P --> Q[Growth Arrest]
+    
+    %% Integration
+    K --> R[Dormancy Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Non-Replicating State]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Metabolic Adaptation -->
+            <div class="process-item" id="metabolic-adaptation">
+                <h3>2. Metabolic Adaptation</h3>
+                <p>Detailed analysis of M. tuberculosis Metabolic Adaptation using the Programming Framework, revealing computational logic and regulatory patterns for energy conservation and survival.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Energy Source Detection
+    A[Glucose Depletion] --> B[Fatty Acid Metabolism]
+    C[Oxygen Limitation] --> D[Anaerobic Respiration]
+    E[Host Lipid Availability] --> F[Cholesterol Utilization]
+    G[Iron Limitation] --> H[Iron Scavenging]
+    
+    %% Fatty Acid Metabolism
+    B --> I[β-Oxidation Activation]
+    I --> J[Acetyl-CoA Production]
+    J --> K[TCA Cycle Adaptation]
+    
+    %% Anaerobic Respiration
+    D --> L[Nitrate Reduction]
+    L --> M[Fumarate Reduction]
+    M --> N[Anaerobic ATP Production]
+    
+    %% Cholesterol Metabolism
+    F --> O[Cholesterol Uptake]
+    O --> P[Cholesterol Degradation]
+    P --> Q[Propionyl-CoA Production]
+    
+    %% Integration
+    K --> R[Energy Conservation]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Metabolic Dormancy]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Immune Evasion -->
+            <div class="process-item" id="immune-evasion">
+                <h3>3. Immune Evasion</h3>
+                <p>Detailed analysis of M. tuberculosis Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for avoiding host immune detection.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Immune Detection
+    A[Host Immune Response] --> B[Antigen Masking]
+    C[Phagosome Recognition] --> D[Phagosome Arrest]
+    E[TLR Activation] --> F[TLR Inhibition]
+    G[Inflammatory Signals] --> H[Anti-Inflammatory Response]
+    
+    %% Antigen Masking
+    B --> I[Cell Wall Modification]
+    I --> J[Antigen Concealment]
+    J --> K[Immune Recognition Block]
+    
+    %% Phagosome Arrest
+    D --> L[V-ATPase Inhibition]
+    L --> M[Phagosome Acidification Block]
+    M --> N[Lysosome Fusion Prevention]
+    
+    %% TLR Inhibition
+    F --> O[TLR Signaling Block]
+    O --> P[Inflammatory Response Suppression]
+    P --> Q[Immune Evasion]
+    
+    %% Integration
+    K --> R[Immune System Evasion]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>4. Stress Response</h3>
+                <p>Detailed analysis of M. tuberculosis Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Detection
+    A[Oxidative Stress] --> B[OxyR Activation]
+    C[Heat Stress] --> D[σH Activation]
+    E[DNA Damage] --> F[SOS Response]
+    G[Protein Misfolding] --> H[σE Activation]
+    
+    %% Oxidative Stress Response
+    B --> I[Catalase Production]
+    I --> J[Superoxide Dismutase]
+    J --> K[ROS Scavenging]
+    
+    %% Heat Shock Response
+    D --> L[Heat Shock Proteins]
+    L --> M[Protein Protection]
+    M --> N[Thermal Adaptation]
+    
+    %% DNA Damage Response
+    F --> O[DNA Repair Enzymes]
+    O --> P[DNA Damage Repair]
+    P --> Q[Genome Stability]
+    
+    %% Protein Stress Response
+    H --> R[Chaperone Production]
+    R --> S[Protein Folding]
+    S --> T[Proteostasis]
+    
+    %% Integration
+    K --> U[Stress Adaptation]
+    N --> U
+    Q --> U
+    T --> U
+    U --> V[Environmental Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#74c0fc,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Drug Tolerance -->
+            <div class="process-item" id="drug-tolerance">
+                <h3>5. Drug Tolerance</h3>
+                <p>Detailed analysis of M. tuberculosis Drug Tolerance using the Programming Framework, revealing computational logic and regulatory patterns for antibiotic resistance and tolerance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Drug Detection
+    A[Isoniazid Presence] --> B[KatG Activation]
+    C[Rifampin Presence] --> D[RpoB Modification]
+    E[Ethambutol Presence] --> F[EmbB Mutation]
+    G[Pyrazinamide Presence] --> H[PncA Inactivation]
+    
+    %% Drug Inactivation
+    B --> I[Isoniazid Activation]
+    I --> J[INH-NAD Adduct Formation]
+    J --> K[INH Resistance]
+    
+    %% Target Modification
+    D --> L[RpoB Mutation]
+    L --> M[Rifampin Resistance]
+    F --> N[EmbB Mutation]
+    N --> O[Ethambutol Resistance]
+    
+    %% Drug Efflux
+    H --> P[Pyrazinamide Resistance]
+    P --> Q[Efflux Pump Activation]
+    Q --> R[Drug Export]
+    
+    %% Integration
+    K --> S[Multi-Drug Tolerance]
+    M --> S
+    O --> S
+    R --> S
+    S --> T[Treatment Failure]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#ffd43b,color:#000
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#ffd43b,color:#000
+    style R fill:#51cf66,color:#fff
+    style S fill:#74c0fc,color:#fff
+    style T fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Granuloma Formation -->
+            <div class="process-item" id="granuloma-formation">
+                <h3>6. Granuloma Formation</h3>
+                <p>Detailed analysis of M. tuberculosis Granuloma Formation using the Programming Framework, revealing computational logic and regulatory patterns for host tissue manipulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Initial Infection
+    A[Macrophage Infection] --> B[Mycobacterial Replication]
+    C[Host Immune Response] --> D[Inflammatory Cytokines]
+    E[Cell Death] --> F[Caseous Necrosis]
+    G[Fibroblast Activation] --> H[Fibrosis Formation]
+    
+    %% Granuloma Development
+    B --> I[Macrophage Aggregation]
+    D --> J[Lymphocyte Recruitment]
+    F --> K[Caseous Center Formation]
+    H --> L[Fibrotic Wall]
+    
+    %% Granuloma Structure
+    I --> M[Epithelioid Cells]
+    J --> N[T-Cell Ring]
+    K --> O[Caseous Necrosis Center]
+    L --> P[Fibrotic Capsule]
+    
+    %% Integration
+    M --> Q[Granuloma Structure]
+    N --> Q
+    O --> Q
+    P --> Q
+    Q --> R[Latent Infection]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#74c0fc,color:#fff
+    style O fill:#74c0fc,color:#fff
+    style P fill:#74c0fc,color:#fff
+    style Q fill:#b197fc,color:#fff
+    style R fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Reactivation Signals -->
+            <div class="process-item" id="reactivation-signals">
+                <h3>7. Reactivation Signals</h3>
+                <p>Detailed analysis of M. tuberculosis Reactivation Signals using the Programming Framework, revealing computational logic and regulatory patterns for exiting dormancy.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Reactivation Triggers
+    A[Immune Suppression] --> B[Immune Pressure Reduction]
+    C[Oxygen Availability] --> D[Aerobic Respiration]
+    E[Nutrient Availability] --> F[Metabolic Reactivation]
+    G[Host Stress] --> H[Opportunistic Growth]
+    
+    %% DosR Inactivation
+    B --> I[DosR Dephosphorylation]
+    I --> J[DosR-DNA Dissociation]
+    J --> K[Dormancy Gene Repression]
+    
+    %% Metabolic Reactivation
+    D --> L[Oxidative Phosphorylation]
+    L --> M[ATP Production]
+    M --> N[Growth Resumption]
+    
+    %% Gene Expression
+    F --> O[Growth Gene Expression]
+    O --> P[Cell Division Activation]
+    P --> Q[Replication Resumption]
+    
+    %% Integration
+    K --> R[Reactivation Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Active Replication]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Persistence Mechanisms -->
+            <div class="process-item" id="persistence-mechanisms">
+                <h3>8. Persistence Mechanisms</h3>
+                <p>Detailed analysis of M. tuberculosis Persistence Mechanisms using the Programming Framework, revealing computational logic and regulatory patterns for long-term survival.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Persistence Strategies
+    A[Host Environment] --> B[Metabolic Flexibility]
+    C[Immune Pressure] --> D[Antigenic Variation]
+    E[Antibiotic Pressure] --> F[Drug Resistance]
+    G[Host Stress] --> H[Opportunistic Growth]
+    
+    %% Metabolic Flexibility
+    B --> I[Multiple Carbon Sources]
+    I --> J[Energy Conservation]
+    J --> K[Metabolic Dormancy]
+    
+    %% Antigenic Variation
+    D --> L[Surface Protein Variation]
+    L --> M[Immune Evasion]
+    M --> N[Host Adaptation]
+    
+    %% Drug Resistance
+    F --> O[Resistance Gene Expression]
+    O --> P[Drug Efflux Systems]
+    P --> Q[Treatment Tolerance]
+    
+    %% Integration
+    K --> R[Long-Term Persistence]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Decades of Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of M. tuberculosis dormancy and persistence systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Dormancy & Persistence</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
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+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

neural_plasticity_batch01_synaptic_plasticity.html

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+<html lang="en">
+<head>
+    <meta charset="UTF-8">
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+    <title>Neural Plasticity: Synaptic Plasticity Mechanisms</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
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+        .footer { 
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+        .footer p { 
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+        
+        @media (max-width: 768px) { 
+            .header h1 { 
+                font-size: 2em; 
+            } 
+        } 
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🧠 Neural Plasticity Systems</h1>
+            <p>Synaptic Plasticity Mechanisms: Biological Computation of Learning and Memory</p>
+            <div class="stats">
+                <div class="stat">
+                    <span class="stat-number">8</span>
+                    <span class="stat-label">Processes</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">4</span>
+                    <span class="stat-label">Categories</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">100%</span>
+                    <span class="stat-label">Complete</span>
+                </div>
+            </div>
+        </div>
+        
+        <div class="intro">
+            <h2>🎯 Neural Plasticity Overview</h2>
+            <p>This document showcases <strong>Synaptic Plasticity Mechanisms</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the fundamental computational mechanisms by which neural systems learn, adapt, and store information.</p>
+            <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how neural plasticity operates as sophisticated biological computation with precise molecular algorithms for synaptic strength modification.</p>
+            <p>The processes are organized into four main categories: <strong>Long-Term Potentiation (LTP)</strong>, <strong>Long-Term Depression (LTD)</strong>, <strong>Synaptic Scaling</strong>, and <strong>Structural Plasticity</strong>.</p>
+        </div>
+        
+        <div class="content">
+            <div class="color-legend">
+                <h4>🎨 Programming Framework Color Coding</h4>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ff6b6b;"></div>
+                    <span><strong>Triggers:</strong> Neural activity, calcium signals, neurotransmitter release</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ffd43b;"></div>
+                    <span><strong>Enzymes:</strong> Kinases, phosphatases, proteases, calcium-binding proteins</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #74c0fc;"></div>
+                    <span><strong>Intermediates:</strong> Calcium ions, second messengers, signaling complexes</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #51cf66;"></div>
+                    <span><strong>Processing:</strong> Phosphorylation, protein synthesis, receptor trafficking</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #b197fc;"></div>
+                    <span><strong>Products:</strong> Synaptic strength changes, structural modifications, memory formation</span>
+                </div>
+            </div>
+
+            <!-- Long-Term Potentiation -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>⚡ Long-Term Potentiation (LTP)</h2>
+                    <p>Synaptic strengthening mechanisms for memory formation</p>
+                </div>
+                <div class="process-content">
+                    <h3>1. NMDA Receptor-Dependent LTP</h3>
+                    <p class="process-description">The primary mechanism for synaptic strengthening in excitatory synapses, involving calcium influx through NMDA receptors and subsequent activation of calcium-dependent signaling cascades.</p>
+                    <div class="mermaid">
+graph TD
+    A[High Frequency Stimulation] --> B[Glutamate Release]
+    B --> C[AMPA Receptor Activation]
+    C --> D[Postsynaptic Depolarization]
+    D --> E[Mg2+ Block Relief]
+    E --> F[NMDA Receptor Opening]
+    F --> G[Calcium Influx]
+    G --> H[Calcium-Calmodulin Complex]
+    H --> I[CaMKII Activation]
+    I --> J[CaMKII Autophosphorylation]
+    J --> K[AMPA Receptor Phosphorylation]
+    K --> L[AMPA Receptor Trafficking]
+    L --> M[Synaptic Strength Increase]
+    
+    N[Calcium Signal] --> O[Calcineurin Activation]
+    O --> P[PP1 Activation]
+    P --> Q[Inhibitor-1 Phosphorylation]
+    Q --> R[PP1 Inhibition]
+    R --> S[CaMKII Persistence]
+    S --> T[LTP Maintenance]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#b197fc,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Long-Term Depression -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>📉 Long-Term Depression (LTD)</h2>
+                    <p>Synaptic weakening mechanisms for memory refinement</p>
+                </div>
+                <div class="process-content">
+                    <h3>2. NMDA Receptor-Dependent LTD</h3>
+                    <p class="process-description">Synaptic weakening mechanism that occurs with low-frequency stimulation, involving calcium-dependent activation of phosphatases and removal of AMPA receptors from the synapse.</p>
+                    <div class="mermaid">
+graph TD
+    A[Low Frequency Stimulation] --> B[Glutamate Release]
+    B --> C[AMPA Receptor Activation]
+    C --> D[Weak Postsynaptic Depolarization]
+    D --> E[Partial Mg2+ Block Relief]
+    E --> F[Limited NMDA Opening]
+    F --> G[Moderate Calcium Influx]
+    G --> H[Calcium-Calmodulin Complex]
+    H --> I[Calcineurin Activation]
+    I --> J[PP1 Activation]
+    J --> K[AMPA Receptor Dephosphorylation]
+    K --> L[AMPA Receptor Endocytosis]
+    L --> M[Synaptic Strength Decrease]
+    
+    N[Calcium Signal] --> O[Calcium-Calmodulin]
+    O --> P[Calcineurin Complex]
+    P --> Q[PP1 Recruitment]
+    Q --> R[AMPA Receptor Removal]
+    R --> S[Synaptic Depression]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#b197fc,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style O fill:#74c0fc,color:#fff
+    style P fill:#74c0fc,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Synaptic Scaling -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>⚖️ Synaptic Scaling</h2>
+                    <p>Homeostatic regulation of synaptic strength</p>
+                </div>
+                <div class="process-content">
+                    <h3>3. Activity-Dependent Synaptic Scaling</h3>
+                    <p class="process-description">Homeostatic mechanism that globally adjusts synaptic strength in response to changes in neuronal activity, maintaining network stability and preventing runaway excitation or depression.</p>
+                    <div class="mermaid">
+graph TD
+    A[Chronic Activity Changes] --> B[Calcium Signal Integration]
+    B --> C[Activity Sensor Activation]
+    C --> D[Transcription Factor Activation]
+    D --> E[Gene Expression Changes]
+    E --> F[Protein Synthesis]
+    F --> G[AMPA Receptor Subunit Changes]
+    G --> H[Synaptic Strength Adjustment]
+    
+    I[Low Activity] --> J[Calcium Decrease]
+    J --> K[CREB Activation]
+    K --> L[BDNF Expression]
+    L --> M[AMPA Receptor Insertion]
+    M --> N[Synaptic Strengthening]
+    
+    O[High Activity] --> P[Calcium Increase]
+    P --> Q[TNF-α Expression]
+    Q --> R[AMPA Receptor Removal]
+    R --> S[Synaptic Weakening]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    style C fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style E fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style J fill:#74c0fc,color:#fff
+    style K fill:#ffd43b,color:#000
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#ff6b6b,color:#fff
+    style P fill:#74c0fc,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Structural Plasticity -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🏗️ Structural Plasticity</h2>
+                    <p>Morphological changes in synaptic structure</p>
+                </div>
+                <div class="process-content">
+                    <h3>4. Dendritic Spine Remodeling</h3>
+                    <p class="process-description">Long-term structural changes in dendritic spines that underlie persistent synaptic modifications, involving actin cytoskeleton reorganization and protein synthesis.</p>
+                    <div class="mermaid">
+graph TD
+    A[Synaptic Activity] --> B[Calcium Signal]
+    B --> C[Rho GTPase Activation]
+    C --> D[Actin Polymerization]
+    D --> E[Spine Head Enlargement]
+    E --> F[PSD Expansion]
+    F --> G[Structural LTP]
+    
+    H[Activity Pattern] --> I[Calcium Dynamics]
+    I --> J[Protease Activation]
+    J --> K[Actin Depolymerization]
+    K --> L[Spine Retraction]
+    L --> M[Synapse Elimination]
+    
+    N[BDNF Signaling] --> O[TrkB Activation]
+    O --> P[PI3K Activation]
+    P --> Q[Protein Synthesis]
+    Q --> R[Spine Growth]
+    R --> S[New Synapse Formation]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    style C fill:#ffd43b,color:#000
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style I fill:#74c0fc,color:#fff
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#b197fc,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This analysis demonstrates the computational nature of neural plasticity systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        // Initialize Mermaid with enhanced compatibility for Hugging Face Spaces
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+            startOnLoad: false, 
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+                    console.log('Mermaid initialized successfully');
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+                    console.error('Mermaid initialization error:', error);
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+                console.error('Mermaid library not loaded');
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+        
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+                    mermaid.init(undefined, '.mermaid');
+                    console.log('Mermaid re-initialized after delay');
+                } catch (error) {
+                    console.error('Delayed Mermaid initialization error:', error);
+                }
+            }
+        }, 1000);
+    </script>
+</body>
+</html>

neural_plasticity_batch02_sensory_processing.html

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+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Neural Computation: Sensory Processing Algorithms</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
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+            } 
+        } 
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>👁️ Sensory Processing Systems</h1>
+            <p>Neural Algorithms for Sensory Information Processing and Feature Detection</p>
+            <div class="stats">
+                <div class="stat">
+                    <span class="stat-number">8</span>
+                    <span class="stat-label">Processes</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">4</span>
+                    <span class="stat-label">Categories</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">100%</span>
+                    <span class="stat-label">Complete</span>
+                </div>
+            </div>
+        </div>
+        
+        <div class="intro">
+            <h2>🎯 Sensory Processing Overview</h2>
+            <p>This document showcases <strong>Sensory Processing Algorithms</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the sophisticated computational mechanisms by which neural systems extract, filter, and interpret sensory information from the environment.</p>
+            <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how sensory processing operates as biological computation with precise algorithms for feature detection, signal filtering, and information integration.</p>
+            <p>The processes are organized into four main categories: <strong>Visual Processing</strong>, <strong>Auditory Processing</strong>, <strong>Olfactory Processing</strong>, and <strong>Multisensory Integration</strong>.</p>
+        </div>
+        
+        <div class="content">
+            <div class="color-legend">
+                <h4>🎨 Programming Framework Color Coding</h4>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ff6b6b;"></div>
+                    <span><strong>Triggers:</strong> Sensory stimuli, light, sound, chemical signals</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ffd43b;"></div>
+                    <span><strong>Enzymes:</strong> Transduction proteins, ion channels, signaling molecules</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #74c0fc;"></div>
+                    <span><strong>Intermediates:</strong> Action potentials, synaptic signals, neural representations</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #51cf66;"></div>
+                    <span><strong>Processing:</strong> Feature detection, signal filtering, pattern recognition</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #b197fc;"></div>
+                    <span><strong>Products:</strong> Perceptual representations, behavioral responses, cognitive integration</span>
+                </div>
+            </div>
+
+            <!-- Visual Processing -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>👁️ Visual Processing</h2>
+                    <p>Computational algorithms for visual information processing</p>
+                </div>
+                <div class="process-content">
+                    <h3>1. Retinal Processing and Feature Detection</h3>
+                    <p class="process-description">The initial computational stage of visual processing where retinal circuits extract basic visual features through parallel processing pathways, including edge detection, motion sensitivity, and contrast enhancement.</p>
+                    <div class="mermaid">
+graph TD
+    A[Light Stimulus] --> B[Photoreceptor Activation]
+    B --> C[Phototransduction Cascade]
+    C --> D[Hyperpolarization]
+    D --> E[Bipolar Cell Activation]
+    E --> F[Ganglion Cell Response]
+    F --> G[Action Potential Generation]
+    
+    H[Edge Detection] --> I[Center-Surround Organization]
+    I --> J[Lateral Inhibition]
+    J --> K[Contrast Enhancement]
+    K --> L[Feature Extraction]
+    
+    M[Motion Detection] --> N[Temporal Filtering]
+    N --> O[Motion-Sensitive Circuits]
+    O --> P[Direction Selectivity]
+    P --> Q[Motion Representation]
+    
+    R[Color Processing] --> S[Cone Type Activation]
+    S --> T[Color Opponency]
+    T --> U[Color Channel Separation]
+    U --> V[Color Representation]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style C fill:#51cf66,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#74c0fc,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
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+    style J fill:#51cf66,color:#fff
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+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
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+    style R fill:#ff6b6b,color:#fff
+    style S fill:#ffd43b,color:#000
+    style T fill:#51cf66,color:#fff
+    style U fill:#51cf66,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Auditory Processing -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>👂 Auditory Processing</h2>
+                    <p>Neural algorithms for sound processing and analysis</p>
+                </div>
+                <div class="process-content">
+                    <h3>2. Cochlear Processing and Frequency Analysis</h3>
+                    <p class="process-description">The computational transformation of sound waves into neural representations through mechanical-to-electrical transduction, frequency decomposition, and temporal pattern analysis.</p>
+                    <div class="mermaid">
+graph TD
+    A[Sound Wave] --> B[Cochlear Fluid Movement]
+    B --> C[Basilar Membrane Vibration]
+    C --> D[Hair Cell Deflection]
+    D --> E[Ion Channel Opening]
+    E --> F[Receptor Potential]
+    F --> G[Neurotransmitter Release]
+    G --> H[Spiral Ganglion Activation]
+    H --> I[Auditory Nerve Signal]
+    
+    J[Frequency Analysis] --> K[Tonotopic Organization]
+    K --> L[Frequency Tuning]
+    L --> M[Frequency Representation]
+    
+    N[Temporal Processing] --> O[Phase Locking]
+    O --> P[Temporal Coding]
+    P --> Q[Timing Information]
+    
+    R[Intensity Coding] --> S[Rate Coding]
+    S --> T[Loudness Representation]
+    T --> U[Intensity Discrimination]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#ffd43b,color:#000
+    style E fill:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#b197fc,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style K fill:#51cf66,color:#fff
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+    style Q fill:#b197fc,color:#fff
+    style R fill:#ff6b6b,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Olfactory Processing -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>👃 Olfactory Processing</h2>
+                    <p>Chemical signal processing and odor recognition</p>
+                </div>
+                <div class="process-content">
+                    <h3>3. Olfactory Receptor Processing</h3>
+                    <p class="process-description">The computational transformation of chemical signals into neural representations through receptor-ligand interactions, signal amplification, and combinatorial coding of odor identity.</p>
+                    <div class="mermaid">
+graph TD
+    A[Odorant Molecule] --> B[Olfactory Receptor Binding]
+    B --> C[G-Protein Activation]
+    C --> D[Adenylyl Cyclase Activation]
+    D --> E[cAMP Production]
+    E --> F[Ion Channel Opening]
+    F --> G[Depolarization]
+    G --> H[Action Potential Generation]
+    H --> I[Olfactory Bulb Signal]
+    
+    J[Receptor Specificity] --> K[Ligand-Receptor Matching]
+    K --> L[Combinatorial Coding]
+    L --> M[Odor Identity]
+    
+    N[Concentration Coding] --> O[Receptor Sensitivity]
+    O --> P[Intensity Representation]
+    P --> Q[Concentration Discrimination]
+    
+    R[Temporal Dynamics] --> S[Adaptation Mechanisms]
+    S --> T[Response Modulation]
+    T --> U[Temporal Coding]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style C fill:#51cf66,color:#fff
+    style D fill:#ffd43b,color:#000
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+    style T fill:#51cf66,color:#fff
+    style U fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Multisensory Integration -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🔄 Multisensory Integration</h2>
+                    <p>Cross-modal information processing and integration</p>
+                </div>
+                <div class="process-content">
+                    <h3>4. Cross-Modal Integration Algorithms</h3>
+                    <p class="process-description">The computational integration of information from multiple sensory modalities to create unified perceptual representations and enhance detection, localization, and recognition of environmental stimuli.</p>
+                    <div class="mermaid">
+graph TD
+    A[Visual Input] --> B[Visual Processing Stream]
+    C[Auditory Input] --> D[Auditory Processing Stream]
+    E[Somatosensory Input] --> F[Somatosensory Stream]
+    
+    B --> G[Multisensory Convergence]
+    D --> G
+    F --> G
+    G --> H[Cross-Modal Integration]
+    H --> I[Unified Representation]
+    I --> J[Enhanced Detection]
+    
+    K[Temporal Synchrony] --> L[Coincidence Detection]
+    L --> M[Spatial Alignment]
+    M --> N[Integration Enhancement]
+    
+    O[Modality-Specific Processing] --> P[Feature Extraction]
+    P --> Q[Cross-Modal Matching]
+    Q --> R[Integration Decision]
+    R --> S[Behavioral Response]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#b197fc,color:#fff
+    style J fill:#b197fc,color:#fff
+    style K fill:#ff6b6b,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#ff6b6b,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This analysis demonstrates the computational nature of sensory processing systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            </div>
+        </div>
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+                    console.log('Mermaid initialized successfully');
+                } catch (error) {
+                    console.error('Mermaid initialization error:', error);
+                }
+            } else {
+                console.error('Mermaid library not loaded');
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+        
+        // Also try to render after a short delay
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+                    console.log('Mermaid re-initialized after delay');
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+                    console.error('Delayed Mermaid initialization error:', error);
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+        }, 1000);
+    </script>
+</body>
+</html>

neural_plasticity_batch03_memory_formation.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Neural Computation: Memory Formation Systems</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        // Fallback if Mermaid fails to load
+        window.addEventListener('load', function() {
+            if (typeof mermaid === 'undefined') {
+                console.error('Mermaid library failed to load');
+                // Show fallback message
+                const mermaidDivs = document.querySelectorAll('.mermaid');
+                mermaidDivs.forEach(function(div) {
+                    div.innerHTML = '<div style="padding: 20px; text-align: center; color: #666; border: 2px dashed #ccc; border-radius: 8px;"><p><strong>Mermaid Diagram</strong></p><p>Chart loading failed. Please refresh the page or check your internet connection.</p></div>';
+                });
+            }
+        });
+    </script>
+    <style>
+        body { 
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+        @media (max-width: 768px) { 
+            .header h1 { 
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+            } 
+        } 
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🧠 Memory Formation Systems</h1>
+            <p>Neural Algorithms for Memory Encoding, Consolidation, and Retrieval</p>
+            <div class="stats">
+                <div class="stat">
+                    <span class="stat-number">8</span>
+                    <span class="stat-label">Processes</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">4</span>
+                    <span class="stat-label">Categories</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">100%</span>
+                    <span class="stat-label">Complete</span>
+                </div>
+            </div>
+        </div>
+        
+        <div class="intro">
+            <h2>🎯 Memory Formation Overview</h2>
+            <p>This document showcases <strong>Memory Formation Systems</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the sophisticated computational mechanisms by which neural systems encode, store, consolidate, and retrieve information over time.</p>
+            <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how memory formation operates as biological computation with precise algorithms for information processing, storage, and retrieval.</p>
+            <p>The processes are organized into four main categories: <strong>Memory Consolidation</strong>, <strong>Memory Retrieval</strong>, <strong>Memory Extinction</strong>, and <strong>Working Memory</strong>.</p>
+        </div>
+        
+        <div class="content">
+            <div class="color-legend">
+                <h4>🎨 Programming Framework Color Coding</h4>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ff6b6b;"></div>
+                    <span><strong>Triggers:</strong> Learning events, retrieval cues, consolidation signals</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ffd43b;"></div>
+                    <span><strong>Enzymes:</strong> Transcription factors, kinases, memory-related proteins</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #74c0fc;"></div>
+                    <span><strong>Intermediates:</strong> Neural patterns, synaptic states, memory traces</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #51cf66;"></div>
+                    <span><strong>Processing:</strong> Pattern completion, consolidation, retrieval algorithms</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #b197fc;"></div>
+                    <span><strong>Products:</strong> Stable memories, behavioral responses, cognitive integration</span>
+                </div>
+            </div>
+
+            <!-- Memory Consolidation -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>💾 Memory Consolidation</h2>
+                    <p>Hippocampal-cortical transfer and stabilization</p>
+                </div>
+                <div class="process-content">
+                    <h3>1. Hippocampal-Cortical Memory Transfer</h3>
+                    <p class="process-description">The computational process by which newly encoded memories in the hippocampus are gradually transferred to cortical regions for long-term storage, involving replay mechanisms and synaptic consolidation.</p>
+                    <div class="mermaid">
+graph TD
+    A[Learning Event] --> B[Hippocampal Encoding]
+    B --> C[Memory Trace Formation]
+    C --> D[Sharp Wave Ripples]
+    D --> E[Memory Replay]
+    E --> F[Cortical Activation]
+    F --> G[Synaptic Strengthening]
+    G --> H[Memory Consolidation]
+    
+    I[Sleep Cycles] --> J[Slow Wave Sleep]
+    J --> K[Hippocampal Replay]
+    K --> L[Cortical Replay]
+    L --> M[Memory Integration]
+    M --> N[Stable Memory]
+    
+    O[Repeated Retrieval] --> P[Memory Strengthening]
+    P --> Q[Synaptic Consolidation]
+    Q --> R[Long-term Storage]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#ff6b6b,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Memory Retrieval -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🔍 Memory Retrieval</h2>
+                    <p>Pattern completion and memory reconstruction</p>
+                </div>
+                <div class="process-content">
+                    <h3>2. Pattern Completion Algorithms</h3>
+                    <p class="process-description">The computational mechanism by which partial cues activate distributed memory networks to reconstruct complete memories through pattern completion and associative recall.</p>
+                    <div class="mermaid">
+graph TD
+    A[Retrieval Cue] --> B[Pattern Activation]
+    B --> C[Distributed Network]
+    C --> D[Pattern Completion]
+    D --> E[Memory Reconstruction]
+    E --> F[Associative Recall]
+    F --> G[Memory Retrieval]
+    
+    H[Context Cues] --> I[Contextual Activation]
+    I --> J[Memory Network]
+    J --> K[Pattern Matching]
+    K --> L[Memory Selection]
+    L --> M[Retrieval Success]
+    
+    N[Multiple Cues] --> O[Cue Integration]
+    O --> P[Convergent Activation]
+    P --> Q[Stronger Retrieval]
+    Q --> R[Memory Confidence]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#74c0fc,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#b197fc,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Memory Extinction -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🗑️ Memory Extinction</h2>
+                    <p>Forgetting mechanisms and memory suppression</p>
+                </div>
+                <div class="process-content">
+                    <h3>3. Active Forgetting Mechanisms</h3>
+                    <p class="process-description">The computational processes by which memories are actively suppressed or forgotten through extinction learning, interference, and synaptic weakening mechanisms.</p>
+                    <div class="mermaid">
+graph TD
+    A[Extinction Training] --> B[New Learning]
+    B --> C[Competing Memory]
+    C --> D[Memory Interference]
+    D --> E[Original Memory Suppression]
+    E --> F[Forgetting]
+    
+    G[Time Passage] --> H[Memory Decay]
+    H --> I[Synaptic Weakening]
+    I --> J[Memory Fading]
+    J --> K[Natural Forgetting]
+    
+    L[Interference Events] --> M[Memory Competition]
+    M --> N[Pattern Interference]
+    N --> O[Memory Confusion]
+    O --> P[Retrieval Failure]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Working Memory -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>⚡ Working Memory</h2>
+                    <p>Prefrontal cortical computation and maintenance</p>
+                </div>
+                <div class="process-content">
+                    <h3>4. Prefrontal Cortical Working Memory</h3>
+                    <p class="process-description">The computational system for temporarily holding and manipulating information in mind, involving persistent neural activity and dynamic maintenance mechanisms in prefrontal cortical circuits.</p>
+                    <div class="mermaid">
+graph TD
+    A[Sensory Input] --> B[Information Encoding]
+    B --> C[Working Memory Buffer]
+    C --> D[Persistent Activity]
+    D --> E[Information Maintenance]
+    E --> F[Manipulation Operations]
+    F --> G[Working Memory Output]
+    
+    H[Attention Focus] --> I[Selective Maintenance]
+    I --> J[Distractor Filtering]
+    J --> K[Memory Stability]
+    K --> L[Task Performance]
+    
+    M[Executive Control] --> N[Memory Operations]
+    N --> O[Information Updating]
+    O --> P[Memory Manipulation]
+    P --> Q[Cognitive Control]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#b197fc,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This analysis demonstrates the computational nature of memory formation systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        // Initialize Mermaid with enhanced compatibility for Hugging Face Spaces
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+            startOnLoad: false, 
+            theme: 'default', 
+            flowchart: { 
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+                padding: 10 
+            }, 
+            themeVariables: { 
+                fontFamily: 'Arial, sans-serif', 
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+            },
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+            logLevel: 1
+        });
+        
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+                try {
+                    mermaid.init(undefined, '.mermaid');
+                    console.log('Mermaid initialized successfully');
+                } catch (error) {
+                    console.error('Mermaid initialization error:', error);
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+            } else {
+                console.error('Mermaid library not loaded');
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+        
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+                    console.log('Mermaid re-initialized after delay');
+                } catch (error) {
+                    console.error('Delayed Mermaid initialization error:', error);
+                }
+            }
+        }, 1000);
+    </script>
+</body>
+</html>

neural_plasticity_batch04_motor_control.html

@@ -0,0 +1,576 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Neural Computation: Motor Control Systems</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        // Fallback if Mermaid fails to load
+        window.addEventListener('load', function() {
+            if (typeof mermaid === 'undefined') {
+                console.error('Mermaid library failed to load');
+                // Show fallback message
+                const mermaidDivs = document.querySelectorAll('.mermaid');
+                mermaidDivs.forEach(function(div) {
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+                });
+            }
+        });
+    </script>
+    <style>
+        body { 
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+        .intro p { 
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+            margin-bottom: 15px; 
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+            min-height: 200px;
+            border: 1px solid #dee2e6;
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+        }
+        
+        .mermaid::before {
+            content: "Loading chart...";
+            position: absolute;
+            top: 50%;
+            left: 50%;
+            transform: translate(-50%, -50%);
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+            font-style: italic;
+            z-index: 1;
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+        
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+            color: #495057; 
+            font-size: 1.2rem;
+            font-weight: 500;
+        }
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+        .color-item { 
+            display: flex; 
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+            margin: 8px 0; 
+            padding: 8px;
+            border-radius: 4px;
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+        }
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+        .color-box { 
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+            height: 20px; 
+            border-radius: 3px; 
+            margin-right: 10px; 
+            border: 1px solid rgba(0,0,0,0.1);
+        }
+        
+        .footer { 
+            background: #495057; 
+            color: white; 
+            text-align: center; 
+            padding: 30px; 
+            margin-top: 40px; 
+        }
+        
+        .footer p { 
+            margin: 0; 
+            opacity: 0.8; 
+        }
+        
+        @media (max-width: 768px) { 
+            .header h1 { 
+                font-size: 2em; 
+            } 
+        } 
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🏃 Motor Control Systems</h1>
+            <p>Neural Algorithms for Movement Planning, Execution, and Learning</p>
+            <div class="stats">
+                <div class="stat">
+                    <span class="stat-number">8</span>
+                    <span class="stat-label">Processes</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">4</span>
+                    <span class="stat-label">Categories</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">100%</span>
+                    <span class="stat-label">Complete</span>
+                </div>
+            </div>
+        </div>
+        
+        <div class="intro">
+            <h2>🎯 Motor Control Overview</h2>
+            <p>This document showcases <strong>Motor Control Systems</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the sophisticated computational mechanisms by which neural systems plan, execute, and learn complex motor behaviors.</p>
+            <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how motor control operates as biological computation with precise algorithms for movement planning, execution, and adaptation.</p>
+            <p>The processes are organized into four main categories: <strong>Motor Planning</strong>, <strong>Motor Execution</strong>, <strong>Motor Learning</strong>, and <strong>Motor Coordination</strong>.</p>
+        </div>
+        
+        <div class="content">
+            <div class="color-legend">
+                <h4>🎨 Programming Framework Color Coding</h4>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ff6b6b;"></div>
+                    <span><strong>Triggers:</strong> Movement goals, sensory feedback, motor commands</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ffd43b;"></div>
+                    <span><strong>Enzymes:</strong> Motor neurons, muscle proteins, signaling molecules</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #74c0fc;"></div>
+                    <span><strong>Intermediates:</strong> Motor plans, muscle contractions, movement states</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #51cf66;"></div>
+                    <span><strong>Processing:</strong> Movement planning, execution, coordination algorithms</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #b197fc;"></div>
+                    <span><strong>Products:</strong> Coordinated movements, behavioral responses, motor skills</span>
+                </div>
+            </div>
+
+            <!-- Motor Planning -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🎯 Motor Planning</h2>
+                    <p>Premotor cortical algorithms for movement preparation</p>
+                </div>
+                <div class="process-content">
+                    <h3>1. Premotor Cortical Planning</h3>
+                    <p class="process-description">The computational process by which the premotor cortex transforms movement goals into motor plans, involving spatial mapping, trajectory planning, and motor program selection.</p>
+                    <div class="mermaid">
+graph TD
+    A[Movement Goal] --> B[Goal Representation]
+    B --> C[Spatial Planning]
+    C --> D[Trajectory Computation]
+    D --> E[Motor Program Selection]
+    E --> F[Planning Completion]
+    F --> G[Motor Command]
+    
+    H[Sensory Context] --> I[Context Integration]
+    I --> J[Planning Modulation]
+    J --> K[Adaptive Planning]
+    K --> L[Context-Appropriate Movement]
+    
+    M[Multiple Goals] --> N[Goal Prioritization]
+    N --> O[Planning Competition]
+    O --> P[Winner Selection]
+    P --> Q[Selected Movement Plan]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#74c0fc,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#b197fc,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Motor Execution -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>⚡ Motor Execution</h2>
+                    <p>Spinal cord computation and muscle activation</p>
+                </div>
+                <div class="process-content">
+                    <h3>2. Spinal Cord Motor Execution</h3>
+                    <p class="process-description">The computational transformation of motor commands into coordinated muscle contractions through spinal cord circuits, involving motor neuron recruitment and muscle synergy activation.</p>
+                    <div class="mermaid">
+graph TD
+    A[Motor Command] --> B[Spinal Cord Processing]
+    B --> C[Motor Neuron Recruitment]
+    C --> D[Muscle Fiber Activation]
+    D --> E[Muscle Contraction]
+    E --> F[Movement Execution]
+    
+    G[Feedback Signals] --> H[Sensory Integration]
+    H --> I[Execution Adjustment]
+    I --> J[Movement Refinement]
+    J --> K[Coordinated Movement]
+    
+    L[Multiple Muscles] --> M[Synergy Activation]
+    M --> N[Coordinated Contraction]
+    N --> O[Balanced Movement]
+    O --> P[Smooth Execution]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#ffd43b,color:#000
+    style D fill:#51cf66,color:#fff
+    style E fill:#74c0fc,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Motor Learning -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🎓 Motor Learning</h2>
+                    <p>Cerebellar adaptation and skill acquisition</p>
+                </div>
+                <div class="process-content">
+                    <h3>3. Cerebellar Motor Learning</h3>
+                    <p class="process-description">The computational mechanism by which the cerebellum adapts motor programs through error-driven learning, involving prediction error computation and synaptic plasticity for skill acquisition.</p>
+                    <div class="mermaid">
+graph TD
+    A[Motor Error] --> B[Error Detection]
+    B --> C[Cerebellar Processing]
+    C --> D[Error Correction]
+    D --> E[Motor Adaptation]
+    E --> F[Skill Improvement]
+    
+    G[Prediction Error] --> H[Error Signal]
+    H --> I[Synaptic Plasticity]
+    I --> J[Circuit Modification]
+    J --> K[Adaptive Response]
+    K --> L[Improved Performance]
+    
+    M[Repeated Practice] --> N[Error Reduction]
+    N --> O[Skill Consolidation]
+    O --> P[Automatic Performance]
+    P --> Q[Motor Expertise]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#b197fc,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Motor Coordination -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🤝 Motor Coordination</h2>
+                    <p>Basal ganglia selection and movement coordination</p>
+                </div>
+                <div class="process-content">
+                    <h3>4. Basal Ganglia Movement Selection</h3>
+                    <p class="process-description">The computational system for selecting and coordinating motor actions through the basal ganglia, involving action selection, inhibition of competing movements, and coordination of multiple motor systems.</p>
+                    <div class="mermaid">
+graph TD
+    A[Multiple Actions] --> B[Action Competition]
+    B --> C[Basal Ganglia Processing]
+    C --> D[Action Selection]
+    D --> E[Selected Movement]
+    E --> F[Coordinated Action]
+    
+    G[Competing Movements] --> H[Inhibition Processing]
+    H --> I[Competitor Suppression]
+    I --> J[Selected Action Enhancement]
+    J --> K[Clear Movement Choice]
+    
+    L[Multiple Systems] --> M[System Coordination]
+    M --> N[Temporal Synchronization]
+    N --> O[Spatial Coordination]
+    O --> P[Integrated Movement]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This analysis demonstrates the computational nature of motor control systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        // Initialize Mermaid with enhanced compatibility for Hugging Face Spaces
+        mermaid.initialize({ 
+            startOnLoad: false, 
+            theme: 'default', 
+            flowchart: { 
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+        
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+                    console.log('Mermaid re-initialized after delay');
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+                    console.error('Delayed Mermaid initialization error:', error);
+                }
+            }
+        }, 1000);
+    </script>
+</body>
+</html>

neural_plasticity_batch05_decision_making.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Neural Computation: Decision-Making Systems</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        // Fallback if Mermaid fails to load
+        window.addEventListener('load', function() {
+            if (typeof mermaid === 'undefined') {
+                console.error('Mermaid library failed to load');
+                // Show fallback message
+                const mermaidDivs = document.querySelectorAll('.mermaid');
+                mermaidDivs.forEach(function(div) {
+                    div.innerHTML = '<div style="padding: 20px; text-align: center; color: #666; border: 2px dashed #ccc; border-radius: 8px;"><p><strong>Mermaid Diagram</strong></p><p>Chart loading failed. Please refresh the page or check your internet connection.</p></div>';
+                });
+            }
+        });
+    </script>
+    <style>
+        body { 
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
+            line-height: 1.6; 
+            margin: 0; 
+            padding: 20px; 
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); 
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+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+        }
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+        .container { 
+            max-width: 1400px; 
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+            background: white; 
+            border-radius: 15px; 
+            box-shadow: 0 20px 40px rgba(0,0,0,0.1); 
+            overflow: hidden; 
+        }
+        
+        .header { 
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); 
+            color: white; 
+            padding: 40px; 
+            text-align: center; 
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+        .header h1 { 
+            font-size: 2.5em; 
+            margin: 0; 
+            text-shadow: 2px 2px 4px rgba(0,0,0,0.3); 
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+            border-bottom: 1px solid #e9ecef; 
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+        }
+        
+        .process-section { 
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+            background: white; 
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+        .process-header { 
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+            color: white; 
+            padding: 30px; 
+            text-align: center; 
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+        
+        .process-header h2 { 
+            margin: 0; 
+            font-size: 2em; 
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+        .process-header p { 
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+        .process-content { 
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+        .process-description { 
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+            font-size: 1.1em; 
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+        
+        .mermaid { 
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+            font-family: Arial, sans-serif !important;
+            font-size: 14px !important; 
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+            min-height: 200px;
+            border: 1px solid #dee2e6;
+            position: relative;
+        }
+        
+        .mermaid::before {
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+        .color-legend { 
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+            border-radius: 8px; 
+            padding: 20px; 
+            margin: 20px 0; 
+            border-left: 4px solid #667eea; 
+            display: block;
+        }
+        
+        .color-legend h4 { 
+            margin: 0 0 15px 0; 
+            color: #495057; 
+            font-size: 1.2rem;
+            font-weight: 500;
+        }
+        
+        .color-item { 
+            display: flex; 
+            align-items: center; 
+            margin: 8px 0; 
+            padding: 8px;
+            border-radius: 4px;
+            background: white;
+        }
+        
+        .color-box { 
+            width: 20px; 
+            height: 20px; 
+            border-radius: 3px; 
+            margin-right: 10px; 
+            border: 1px solid rgba(0,0,0,0.1);
+        }
+        
+        .footer { 
+            background: #495057; 
+            color: white; 
+            text-align: center; 
+            padding: 30px; 
+            margin-top: 40px; 
+        }
+        
+        .footer p { 
+            margin: 0; 
+            opacity: 0.8; 
+        }
+        
+        @media (max-width: 768px) { 
+            .header h1 { 
+                font-size: 2em; 
+            } 
+        } 
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🧠 Neural Decision-Making</h1>
+            <p>Computational Algorithms for Neural Circuit Decision Processes</p>
+            <div class="stats">
+                <div class="stat">
+                    <span class="stat-number">8</span>
+                    <span class="stat-label">Processes</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">4</span>
+                    <span class="stat-label">Categories</span>
+                </div>
+                <div class="stat">
+                    <span class="stat-number">100%</span>
+                    <span class="stat-label">Complete</span>
+                </div>
+            </div>
+        </div>
+        
+        <div class="intro">
+            <h2>🎯 Neural Decision-Making Overview</h2>
+            <p>This document showcases <strong>Neural Circuit Decision-Making Systems</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the sophisticated computational mechanisms by which neural circuits make decisions, select actions, and resolve conflicts between competing options.</p>
+            <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how decision-making operates as biological computation with precise algorithms for competitive selection, threshold detection, and response generation.</p>
+            <p>The processes are organized into four main categories: <strong>Winner-Take-All Networks</strong>, <strong>Lateral Inhibition</strong>, <strong>Attentional Mechanisms</strong>, and <strong>Decision Thresholding</strong>.</p>
+        </div>
+        
+        <div class="content">
+            <div class="color-legend">
+                <h4>🎨 Programming Framework Color Coding</h4>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ff6b6b;"></div>
+                    <span><strong>Triggers:</strong> Decision inputs, competing options, threshold signals</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #ffd43b;"></div>
+                    <span><strong>Enzymes:</strong> Inhibitory neurons, excitatory neurons, decision circuits</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #74c0fc;"></div>
+                    <span><strong>Intermediates:</strong> Neural activity patterns, decision states, competitive dynamics</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #51cf66;"></div>
+                    <span><strong>Processing:</strong> Competition algorithms, inhibition processing, selection mechanisms</span>
+                </div>
+                <div class="color-item">
+                    <div class="color-box" style="background: #b197fc;"></div>
+                    <span><strong>Products:</strong> Selected decisions, behavioral responses, cognitive outcomes</span>
+                </div>
+            </div>
+
+            <!-- Winner-Take-All Networks -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🏆 Winner-Take-All Networks</h2>
+                    <p>Competitive selection and decision resolution</p>
+                </div>
+                <div class="process-content">
+                    <h3>1. Competitive Decision Networks</h3>
+                    <p class="process-description">The computational mechanism by which neural networks resolve competition between multiple options through mutual inhibition, leading to the selection of a single winning option while suppressing all others.</p>
+                    <div class="mermaid">
+graph TD
+    A[Multiple Options] --> B[Competition Initiation]
+    B --> C[Mutual Inhibition]
+    C --> D[Activity Competition]
+    D --> E[Winner Emergence]
+    E --> F[Loser Suppression]
+    F --> G[Decision Resolution]
+    
+    H[Competing Signals] --> I[Signal Integration]
+    I --> J[Competition Dynamics]
+    J --> K[Threshold Crossing]
+    K --> L[Winner Selection]
+    
+    M[Feedback Inhibition] --> N[Competitor Suppression]
+    N --> O[Winner Stabilization]
+    O --> P[Decision Commitment]
+    P --> Q[Stable Choice]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#b197fc,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#74c0fc,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#b197fc,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Lateral Inhibition -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>🚫 Lateral Inhibition</h2>
+                    <p>Contrast enhancement and signal sharpening</p>
+                </div>
+                <div class="process-content">
+                    <h3>2. Contrast Enhancement Mechanisms</h3>
+                    <p class="process-description">The computational process by which lateral inhibition sharpens neural representations by suppressing neighboring activity, enhancing contrast and improving signal-to-noise ratios in decision-making circuits.</p>
+                    <div class="mermaid">
+graph TD
+    A[Neural Activity] --> B[Lateral Inhibition]
+    B --> C[Neighbor Suppression]
+    C --> D[Contrast Enhancement]
+    D --> E[Signal Sharpening]
+    E --> F[Enhanced Representation]
+    
+    G[Inhibitory Interneurons] --> H[Inhibition Spread]
+    H --> I[Activity Suppression]
+    I --> J[Contrast Formation]
+    J --> K[Sharpened Signals]
+    
+    L[Multiple Inputs] --> M[Inhibition Processing]
+    M --> N[Competitive Suppression]
+    N --> O[Winner Enhancement]
+    O --> P[Clear Decision Signal]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ffd43b,color:#000
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Attentional Mechanisms -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>👁️ Attentional Mechanisms</h2>
+                    <p>Focus and filtering in decision processes</p>
+                </div>
+                <div class="process-content">
+                    <h3>3. Attention and Focus Algorithms</h3>
+                    <p class="process-description">The computational system for directing attention and filtering information in decision-making, involving selective enhancement of relevant signals and suppression of distracting information.</p>
+                    <div class="mermaid">
+graph TD
+    A[Multiple Stimuli] --> B[Attention Selection]
+    B --> C[Target Enhancement]
+    C --> D[Distractor Suppression]
+    D --> E[Focused Processing]
+    E --> F[Enhanced Decision]
+    
+    G[Attentional Control] --> H[Top-Down Modulation]
+    H --> I[Selective Enhancement]
+    I --> J[Filtering Processing]
+    J --> K[Focused Attention]
+    
+    L[Competing Signals] --> M[Priority Computation]
+    M --> N[Signal Ranking]
+    N --> O[Attention Allocation]
+    O --> P[Optimal Focus]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#74c0fc,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Decision Thresholding -->
+            <div class="process-section">
+                <div class="process-header">
+                    <h2>⚖️ Decision Thresholding</h2>
+                    <p>Response selection and threshold crossing</p>
+                </div>
+                <div class="process-content">
+                    <h3>4. Response Selection Mechanisms</h3>
+                    <p class="process-description">The computational process by which neural circuits determine when sufficient evidence has accumulated to trigger a decision response, involving threshold detection and response generation.</p>
+                    <div class="mermaid">
+graph TD
+    A[Evidence Accumulation] --> B[Threshold Monitoring]
+    B --> C[Evidence Integration]
+    C --> D[Threshold Comparison]
+    D --> E[Decision Trigger]
+    E --> F[Response Generation]
+    
+    G[Multiple Thresholds] --> H[Threshold Selection]
+    H --> I[Decision Criteria]
+    I --> J[Response Selection]
+    J --> K[Behavioral Output]
+    
+    L[Time Pressure] --> M[Urgency Signal]
+    M --> N[Threshold Lowering]
+    N --> O[Faster Decision]
+    O --> P[Timely Response]
+    
+    style A fill:#ff6b6b,color:#fff
+    style B fill:#51cf66,color:#fff
+    style C fill:#74c0fc,color:#fff
+    style D fill:#51cf66,color:#fff
+    style E fill:#51cf66,color:#fff
+    style F fill:#b197fc,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#74c0fc,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This analysis demonstrates the computational nature of neural decision-making systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        // Initialize Mermaid with enhanced compatibility for Hugging Face Spaces
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+            startOnLoad: false, 
+            theme: 'default', 
+            flowchart: { 
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+                curve: 'linear', 
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+                rankSpacing: 40, 
+                padding: 10 
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+        });
+        
+        // Force re-render when DOM is loaded
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+                    console.error('Mermaid initialization error:', error);
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+                console.error('Mermaid library not loaded');
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+        
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+                    console.error('Delayed Mermaid initialization error:', error);
+                }
+            }
+        }, 1000);
+    </script>
+</body>
+</html>

p_aeruginosa_batch01_virulence_pathogenicity.html

@@ -0,0 +1,723 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>P. aeruginosa Batch 01: Virulence & Pathogenicity - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 P. aeruginosa Batch 01: Virulence & Pathogenicity</h1>
+            <p>Programming Framework Analysis - 8 Virulence Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Virulence & Pathogenicity Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental P. aeruginosa processes responsible for virulence and pathogenicity. These processes represent the core computational systems that enable this opportunistic pathogen to cause serious infections in immunocompromised hosts.</p>
+                <p>Each process demonstrates sophisticated biological programming with quorum sensing, biofilm formation, antibiotic resistance, and virulence factor production.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Virulence Processes</h2>
+                <ul>
+                    <li><a href="#quorum-sensing">1. Quorum Sensing</a></li>
+                    <li><a href="#biofilm-formation">2. Biofilm Formation</a></li>
+                    <li><a href="#antibiotic-resistance">3. Antibiotic Resistance</a></li>
+                    <li><a href="#toxin-production">4. Toxin Production</a></li>
+                    <li><a href="#iron-acquisition">5. Iron Acquisition</a></li>
+                    <li><a href="#motility-chemotaxis">6. Motility & Chemotaxis</a></li>
+                    <li><a href="#secretion-systems">7. Secretion Systems</a></li>
+                    <li><a href="#stress-response">8. Stress Response</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Quorum Sensing -->
+            <div class="process-item" id="quorum-sensing">
+                <h3>1. Quorum Sensing</h3>
+                <p>Detailed analysis of P. aeruginosa Quorum Sensing using the Programming Framework, revealing computational logic and regulatory patterns for population density communication.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Autoinducer Production
+    A[LasI Synthesis] --> B[N-3-Oxo-Dodecanoyl-HSL]
+    C[RhlI Synthesis] --> D[N-Butyryl-HSL]
+    E[PQS Synthesis] --> F[2-Heptyl-3-Hydroxy-4-Quinolone]
+    
+    %% Autoinducer Secretion
+    B --> G[Autoinducer Secretion]
+    D --> G
+    F --> G
+    G --> H[Extracellular Accumulation]
+    
+    %% Signal Detection
+    H --> I[LasR Receptor]
+    H --> J[RhlR Receptor]
+    H --> K[PqsR Receptor]
+    
+    %% Threshold Detection
+    I --> L{Threshold Reached?}
+    J --> M{Threshold Reached?}
+    K --> N{Threshold Reached?}
+    
+    %% Gene Expression Activation
+    L -->|Yes| O[Virulence Gene Expression]
+    M -->|Yes| P[Biofilm Gene Expression]
+    N -->|Yes| Q[Secondary Metabolite Expression]
+    
+    %% Integration
+    O --> R[Population Response]
+    P --> R
+    Q --> R
+    R --> S[Coordinated Behavior]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#74c0fc,color:#fff
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#74c0fc,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#74c0fc,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#b197fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Biofilm Formation -->
+            <div class="process-item" id="biofilm-formation">
+                <h3>2. Biofilm Formation</h3>
+                <p>Detailed analysis of P. aeruginosa Biofilm Formation using the Programming Framework, revealing computational logic and regulatory patterns for multicellular community development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Initial Attachment
+    A[Surface Recognition] --> B[Flagellar Attachment]
+    C[Pili-Mediated Adhesion] --> D[Surface Binding]
+    E[EPS Production] --> F[Extracellular Matrix]
+    
+    %% Microcolony Formation
+    B --> G[Cell Aggregation]
+    D --> G
+    F --> G
+    G --> H[Microcolony Development]
+    
+    %% Biofilm Maturation
+    H --> I[Quorum Sensing Activation]
+    I --> J[Alginate Production]
+    J --> K[Biofilm Matrix]
+    K --> L[3D Structure Formation]
+    
+    %% Biofilm Architecture
+    L --> M[Water Channels]
+    M --> N[Nutrient Gradients]
+    N --> O[Oxygen Gradients]
+    O --> P[Mature Biofilm]
+    
+    %% Integration
+    P --> Q[Biofilm Community]
+    Q --> R[Antibiotic Resistance]
+    R --> S[Chronic Infection]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#51cf66,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#74c0fc,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#74c0fc,color:#fff
+    style O fill:#74c0fc,color:#fff
+    style P fill:#b197fc,color:#fff
+    style Q fill:#b197fc,color:#fff
+    style R fill:#b197fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Antibiotic Resistance -->
+            <div class="process-item" id="antibiotic-resistance">
+                <h3>3. Antibiotic Resistance</h3>
+                <p>Detailed analysis of P. aeruginosa Antibiotic Resistance using the Programming Framework, revealing computational logic and regulatory patterns for multi-drug resistance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Drug Detection
+    A[Antibiotic Presence] --> B[Efflux Pump Activation]
+    C[β-Lactam Antibiotics] --> D[β-Lactamase Production]
+    E[Aminoglycosides] --> F[Modifying Enzymes]
+    G[Quinolones] --> H[DNA Gyrase Mutation]
+    
+    %% Efflux Systems
+    B --> I[MexAB-OprM Pump]
+    B --> J[MexCD-OprJ Pump]
+    B --> K[MexEF-OprN Pump]
+    I --> L[Drug Export]
+    J --> L
+    K --> L
+    
+    %% Enzymatic Resistance
+    D --> M[β-Lactam Hydrolysis]
+    F --> N[Aminoglycoside Modification]
+    H --> O[Target Modification]
+    
+    %% Resistance Mechanisms
+    L --> P[Reduced Drug Accumulation]
+    M --> Q[β-Lactam Inactivation]
+    N --> R[Aminoglycoside Inactivation]
+    O --> S[Target Protection]
+    
+    %% Integration
+    P --> T[Multi-Drug Resistance]
+    Q --> T
+    R --> T
+    S --> T
+    T --> U[Treatment Failure]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#74c0fc,color:#fff
+    style Q fill:#74c0fc,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#74c0fc,color:#fff
+    style T fill:#b197fc,color:#fff
+    style U fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Toxin Production -->
+            <div class="process-item" id="toxin-production">
+                <h3>4. Toxin Production</h3>
+                <p>Detailed analysis of P. aeruginosa Toxin Production using the Programming Framework, revealing computational logic and regulatory patterns for virulence factor synthesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Toxin Gene Regulation
+    A[Quorum Sensing Signal] --> B[LasR Activation]
+    C[Iron Limitation] --> D[Fur Repression Release]
+    E[Stress Conditions] --> F[Toxin Gene Expression]
+    
+    %% Exotoxin Production
+    B --> G[Exotoxin A Synthesis]
+    G --> H[ADP-Ribosylation]
+    H --> I[Protein Synthesis Inhibition]
+    
+    %% Cytotoxin Production
+    D --> J[Pyocyanin Synthesis]
+    J --> K[ROS Generation]
+    K --> L[Oxidative Damage]
+    
+    %% Protease Production
+    F --> M[Elastase Production]
+    F --> N[Alkaline Protease]
+    M --> O[Tissue Degradation]
+    N --> O
+    
+    %% Integration
+    I --> P[Host Cell Death]
+    L --> P
+    O --> Q[Tissue Damage]
+    P --> R[Virulence]
+    Q --> R
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#51cf66,color:#fff
+    style J fill:#ffd43b,color:#000
+    style K fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#51cf66,color:#fff
+    style P fill:#b197fc,color:#fff
+    style Q fill:#b197fc,color:#fff
+    style R fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Iron Acquisition -->
+            <div class="process-item" id="iron-acquisition">
+                <h3>5. Iron Acquisition</h3>
+                <p>Detailed analysis of P. aeruginosa Iron Acquisition using the Programming Framework, revealing computational logic and regulatory patterns for iron scavenging systems.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Iron Limitation Detection
+    A[Low Iron Environment] --> B[Fur Repression Release]
+    C[Host Iron Restriction] --> D[Siderophore Gene Expression]
+    E[Iron Deficiency] --> F[Iron Uptake Activation]
+    
+    %% Siderophore Production
+    D --> G[Pyoverdine Synthesis]
+    D --> H[Pyochelin Synthesis]
+    G --> I[Iron Chelation]
+    H --> I
+    
+    %% Iron Transport
+    I --> J[Iron-Siderophore Complex]
+    J --> K[Outer Membrane Receptor]
+    K --> L[Periplasmic Binding Protein]
+    L --> M[Inner Membrane Transporter]
+    
+    %% Iron Release
+    M --> N[Iron Release]
+    N --> O[Iron Storage]
+    O --> P[Metabolic Integration]
+    
+    %% Integration
+    P --> Q[Iron Homeostasis]
+    Q --> R[Virulence Expression]
+    R --> S[Pathogenicity]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#51cf66,color:#fff
+    style J fill:#74c0fc,color:#fff
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#51cf66,color:#fff
+    style O fill:#74c0fc,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+    style R fill:#b197fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Motility & Chemotaxis -->
+            <div class="process-item" id="motility-chemotaxis">
+                <h3>6. Motility & Chemotaxis</h3>
+                <p>Detailed analysis of P. aeruginosa Motility & Chemotaxis using the Programming Framework, revealing computational logic and regulatory patterns for movement and navigation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Flagellar Assembly
+    A[Flagellar Gene Expression] --> B[Flagellar Assembly]
+    C[Chemotaxis Proteins] --> D[Chemotaxis System]
+    E[Pili Synthesis] --> F[Twitching Motility]
+    
+    %% Signal Detection
+    G[Nutrient Gradient] --> H[Chemoreceptor Binding]
+    I[Oxygen Gradient] --> J[Aerotaxis Response]
+    K[Host Signals] --> L[Host-Directed Movement]
+    
+    %% Signal Transduction
+    H --> M[CheA Phosphorylation]
+    J --> M
+    L --> M
+    M --> N[CheY Phosphorylation]
+    
+    %% Motor Control
+    N --> O[Flagellar Motor]
+    O --> P[Swimming Motility]
+    F --> Q[Surface Motility]
+    
+    %% Navigation
+    P --> R[Gradient Following]
+    Q --> S[Surface Exploration]
+    R --> T[Host Colonization]
+    S --> T
+    
+    %% Integration
+    T --> U[Infection Establishment]
+    U --> V[Virulence Expression]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style K fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#74c0fc,color:#fff
+    style U fill:#b197fc,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Secretion Systems -->
+            <div class="process-item" id="secretion-systems">
+                <h3>7. Secretion Systems</h3>
+                <p>Detailed analysis of P. aeruginosa Secretion Systems using the Programming Framework, revealing computational logic and regulatory patterns for virulence factor delivery.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Type III Secretion
+    A[Contact with Host Cell] --> B[Type III Apparatus Assembly]
+    C[Virulence Factor Synthesis] --> D[Effector Protein Production]
+    E[Host Cell Recognition] --> F[Needle Complex Formation]
+    
+    %% Effector Delivery
+    B --> G[Translocon Formation]
+    D --> H[Effector Loading]
+    F --> I[Injection Apparatus]
+    G --> J[Effector Injection]
+    H --> J
+    I --> J
+    
+    %% Type II Secretion
+    K[Exoenzyme Synthesis] --> L[Sec Pathway]
+    L --> M[Periplasmic Processing]
+    M --> N[Type II Apparatus]
+    N --> O[Exoenzyme Secretion]
+    
+    %% Type VI Secretion
+    P[Competition Signal] --> Q[Type VI Assembly]
+    Q --> R[Toxin Loading]
+    R --> S[Target Cell Injection]
+    
+    %% Integration
+    J --> T[Host Cell Manipulation]
+    O --> U[Tissue Damage]
+    S --> V[Competitive Advantage]
+    T --> W[Virulence]
+    U --> W
+    V --> W
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style K fill:#ff6b6b,color:#fff
+    style P fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#ffd43b,color:#000
+    style O fill:#51cf66,color:#fff
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#b197fc,color:#fff
+    style U fill:#b197fc,color:#fff
+    style V fill:#b197fc,color:#fff
+    style W fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>8. Stress Response</h3>
+                <p>Detailed analysis of P. aeruginosa Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Detection
+    A[Oxidative Stress] --> B[OxyR Activation]
+    C[Heat Stress] --> D[σ32 Activation]
+    E[Osmotic Stress] --> F[σE Activation]
+    G[Antibiotic Stress] --> H[MarR Activation]
+    
+    %% Oxidative Stress Response
+    B --> I[Catalase Production]
+    I --> J[ROS Scavenging]
+    J --> K[Oxidative Defense]
+    
+    %% Heat Shock Response
+    D --> L[Heat Shock Proteins]
+    L --> M[Protein Protection]
+    M --> N[Thermal Adaptation]
+    
+    %% Osmotic Stress Response
+    F --> O[Osmolyte Synthesis]
+    O --> P[Osmotic Balance]
+    P --> Q[Osmotic Adaptation]
+    
+    %% Antibiotic Stress Response
+    H --> R[Efflux Pump Induction]
+    R --> S[Antibiotic Resistance]
+    S --> T[Stress Survival]
+    
+    %% Integration
+    K --> U[Environmental Adaptation]
+    N --> U
+    Q --> U
+    T --> U
+    U --> V[Pathogen Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#b197fc,color:#fff
+    style R fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#b197fc,color:#fff
+    style U fill:#b197fc,color:#fff
+    style V fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of P. aeruginosa virulence and pathogenicity systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Virulence & Pathogenicity</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

s_aureus_batch01_pathogenicity_biofilm.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>S. aureus Batch 01: Pathogenicity & Biofilm - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 S. aureus Batch 01: Pathogenicity & Biofilm</h1>
+            <p>Programming Framework Analysis - 8 Bacterial Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Pathogenicity & Biofilm Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental S. aureus processes responsible for pathogenicity and biofilm formation. These processes represent the core computational systems that enable this opportunistic pathogen to cause infections, form biofilms, and develop antibiotic resistance.</p>
+                <p>Each process demonstrates sophisticated biological programming with virulence factor production, biofilm formation, immune evasion, and resistance mechanisms.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Bacterial Processes</h2>
+                <ul>
+                    <li><a href="#virulence-regulation">1. Virulence Regulation</a></li>
+                    <li><a href="#toxin-production">2. Toxin Production</a></li>
+                    <li><a href="#biofilm-formation">3. Biofilm Formation</a></li>
+                    <li><a href="#immune-evasion">4. Immune Evasion</a></li>
+                    <li><a href="#antibiotic-resistance">5. Antibiotic Resistance</a></li>
+                    <li><a href="#quorum-sensing">6. Quorum Sensing</a></li>
+                    <li><a href="#adhesion">7. Adhesion & Colonization</a></li>
+                    <li><a href="#persistence">8. Persistence Mechanisms</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Virulence Regulation -->
+            <div class="process-item" id="virulence-regulation">
+                <h3>1. Virulence Regulation</h3>
+                <p>Detailed analysis of S. aureus Virulence Regulation using the Programming Framework, revealing computational logic and regulatory patterns for virulence factor expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Environmental Signals
+    A[Host Environment] --> B[Agr System]
+    C[Stress Conditions] --> D[SigB Activation]
+    E[Iron Limitation] --> F[Fur Regulation]
+    G[Oxygen Levels] --> H[SrrAB System]
+    
+    %% Agr Quorum Sensing
+    B --> I[AgrA Phosphorylation]
+    I --> J[RNAIII Production]
+    J --> K[Virulence Gene Expression]
+    
+    %% Stress Response
+    D --> L[Stress Response Genes]
+    L --> M[Environmental Adaptation]
+    M --> N[Stress Survival]
+    
+    %% Iron Regulation
+    F --> O[Iron Uptake Systems]
+    O --> P[Siderophore Production]
+    P --> Q[Iron Acquisition]
+    
+    %% Integration
+    K --> R[Virulence Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Pathogenic Success]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Toxin Production -->
+            <div class="process-item" id="toxin-production">
+                <h3>2. Toxin Production</h3>
+                <p>Detailed analysis of S. aureus Toxin Production using the Programming Framework, revealing computational logic and regulatory patterns for exotoxin synthesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Toxin Induction
+    A[Host Contact] --> B[Alpha-Hemolysin]
+    C[Immune Pressure] --> D[Panton-Valentine Leukocidin]
+    E[Tissue Damage] --> F[Enterotoxins]
+    G[Inflammatory Response] --> H[Superantigens]
+    
+    %% Alpha-Hemolysin
+    B --> I[Hla Expression]
+    I --> J[Pore Formation]
+    J --> K[Cell Lysis]
+    
+    %% PVL Production
+    D --> L[PVL Genes]
+    L --> M[Leukocyte Destruction]
+    M --> N[Immune Suppression]
+    
+    %% Enterotoxin Synthesis
+    F --> O[SEA-SEE Production]
+    O --> P[Food Poisoning]
+    P --> Q[Gastrointestinal Toxicity]
+    
+    %% Integration
+    K --> R[Toxin Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Damage]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Biofilm Formation -->
+            <div class="process-item" id="biofilm-formation">
+                <h3>3. Biofilm Formation</h3>
+                <p>Detailed analysis of S. aureus Biofilm Formation using the Programming Framework, revealing computational logic and regulatory patterns for biofilm development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Biofilm Initiation
+    A[Surface Contact] --> B[Adhesion Proteins]
+    C[Quorum Sensing] --> D[EPS Production]
+    E[Environmental Stress] --> F[Biofilm Matrix]
+    G[Cell Aggregation] --> H[Microcolony Formation]
+    
+    %% Adhesion Phase
+    B --> I[Surface Proteins]
+    I --> J[Initial Attachment]
+    J --> K[Reversible Adhesion]
+    
+    %% Matrix Production
+    D --> L[Polysaccharide Synthesis]
+    L --> M[Extracellular DNA]
+    M --> N[Protein Matrix]
+    
+    %% Biofilm Maturation
+    F --> O[3D Structure]
+    O --> P[Water Channels]
+    P --> Q[Mature Biofilm]
+    
+    %% Integration
+    K --> R[Biofilm Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Antibiotic Resistance]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Immune Evasion -->
+            <div class="process-item" id="immune-evasion">
+                <h3>4. Immune Evasion</h3>
+                <p>Detailed analysis of S. aureus Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for host immune system avoidance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Immune Detection
+    A[Host Immune Response] --> B[Protein A]
+    C[Phagocytosis] --> D[Staphyloxanthin]
+    E[Complement System] --> F[SCIN Proteins]
+    G[Antibody Response] --> H[SpA Binding]
+    
+    %% Protein A Function
+    B --> I[IgG Binding]
+    I --> J[Antibody Inactivation]
+    J --> K[Immune Recognition Block]
+    
+    %% Antioxidant Protection
+    D --> L[ROS Scavenging]
+    L --> M[Oxidative Protection]
+    M --> N[Phagocyte Survival]
+    
+    %% Complement Inhibition
+    F --> O[C3b Inactivation]
+    O --> P[Complement Block]
+    P --> Q[Opsonization Prevention]
+    
+    %% Integration
+    K --> R[Immune Evasion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Antibiotic Resistance -->
+            <div class="process-item" id="antibiotic-resistance">
+                <h3>5. Antibiotic Resistance</h3>
+                <p>Detailed analysis of S. aureus Antibiotic Resistance using the Programming Framework, revealing computational logic and regulatory patterns for resistance mechanisms.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Resistance Mechanisms
+    A[Methicillin] --> B[mecA Gene]
+    C[Vancomycin] --> D[Cell Wall Thickening]
+    E[Penicillin] --> F[Beta-Lactamase]
+    G[Multiple Drugs] --> H[Efflux Pumps]
+    
+    %% MRSA Resistance
+    B --> I[PBP2a Production]
+    I --> J[Altered PBP]
+    J --> K[Beta-Lactam Resistance]
+    
+    %% Vancomycin Resistance
+    D --> L[Cell Wall Modification]
+    L --> M[Peptidoglycan Changes]
+    M --> N[VISA Phenotype]
+    
+    %% Beta-Lactamase
+    F --> O[BlaZ Expression]
+    O --> P[Antibiotic Hydrolysis]
+    P --> Q[Penicillin Inactivation]
+    
+    %% Integration
+    K --> R[Resistance Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Treatment Failure]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Quorum Sensing -->
+            <div class="process-item" id="quorum-sensing">
+                <h3>6. Quorum Sensing</h3>
+                <p>Detailed analysis of S. aureus Quorum Sensing using the Programming Framework, revealing computational logic and regulatory patterns for cell-cell communication.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Quorum Sensing Systems
+    A[Cell Density] --> B[Agr System]
+    C[Autoinducer Peptides] --> D[AgrC Receptor]
+    E[Population Size] --> F[AgrD Processing]
+    G[Environmental Signals] --> H[AgrB Export]
+    
+    %% Agr Activation
+    B --> I[AgrA Phosphorylation]
+    I --> J[P2/P3 Promoter Activation]
+    J --> K[RNAII/RNAIII Production]
+    
+    %% Autoinducer Synthesis
+    D --> L[AgrD Processing]
+    L --> M[AIP Production]
+    M --> N[Cell Communication]
+    
+    %% Gene Regulation
+    F --> O[Virulence Gene Control]
+    O --> P[Biofilm Regulation]
+    P --> Q[Metabolic Adaptation]
+    
+    %% Integration
+    K --> R[Quorum Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Population Behavior]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Adhesion & Colonization -->
+            <div class="process-item" id="adhesion">
+                <h3>7. Adhesion & Colonization</h3>
+                <p>Detailed analysis of S. aureus Adhesion & Colonization using the Programming Framework, revealing computational logic and regulatory patterns for host tissue attachment.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Adhesion Factors
+    A[Host Tissue] --> B[Surface Proteins]
+    C[Extracellular Matrix] --> D[Adhesins]
+    E[Host Proteins] --> F[Binding Proteins]
+    G[Cell Surfaces] --> H[Colonization Factors]
+    
+    %% Surface Protein Function
+    B --> I[Protein A Expression]
+    I --> J[Fibronectin Binding]
+    J --> K[Host Cell Attachment]
+    
+    %% Adhesin Production
+    D --> L[FnBPs Synthesis]
+    L --> M[ECM Binding]
+    M --> N[Tissue Colonization]
+    
+    %% Binding Protein Activity
+    F --> O[ClfA/ClfB Production]
+    O --> P[Fibrinogen Binding]
+    P --> Q[Blood Clot Attachment]
+    
+    %% Integration
+    K --> R[Adhesion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Colonization]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Persistence Mechanisms -->
+            <div class="process-item" id="persistence">
+                <h3>8. Persistence Mechanisms</h3>
+                <p>Detailed analysis of S. aureus Persistence Mechanisms using the Programming Framework, revealing computational logic and regulatory patterns for long-term survival.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Persistence Triggers
+    A[Antibiotic Pressure] --> B[Persister Formation]
+    C[Host Immune Response] --> D[Intracellular Survival]
+    E[Environmental Stress] --> F[Dormancy Induction]
+    G[Nutrient Limitation] --> H[Metabolic Adaptation]
+    
+    %% Persister Development
+    B --> I[Growth Arrest]
+    I --> J[Metabolic Shutdown]
+    J --> K[Antibiotic Tolerance]
+    
+    %% Intracellular Survival
+    D --> L[Phagosome Escape]
+    L --> M[Cytosolic Replication]
+    M --> N[Host Cell Survival]
+    
+    %% Dormancy Response
+    F --> O[Stringent Response]
+    O --> P[ppGpp Accumulation]
+    P --> Q[Growth Inhibition]
+    
+    %% Integration
+    K --> R[Persistence Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Long-Term Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of S. aureus pathogenicity and biofilm systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Pathogenicity & Biofilm</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

s_cerevisiae_batch01_aging_fermentation.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>S. cerevisiae Batch 01: Aging & Fermentation - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
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+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
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+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🍺 S. cerevisiae Batch 01: Aging & Fermentation</h1>
+            <p>Programming Framework Analysis - 8 Yeast Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🍺 Aging & Fermentation Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental S. cerevisiae processes responsible for aging and fermentation. These processes represent the core computational systems that enable this model yeast to age, respond to stress, and perform alcoholic fermentation.</p>
+                <p>Each process demonstrates sophisticated biological programming with aging regulation, stress adaptation, metabolic switching, and cell cycle control.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Yeast Processes</h2>
+                <ul>
+                    <li><a href="#replicative-aging">1. Replicative Aging</a></li>
+                    <li><a href="#chronological-aging">2. Chronological Aging</a></li>
+                    <li><a href="#stress-response">3. Stress Response</a></li>
+                    <li><a href="#fermentation">4. Fermentation</a></li>
+                    <li><a href="#metabolic-switching">5. Metabolic Switching</a></li>
+                    <li><a href="#cell-cycle">6. Cell Cycle Control</a></li>
+                    <li><a href="#autophagy">7. Autophagy</a></li>
+                    <li><a href="#quiescence">8. Quiescence</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Replicative Aging -->
+            <div class="process-item" id="replicative-aging">
+                <h3>1. Replicative Aging</h3>
+                <p>Detailed analysis of S. cerevisiae Replicative Aging using the Programming Framework, revealing computational logic and regulatory patterns for cellular senescence.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Aging Triggers
+    A[Budding Division] --> B[Telomere Shortening]
+    C[DNA Damage] --> D[DNA Repair Systems]
+    E[Oxidative Stress] --> F[ROS Accumulation]
+    G[Protein Aggregation] --> H[Proteostasis Decline]
+    
+    %% Telomere Maintenance
+    B --> I[Telomerase Activation]
+    I --> J[Telomere Extension]
+    J --> K[Replicative Potential]
+    
+    %% DNA Damage Response
+    D --> L[Checkpoint Activation]
+    L --> M[Cell Cycle Arrest]
+    M --> N[DNA Repair]
+    
+    %% Oxidative Damage
+    F --> O[Antioxidant Systems]
+    O --> P[ROS Scavenging]
+    P --> Q[Oxidative Protection]
+    
+    %% Integration
+    K --> R[Aging Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Replicative Senescence]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Chronological Aging -->
+            <div class="process-item" id="chronological-aging">
+                <h3>2. Chronological Aging</h3>
+                <p>Detailed analysis of S. cerevisiae Chronological Aging using the Programming Framework, revealing computational logic and regulatory patterns for stationary phase survival.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stationary Phase
+    A[Nutrient Depletion] --> B[Growth Arrest]
+    C[Energy Limitation] --> D[Metabolic Adaptation]
+    E[Stress Accumulation] --> F[Stress Response]
+    G[Time Passage] --> H[Aging Markers]
+    
+    %% Growth Arrest
+    B --> I[Cell Cycle Exit]
+    I --> J[G0 State Entry]
+    J --> K[Quiescent State]
+    
+    %% Metabolic Adaptation
+    D --> L[Glycogen Accumulation]
+    L --> M[Trehalose Synthesis]
+    M --> N[Energy Conservation]
+    
+    %% Stress Response
+    F --> O[Heat Shock Proteins]
+    O --> P[Oxidative Protection]
+    P --> Q[Stress Resistance]
+    
+    %% Integration
+    K --> R[Chronological Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Longevity]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>3. Stress Response</h3>
+                <p>Detailed analysis of S. cerevisiae Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Detection
+    A[Heat Stress] --> B[Hsf1 Activation]
+    C[Oxidative Stress] --> D[Yap1 Activation]
+    E[Osmotic Stress] --> F[Hog1 Activation]
+    G[Nutrient Stress] --> H[Snf1 Activation]
+    
+    %% Heat Shock Response
+    B --> I[Hsp Gene Expression]
+    I --> J[Protein Protection]
+    J --> K[Thermal Adaptation]
+    
+    %% Oxidative Response
+    D --> L[Antioxidant Genes]
+    L --> M[ROS Detoxification]
+    M --> N[Oxidative Protection]
+    
+    %% Osmotic Response
+    F --> O[Glycerol Synthesis]
+    O --> P[Osmolyte Accumulation]
+    P --> Q[Osmotic Balance]
+    
+    %% Integration
+    K --> R[Stress Adaptation]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Environmental Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Fermentation -->
+            <div class="process-item" id="fermentation">
+                <h3>4. Fermentation</h3>
+                <p>Detailed analysis of S. cerevisiae Fermentation using the Programming Framework, revealing computational logic and regulatory patterns for alcoholic fermentation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Glucose Metabolism
+    A[Glucose Uptake] --> B[Glycolysis]
+    C[Pyruvate Production] --> D[Pyruvate Decarboxylase]
+    E[Acetaldehyde] --> F[Alcohol Dehydrogenase]
+    G[NADH Oxidation] --> H[NAD+ Regeneration]
+    
+    %% Glycolytic Pathway
+    B --> I[Hexokinase Activation]
+    I --> J[Fructose-1,6-BP]
+    J --> K[Pyruvate Formation]
+    
+    %% Ethanol Production
+    D --> L[Acetaldehyde Formation]
+    L --> M[CO2 Release]
+    M --> N[Ethanol Synthesis]
+    
+    %% Energy Balance
+    H --> O[ATP Production]
+    O --> P[Energy Conservation]
+    P --> Q[Fermentative Growth]
+    
+    %% Integration
+    K --> R[Fermentation Program]
+    N --> R
+    Q --> R
+    F --> R
+    R --> S[Ethanol Production]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Metabolic Switching -->
+            <div class="process-item" id="metabolic-switching">
+                <h3>5. Metabolic Switching</h3>
+                <p>Detailed analysis of S. cerevisiae Metabolic Switching using the Programming Framework, revealing computational logic and regulatory patterns for respiratory-fermentative transitions.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Environmental Signals
+    A[Oxygen Availability] --> B[Respiratory Activation]
+    C[Glucose Concentration] --> D[Catabolite Repression]
+    E[Energy Demand] --> F[Metabolic Regulation]
+    G[Growth Phase] --> H[Metabolic Switch]
+    
+    %% Respiratory Metabolism
+    B --> I[Cytochrome c Oxidase]
+    I --> J[Electron Transport]
+    J --> K[Oxidative Phosphorylation]
+    
+    %% Fermentative Metabolism
+    D --> L[Glycolytic Genes]
+    L --> M[Fermentation Enzymes]
+    M --> N[Ethanol Production]
+    
+    %% Metabolic Integration
+    F --> O[Snf1/AMPK Activation]
+    O --> P[Metabolic Adaptation]
+    P --> Q[Energy Optimization]
+    
+    %% Integration
+    K --> R[Metabolic Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Metabolic Flexibility]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Cell Cycle Control -->
+            <div class="process-item" id="cell-cycle">
+                <h3>6. Cell Cycle Control</h3>
+                <p>Detailed analysis of S. cerevisiae Cell Cycle Control using the Programming Framework, revealing computational logic and regulatory patterns for cell division.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Cell Cycle Phases
+    A[G1 Phase] --> B[Start Checkpoint]
+    C[S Phase] --> D[DNA Replication]
+    E[G2 Phase] --> F[Mitosis Entry]
+    G[M Phase] --> H[Cell Division]
+    
+    %% G1/S Transition
+    B --> I[Cln3-Cdk1 Activation]
+    I --> J[Cln1/2 Expression]
+    J --> K[G1/S Transition]
+    
+    %% S Phase Control
+    D --> L[DNA Replication Initiation]
+    L --> M[Replication Fork Progression]
+    M --> N[DNA Synthesis Completion]
+    
+    %% G2/M Transition
+    F --> O[Clb1/2-Cdk1 Activation]
+    O --> P[Mitotic Entry]
+    P --> Q[Chromosome Segregation]
+    
+    %% Integration
+    K --> R[Cell Cycle Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Cell Division]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Autophagy -->
+            <div class="process-item" id="autophagy">
+                <h3>7. Autophagy</h3>
+                <p>Detailed analysis of S. cerevisiae Autophagy using the Programming Framework, revealing computational logic and regulatory patterns for cellular recycling.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Autophagy Triggers
+    A[Nutrient Starvation] --> B[TOR Inhibition]
+    C[Protein Aggregation] --> D[Autophagy Induction]
+    E[Organelle Damage] --> F[Selective Autophagy]
+    G[Stress Conditions] --> H[Autophagy Activation]
+    
+    %% Autophagosome Formation
+    B --> I[Atg1 Complex]
+    I --> J[Phagophore Assembly]
+    J --> K[Autophagosome Formation]
+    
+    %% Cargo Recognition
+    D --> L[Cargo Selection]
+    L --> M[Autophagosome Cargo]
+    M --> N[Selective Degradation]
+    
+    %% Lysosomal Fusion
+    F --> O[Vacuolar Fusion]
+    O --> P[Autolysosome Formation]
+    P --> Q[Macromolecule Degradation]
+    
+    %% Integration
+    K --> R[Autophagy Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Cellular Recycling]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Quiescence -->
+            <div class="process-item" id="quiescence">
+                <h3>8. Quiescence</h3>
+                <p>Detailed analysis of S. cerevisiae Quiescence using the Programming Framework, revealing computational logic and regulatory patterns for cellular dormancy.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Quiescence Entry
+    A[Nutrient Limitation] --> B[Growth Arrest]
+    C[Energy Depletion] --> D[Metabolic Shutdown]
+    E[Stress Conditions] --> F[Protective Response]
+    G[Cell Cycle Exit] --> H[G0 State]
+    
+    %% Growth Arrest
+    B --> I[Cell Cycle Inhibition]
+    I --> J[Growth Cessation]
+    J --> K[Quiescent State]
+    
+    %% Metabolic Adaptation
+    D --> L[Energy Conservation]
+    L --> M[Storage Accumulation]
+    M --> N[Metabolic Dormancy]
+    
+    %% Protective Mechanisms
+    F --> O[Stress Resistance]
+    O --> P[Damage Protection]
+    P --> Q[Survival Mechanisms]
+    
+    %% Integration
+    K --> R[Quiescence Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Long-Term Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of S. cerevisiae aging and fermentation systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Aging & Fermentation</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

s_enterica_batch01_invasion_virulence.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>S. enterica Batch 01: Invasion & Virulence - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
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+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
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+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 S. enterica Batch 01: Invasion & Virulence</h1>
+            <p>Programming Framework Analysis - 8 Bacterial Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Invasion & Virulence Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental S. enterica processes responsible for invasion and virulence. These processes represent the core computational systems that enable this enteric pathogen to invade host cells, cause disease, and adapt to different environments.</p>
+                <p>Each process demonstrates sophisticated biological programming with invasion mechanisms, virulence factor production, host adaptation, and survival strategies.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Bacterial Processes</h2>
+                <ul>
+                    <li><a href="#host-invasion">1. Host Invasion</a></li>
+                    <li><a href="#type-iii-secretion">2. Type III Secretion</a></li>
+                    <li><a href="#intracellular-survival">3. Intracellular Survival</a></li>
+                    <li><a href="#virulence-regulation">4. Virulence Regulation</a></li>
+                    <li><a href="#metabolic-adaptation">5. Metabolic Adaptation</a></li>
+                    <li><a href="#stress-response">6. Stress Response</a></li>
+                    <li><a href="#immune-evasion">7. Immune Evasion</a></li>
+                    <li><a href="#persistence">8. Persistence & Transmission</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Host Invasion -->
+            <div class="process-item" id="host-invasion">
+                <h3>1. Host Invasion</h3>
+                <p>Detailed analysis of S. enterica Host Invasion using the Programming Framework, revealing computational logic and regulatory patterns for host cell entry.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Invasion Triggers
+    A[Host Contact] --> B[Adhesion Proteins]
+    C[Environmental Signals] --> D[Invasion Genes]
+    E[Host Cell Recognition] --> F[Surface Proteins]
+    G[Intestinal Environment] --> H[Invasion Factors]
+    
+    %% Adhesion Phase
+    B --> I[Fimbrial Adhesion]
+    I --> J[Host Cell Binding]
+    J --> K[Initial Attachment]
+    
+    %% Invasion Machinery
+    D --> L[SPI-1 Activation]
+    L --> M[T3SS Assembly]
+    M --> N[Effector Secretion]
+    
+    %% Cell Entry
+    F --> O[Membrane Ruffling]
+    O --> P[Phagocytosis Induction]
+    P --> Q[Host Cell Entry]
+    
+    %% Integration
+    K --> R[Invasion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Intracellular Localization]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Type III Secretion -->
+            <div class="process-item" id="type-iii-secretion">
+                <h3>2. Type III Secretion</h3>
+                <p>Detailed analysis of S. enterica Type III Secretion using the Programming Framework, revealing computational logic and regulatory patterns for effector protein delivery.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% T3SS Components
+    A[SPI-1 Genes] --> B[Needle Complex]
+    C[SPI-2 Genes] --> D[Secretion Apparatus]
+    E[Effector Genes] --> F[Translocation System]
+    G[Regulatory Signals] --> H[Secretion Control]
+    
+    %% Needle Assembly
+    B --> I[Base Assembly]
+    I --> J[Needle Formation]
+    J --> K[Translocation Pore]
+    
+    %% Effector Processing
+    D --> L[Effector Recognition]
+    L --> M[Secretion Signal]
+    M --> N[Protein Translocation]
+    
+    %% Host Cell Delivery
+    F --> O[Effector Injection]
+    O --> P[Host Cytoplasm]
+    P --> Q[Target Modification]
+    
+    %% Integration
+    K --> R[T3SS Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Manipulation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Intracellular Survival -->
+            <div class="process-item" id="intracellular-survival">
+                <h3>3. Intracellular Survival</h3>
+                <p>Detailed analysis of S. enterica Intracellular Survival using the Programming Framework, revealing computational logic and regulatory patterns for survival within host cells.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Intracellular Environment
+    A[Phagosome] --> B[SCV Formation]
+    C[Host Defense] --> D[Survival Mechanisms]
+    E[Nutrient Limitation] --> F[Metabolic Adaptation]
+    G[Oxidative Stress] --> H[Stress Response]
+    
+    %% SCV Development
+    B --> I[Vacuole Modification]
+    I --> J[SCV Maturation]
+    J --> K[Intracellular Niche]
+    
+    %% Survival Strategies
+    D --> L[Antioxidant Systems]
+    L --> M[ROS Scavenging]
+    M --> N[Oxidative Protection]
+    
+    %% Metabolic Adaptation
+    F --> O[Alternative Metabolism]
+    O --> P[Energy Conservation]
+    P --> Q[Nutrient Utilization]
+    
+    %% Integration
+    K --> R[Survival Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Intracellular Replication]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: Virulence Regulation -->
+            <div class="process-item" id="virulence-regulation">
+                <h3>4. Virulence Regulation</h3>
+                <p>Detailed analysis of S. enterica Virulence Regulation using the Programming Framework, revealing computational logic and regulatory patterns for virulence factor expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Regulatory Systems
+    A[Environmental Signals] --> B[PhoP/PhoQ System]
+    C[Oxygen Levels] --> D[Fnr Regulation]
+    E[Iron Availability] --> F[Fur Control]
+    G[Host Environment] --> H[Two-Component Systems]
+    
+    %% PhoP/PhoQ Regulation
+    B --> I[PhoQ Sensing]
+    I --> J[PhoP Phosphorylation]
+    J --> K[Virulence Gene Expression]
+    
+    %% Oxygen Response
+    D --> L[Anaerobic Genes]
+    L --> M[Metabolic Adaptation]
+    M --> N[Oxygen Sensing]
+    
+    %% Iron Regulation
+    F --> O[Iron Uptake Systems]
+    O --> P[Siderophore Production]
+    P --> Q[Iron Acquisition]
+    
+    %% Integration
+    K --> R[Virulence Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Pathogenic Success]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Metabolic Adaptation -->
+            <div class="process-item" id="metabolic-adaptation">
+                <h3>5. Metabolic Adaptation</h3>
+                <p>Detailed analysis of S. enterica Metabolic Adaptation using the Programming Framework, revealing computational logic and regulatory patterns for metabolic flexibility.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Metabolic Signals
+    A[Nutrient Availability] --> B[Metabolic Switching]
+    C[Oxygen Levels] --> D[Respiratory Adaptation]
+    E[Host Environment] --> F[Energy Metabolism]
+    G[Stress Conditions] --> H[Metabolic Regulation]
+    
+    %% Metabolic Flexibility
+    B --> I[Carbon Source Utilization]
+    I --> J[Alternative Pathways]
+    J --> K[Metabolic Optimization]
+    
+    %% Respiratory Adaptation
+    D --> L[Aerobic Respiration]
+    L --> M[Anaerobic Respiration]
+    M --> N[Energy Production]
+    
+    %% Energy Metabolism
+    F --> O[ATP Synthesis]
+    O --> P[Energy Conservation]
+    P --> Q[Metabolic Efficiency]
+    
+    %% Integration
+    K --> R[Metabolic Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Environmental Adaptation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Stress Response -->
+            <div class="process-item" id="stress-response">
+                <h3>6. Stress Response</h3>
+                <p>Detailed analysis of S. enterica Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Stress Detection
+    A[Oxidative Stress] --> B[OxyR Activation]
+    C[Heat Stress] --> D[RpoH Activation]
+    E[Acid Stress] --> F[Acid Tolerance]
+    G[Osmotic Stress] --> H[Osmolyte Synthesis]
+    
+    %% Oxidative Response
+    B --> I[Antioxidant Genes]
+    I --> J[ROS Scavenging]
+    J --> K[Oxidative Protection]
+    
+    %% Heat Shock Response
+    D --> L[Heat Shock Proteins]
+    L --> M[Protein Protection]
+    M --> N[Thermal Adaptation]
+    
+    %% Acid Tolerance
+    F --> O[Acid Resistance Systems]
+    O --> P[pH Homeostasis]
+    P --> Q[Acid Survival]
+    
+    %% Integration
+    K --> R[Stress Adaptation]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Environmental Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Immune Evasion -->
+            <div class="process-item" id="immune-evasion">
+                <h3>7. Immune Evasion</h3>
+                <p>Detailed analysis of S. enterica Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for host immune system avoidance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Immune Detection
+    A[Host Immune Response] --> B[Antigen Variation]
+    C[Phagocytosis] --> D[Intracellular Survival]
+    E[Complement System] --> F[Complement Resistance]
+    G[Antibody Response] --> H[Antigen Masking]
+    
+    %% Antigen Variation
+    B --> I[Flagellar Variation]
+    I --> J[Surface Protein Changes]
+    J --> K[Immune Recognition Block]
+    
+    %% Intracellular Evasion
+    D --> L[SCV Formation]
+    L --> M[Phagosome Escape]
+    M --> N[Intracellular Niche]
+    
+    %% Complement Resistance
+    F --> O[Complement Inactivation]
+    O --> P[Opsonization Block]
+    P --> Q[Complement Evasion]
+    
+    %% Integration
+    K --> R[Immune Evasion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Host Survival]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Persistence & Transmission -->
+            <div class="process-item" id="persistence">
+                <h3>8. Persistence & Transmission</h3>
+                <p>Detailed analysis of S. enterica Persistence & Transmission using the Programming Framework, revealing computational logic and regulatory patterns for long-term survival and spread.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Persistence Mechanisms
+    A[Host Environment] --> B[Biofilm Formation]
+    C[Carrier State] --> D[Asymptomatic Colonization]
+    E[Environmental Survival] --> F[Stress Resistance]
+    G[Transmission] --> H[Fecal Shedding]
+    
+    %% Biofilm Development
+    B --> I[EPS Production]
+    I --> J[Cell Aggregation]
+    J --> K[Biofilm Matrix]
+    
+    %% Carrier State
+    D --> L[Intestinal Colonization]
+    L --> M[Immune Tolerance]
+    M --> N[Long-Term Persistence]
+    
+    %% Environmental Survival
+    F --> O[Stress Adaptation]
+    O --> P[Environmental Resistance]
+    P --> Q[Survival Mechanisms]
+    
+    %% Integration
+    K --> R[Persistence Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Transmission Success]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of S. enterica invasion and virulence systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Invasion & Virulence</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>

sars_cov2_batch01_entry_replication.html

@@ -0,0 +1,693 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>SARS-CoV-2 Batch 01: Entry & Replication - Programming Framework Analysis</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <style>
+        body {
+            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
+            line-height: 1.6;
+            margin: 0;
+            padding: 0;
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            min-height: 100vh;
+        }
+        .container {
+            max-width: 1400px;
+            margin: 0 auto;
+            background: white;
+            box-shadow: 0 0 20px rgba(0,0,0,0.1);
+            border-radius: 10px;
+            overflow: hidden;
+        }
+        .header {
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            color: white;
+            padding: 2rem;
+            text-align: center;
+        }
+        .header h1 {
+            margin: 0;
+            font-size: 2.5rem;
+            font-weight: 300;
+        }
+        .content {
+            padding: 2rem;
+        }
+        .intro {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc {
+            background: #f8f9fa;
+            padding: 2rem;
+            border-radius: 8px;
+            margin-bottom: 2rem;
+        }
+        .toc ul {
+            list-style: none;
+            padding: 0;
+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
+        .toc a {
+            color: #007bff;
+            text-decoration: none;
+            font-weight: 500;
+        }
+        .process-item {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            background: #fafafa;
+        }
+        .process-item h3 {
+            color: #495057;
+            margin-bottom: 1rem;
+        }
+        .mermaid-container {
+            background: white;
+            padding: 1rem;
+            border-radius: 8px;
+            margin: 1rem 0;
+            overflow-x: auto;
+        }
+        .footer {
+            background: #f8f9fa;
+            padding: 2rem;
+            text-align: center;
+            border-top: 1px solid #dee2e6;
+            margin-top: 2rem;
+        }
+        .color-legend {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
+            gap: 0.5rem 1rem;
+            margin: 1rem 0 0;
+            font-size: 10pt;
+            color: #333;
+        }
+        .color-box {
+            display: inline-block;
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            margin-right: 4px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <div class="header">
+            <h1>🦠 SARS-CoV-2 Batch 01: Entry & Replication</h1>
+            <p>Programming Framework Analysis - 8 Viral Processes</p>
+        </div>
+        <div class="content">
+            <div class="intro">
+                <h2>🦠 Viral Entry & Replication Systems</h2>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental SARS-CoV-2 processes responsible for viral entry and replication. These processes represent the core computational systems that enable this coronavirus to infect host cells, replicate its genome, and produce viral proteins.</p>
+                <p>Each process demonstrates sophisticated biological programming with viral entry, RNA replication, protein synthesis, and immune response mechanisms.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Viral Processes</h2>
+                <ul>
+                    <li><a href="#viral-entry">1. Viral Entry</a></li>
+                    <li><a href="#genome-release">2. Genome Release</a></li>
+                    <li><a href="#translation">3. Translation & Processing</a></li>
+                    <li><a href="#replication">4. RNA Replication</a></li>
+                    <li><a href="#transcription">5. Subgenomic Transcription</a></li>
+                    <li><a href="#assembly">6. Assembly & Budding</a></li>
+                    <li><a href="#immune-evasion">7. Immune Evasion</a></li>
+                    <li><a href="#pathogenesis">8. Pathogenesis & Spread</a></li>
+                </ul>
+            </div>
+            
+            <!-- Process 1: Viral Entry -->
+            <div class="process-item" id="viral-entry">
+                <h3>1. Viral Entry</h3>
+                <p>Detailed analysis of SARS-CoV-2 Viral Entry using the Programming Framework, revealing computational logic and regulatory patterns for host cell infection.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Entry Triggers
+    A[ACE2 Binding] --> B[S Protein Activation]
+    C[TMPRSS2 Cleavage] --> D[Fusion Activation]
+    E[Endocytosis] --> F[Endosomal Entry]
+    G[Host Cell Contact] --> H[Entry Machinery]
+    
+    %% ACE2 Binding
+    B --> I[S Protein-ACE2]
+    I --> J[Conformational Change]
+    J --> K[Receptor Binding]
+    
+    %% Proteolytic Cleavage
+    D --> L[S Protein Cleavage]
+    L --> M[Fusion Peptide Exposure]
+    M --> N[Membrane Fusion]
+    
+    %% Endosomal Entry
+    F --> O[Endosome Formation]
+    O --> P[Acidification]
+    P --> Q[Cathepsin Activation]
+    
+    %% Integration
+    K --> R[Entry Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Intracellular Localization]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 2: Genome Release -->
+            <div class="process-item" id="genome-release">
+                <h3>2. Genome Release</h3>
+                <p>Detailed analysis of SARS-CoV-2 Genome Release using the Programming Framework, revealing computational logic and regulatory patterns for viral RNA release.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Release Components
+    A[Viral Particle] --> B[Capsid Disassembly]
+    C[Endosomal Acidification] --> D[Protease Activation]
+    E[Host Factors] --> F[RNA Release]
+    G[Intracellular Environment] --> H[Genome Processing]
+    
+    %% Capsid Disassembly
+    B --> I[N Protein Release]
+    I --> J[RNA Uncoating]
+    J --> K[Genome Exposure]
+    
+    %% Protease Activation
+    D --> L[Cathepsin L]
+    L --> M[Proteolytic Cleavage]
+    M --> N[Particle Disruption]
+    
+    %% RNA Release
+    F --> O[Genome Release]
+    O --> P[Cytoplasmic Localization]
+    P --> Q[Translation Initiation]
+    
+    %% Integration
+    K --> R[Release Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral RNA Available]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 3: Translation & Processing -->
+            <div class="process-item" id="translation">
+                <h3>3. Translation & Processing</h3>
+                <p>Detailed analysis of SARS-CoV-2 Translation & Processing using the Programming Framework, revealing computational logic and regulatory patterns for viral protein synthesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Translation Components
+    A[Viral RNA] --> B[Ribosome Binding]
+    C[Host Translation] --> D[Protein Synthesis]
+    E[Proteolytic Processing] --> F[Polyprotein Cleavage]
+    G[Host Proteases] --> H[Protein Processing]
+    
+    %% Initial Translation
+    B --> I[ORF1a Translation]
+    I --> J[Polyprotein Synthesis]
+    J --> K[Proteolytic Processing]
+    
+    %% Polyprotein Processing
+    D --> L[Main Protease]
+    L --> M[Nonstructural Proteins]
+    M --> N[Replication Complex]
+    
+    %% Protein Processing
+    F --> O[Accessory Proteins]
+    O --> P[Structural Proteins]
+    P --> Q[Functional Proteins]
+    
+    %% Integration
+    K --> R[Translation Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral Proteins]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 4: RNA Replication -->
+            <div class="process-item" id="replication">
+                <h3>4. RNA Replication</h3>
+                <p>Detailed analysis of SARS-CoV-2 RNA Replication using the Programming Framework, revealing computational logic and regulatory patterns for viral genome replication.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Replication Components
+    A[Viral RNA] --> B[RdRp Complex]
+    C[Host Factors] --> D[Replication Machinery]
+    E[NTPs] --> F[RNA Synthesis]
+    G[Double-Membrane Vesicles] --> H[Replication Sites]
+    
+    %% RdRp Assembly
+    B --> I[RdRp-Nsp12]
+    I --> J[Accessory Proteins]
+    J --> K[Replication Complex]
+    
+    %% RNA Synthesis
+    D --> L[Minus Strand]
+    L --> M[Plus Strand]
+    M --> N[Genome Replication]
+    
+    %% Replication Sites
+    F --> O[DMV Formation]
+    O --> P[Replication Compartments]
+    P --> Q[RNA Production]
+    
+    %% Integration
+    K --> R[Replication Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral Genomes]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 5: Subgenomic Transcription -->
+            <div class="process-item" id="transcription">
+                <h3>5. Subgenomic Transcription</h3>
+                <p>Detailed analysis of SARS-CoV-2 Subgenomic Transcription using the Programming Framework, revealing computational logic and regulatory patterns for viral gene expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Transcription Components
+    A[Genome Template] --> B[Transcription Complex]
+    C[TRS Elements] --> D[Transcription Regulation]
+    E[Host Factors] --> F[RNA Polymerase]
+    G[Accessory Proteins] --> H[Transcription Control]
+    
+    %% TRS Recognition
+    B --> I[TRS-Binding]
+    I --> J[Template Switching]
+    J --> K[Subgenomic RNA]
+    
+    %% Transcription Regulation
+    D --> L[Nsp1 Inhibition]
+    L --> M[Host Translation Block]
+    M --> N[Viral RNA Synthesis]
+    
+    %% RNA Processing
+    F --> O[5' Cap Addition]
+    O --> P[3' Polyadenylation]
+    P --> Q[Mature sgRNA]
+    
+    %% Integration
+    K --> R[Transcription Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Viral mRNAs]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Assembly & Budding -->
+            <div class="process-item" id="assembly">
+                <h3>6. Assembly & Budding</h3>
+                <p>Detailed analysis of SARS-CoV-2 Assembly & Budding using the Programming Framework, revealing computational logic and regulatory patterns for viral particle formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Assembly Components
+    A[Structural Proteins] --> B[Viral Assembly]
+    C[Viral RNA] --> D[Genome Packaging]
+    E[Host Factors] --> F[Assembly Machinery]
+    G[ER-Golgi] --> H[Assembly Sites]
+    
+    %% Protein Assembly
+    B --> I[N Protein-RNA]
+    I --> J[Nucleocapsid Formation]
+    J --> K[Genome Encapsidation]
+    
+    %% Structural Assembly
+    D --> L[M Protein Assembly]
+    L --> M[E Protein Integration]
+    M --> N[Viral Envelope]
+    
+    %% Budding Process
+    F --> O[ER Budding]
+    O --> P[Golgi Processing]
+    P --> Q[Particle Release]
+    
+    %% Integration
+    K --> R[Assembly Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Mature Virion]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Immune Evasion -->
+            <div class="process-item" id="immune-evasion">
+                <h3>7. Immune Evasion</h3>
+                <p>Detailed analysis of SARS-CoV-2 Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for host immune system avoidance.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Immune Detection
+    A[Host Immune Response] --> B[Interferon Inhibition]
+    C[Innate Immunity] --> D[Pattern Recognition]
+    E[Adaptive Immunity] --> F[Antigen Presentation]
+    G[Inflammatory Response] --> H[Immune Modulation]
+    
+    %% Interferon Block
+    B --> I[Nsp1 Inhibition]
+    I --> J[Translation Block]
+    J --> K[Interferon Suppression]
+    
+    %% Pattern Recognition
+    D --> L[TLR Inhibition]
+    L --> M[RIG-I Block]
+    M --> N[Innate Evasion]
+    
+    %% Antigen Processing
+    F --> O[MHC Inhibition]
+    O --> P[Antigen Presentation Block]
+    P --> Q[Adaptive Evasion]
+    
+    %% Integration
+    K --> R[Immune Evasion Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Immune Escape]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Pathogenesis & Spread -->
+            <div class="process-item" id="pathogenesis">
+                <h3>8. Pathogenesis & Spread</h3>
+                <p>Detailed analysis of SARS-CoV-2 Pathogenesis & Spread using the Programming Framework, revealing computational logic and regulatory patterns for disease development.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Pathogenesis Components
+    A[Viral Replication] --> B[Cell Damage]
+    C[Inflammatory Response] --> D[Cytokine Storm]
+    E[Immune Dysregulation] --> F[Organ Damage]
+    G[Viral Spread] --> H[Transmission]
+    
+    %% Cell Damage
+    B --> I[Apoptosis Induction]
+    I --> J[Cell Death]
+    J --> K[Tissue Damage]
+    
+    %% Cytokine Storm
+    D --> L[Pro-inflammatory Cytokines]
+    L --> M[Immune Hyperactivation]
+    M --> N[Systemic Inflammation]
+    
+    %% Organ Damage
+    F --> O[Lung Damage]
+    O --> P[Multi-organ Failure]
+    P --> Q[Severe Disease]
+    
+    %% Integration
+    K --> R[Pathogenesis Program]
+    N --> R
+    Q --> R
+    H --> R
+    R --> S[Disease Progression]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#ffd43b,color:#000
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,color:#fff
+                    </div>
+                    <div class="color-legend">
+                        <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
+                        <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
+                        <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
+                        <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+        
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of SARS-CoV-2 entry and replication systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 01 of 8: Entry & Replication</em></p>
+            </div>
+        </div>
+    </div>
+    
+    <script>
+        mermaid.initialize({
+            startOnLoad: true,
+            theme: 'default',
+            flowchart: {
+                useMaxWidth: false,
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 30,
+                rankSpacing: 40,
+                padding: 10
+            },
+            themeVariables: {
+                fontFamily: 'Arial, sans-serif',
+                fontSize: '14px',
+                primaryColor: '#ff6b6b',
+                lineColor: '#333333',
+                secondaryColor: '#feca57',
+                tertiaryColor: '#4ecdc4'
+            }
+        });
+    </script>
+</body>
+</html>