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developmental_decision_systems_batch01_cell_fate_choice.html

@@ -225,7 +225,7 @@
                     <span class="stat-label">Categories</span>
                 </div>
                 <div class="stat">
-                    <span class="stat-number">100%</span>
+                    <span class="stat-number">Complete</span>
                     <span class="stat-label">Complete</span>
                 </div>
             </div>

evolutionary_computing_systems_batch01_adaptive_evolution.html

@@ -287,7 +287,6 @@ graph TD
         
         <h3>2. Mutation Generation</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[DNA Replication] --> B[Replication Errors]
     B --> C[Point Mutations]
@@ -328,12 +327,10 @@ graph TD
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style P fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>3. Genetic Drift</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Small Population] --> B[Random Sampling]
     B --> C[Allele Frequency Changes]
@@ -367,12 +364,10 @@ graph TD
     style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>4. Adaptive Evolution</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Environmental Change] --> B[Selection Pressure]
     B --> C[Phenotypic Variation]
@@ -409,12 +404,10 @@ graph TD
     style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>5. Co-evolutionary Arms Race</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Host-Pathogen Interaction] --> B[Host Defense Evolution]
     A --> C[Pathogen Counter-Evolution]
@@ -451,12 +444,10 @@ graph TD
     style L fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>6. Sexual Selection</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Mating Competition] --> B[Sexual Traits]
     B --> C[Mate Choice]
@@ -490,12 +481,10 @@ graph TD
     style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>7. Population Bottleneck Recovery</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Population Bottleneck] --> B[Genetic Diversity Loss]
     B --> C[Inbreeding Depression]
@@ -530,12 +519,10 @@ graph TD
     style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <h3>8. Speciation Decision Tree</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Population Isolation] --> B{Isolation Type?}
     B -->|Geographic| C[Allopatric Speciation]
@@ -575,7 +562,6 @@ graph TD
     style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <div class="color-key">

index.html

@@ -4,6 +4,7 @@
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>Genome Logic Modeling Project (GLMP) - Home</title>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
     <style>
         body {
             font-family: 'Arial', sans-serif;
@@ -174,6 +175,68 @@
             border: 2px solid #333;
         }
         
+        .featured-chart-section {
+            background: #f8f9fa;
+            border: 2px solid #e9ecef;
+            border-radius: 12px;
+            padding: 2rem;
+            margin: 2rem 0;
+            box-shadow: 0 4px 12px rgba(0,0,0,0.1);
+        }
+
+        .chart-description {
+            font-size: 1.1em;
+            color: #495057;
+            margin-bottom: 1.5rem;
+            line-height: 1.6;
+        }
+
+        .chart-container {
+            background: white;
+            border: 1px solid #dee2e6;
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+            text-align: center;
+            max-width: 90%;
+            margin-left: auto;
+            margin-right: auto;
+        }
+
+        .chart-caption {
+            background: #e8f4fd;
+            border-left: 4px solid #007bff;
+            padding: 1rem;
+            margin-top: 1rem;
+            border-radius: 4px;
+            font-size: 0.95em;
+        }
+
+        .chart-color-key {
+            display: grid;
+            grid-template-columns: repeat(5, 1fr);
+            gap: 8px;
+            margin: 15px 0;
+            padding: 10px;
+            background: #f8f9fa;
+            border-radius: 5px;
+            border: 1px solid #ddd;
+            font-size: 0.8em;
+        }
+
+        .chart-color-item {
+            text-align: center;
+            padding: 5px;
+            border-radius: 3px;
+            font-weight: bold;
+        }
+
+        .chart-red { background: #ff6b6b; color: white; }
+        .chart-yellow { background: #ffd43b; color: black; }
+        .chart-green { background: #51cf66; color: white; }
+        .chart-blue { background: #74c0fc; color: white; }
+        .chart-violet { background: #b197fc; color: white; }
+        
         .footer {
             text-align: center;
             margin-top: 40px;
@@ -205,6 +268,20 @@
                 flex-direction: column;
                 align-items: center;
             }
+            
+            .chart-container {
+                max-width: 95%;
+                padding: 1rem;
+            }
+            
+            .featured-chart-section {
+                padding: 1.5rem;
+            }
+            
+            .chart-color-key {
+                grid-template-columns: 1fr;
+                gap: 5px;
+            }
         }
     </style>
 </head>
@@ -238,6 +315,96 @@
         <a href="README.md" class="cta-button">📋 View Complete Collections</a>
     </div>
 
+    <div class="featured-chart-section">
+        <h3>🧬 Featured Example: Bacterial Implementation of Viral Decision Logic</h3>
+        <p class="chart-description">This flowchart demonstrates how viral lysogeny decision logic can be implemented in bacterial cells, showing the universal computational patterns that exist across biological kingdoms. The system processes multiple environmental inputs to make optimal survival decisions.</p>
+        
+        <div class="chart-container">
+            <div class="mermaid">
+graph TD
+    A[Host Stress Signal] --> B{Stress Level?}
+    C[Nutrient Availability] --> D{Nutrient Level?}
+    E[Cell Density] --> F{Density Level?}
+    
+    B -->|High| G[High Stress Response]
+    B -->|Low| H[Low Stress Response]
+    D -->|Low| I[Nutrient Limitation]
+    D -->|High| J[Nutrient Sufficient]
+    F -->|High| K[High Density]
+    F -->|Low| L[Low Density]
+    
+    G --> M[CI-like Repressor Production]
+    H --> N[Cro-like Activator Production]
+    I --> O[Lysogeny Signal]
+    J --> P[Lysis Signal]
+    K --> Q[Quorum Signal]
+    L --> R[No Quorum]
+    
+    M --> S[CI-like Auto-regulation]
+    N --> T[Cro-like Auto-regulation]
+    O --> U[Lysogeny Decision]
+    P --> V[Lysis Decision]
+    Q --> W[Collective Decision]
+    R --> X[Individual Decision]
+    
+    U --> Y[Lysogeny State]
+    V --> Z[Lysis State]
+    W --> AA[Population Response]
+    X --> BB[Individual Response]
+    
+    Y --> CC[Growth Mode]
+    Z --> DD[Dormancy Mode]
+    AA --> EE[Coordinated Response]
+    BB --> FF[Independent Response]
+    
+    style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
+    style C fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
+    style B fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style F fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style M fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style N fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style O fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style P fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style Q fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style R fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style S fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style T fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style U fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style V fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style W fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style X fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style Y fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style Z fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style AA fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style BB fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style CC fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style DD fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style EE fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style FF fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+            </div>
+        </div>
+        
+        <div class="chart-color-key">
+            <div class="chart-color-item chart-red">🔴 Triggers & Conditions</div>
+            <div class="chart-color-item chart-yellow">🟡 Catalysts & Enzymes</div>
+            <div class="chart-color-item chart-green">🟢 Chemical Processing</div>
+            <div class="chart-color-item chart-blue">🔵 Intermediates</div>
+            <div class="chart-color-item chart-violet">🟣 Products</div>
+        </div>
+        
+        <div class="chart-caption">
+            <strong>Computational Logic:</strong> Multi-input decision system with competitive inhibition (CI-like vs Cro-like), demonstrating threshold-based responses to environmental conditions. This example shows how viral decision logic can be implemented in bacterial systems, validating the Programming Framework's prediction of universal computational patterns across biological kingdoms.
+        </div>
+    </div>
+
     <div class="main-content">
         <div class="section">
             <h2>🧪 Experimental Validation Protocols</h2>
@@ -417,5 +584,29 @@
         <p><em>Generated using the Programming Framework methodology</em></p>
         <p><em>This project demonstrates the universal computational nature of biological systems across viral, bacterial, and eukaryotic kingdoms.</em></p>
     </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' 
+            },
+            securityLevel: 'loose'
+        });
+    </script>
 </body>
 </html>

information_processing_systems_batch01_signal_integration.html

@@ -284,246 +284,180 @@ graph TD
 
         <h2>🧠 Complete Information Processing Flowcharts</h2>
         
-        <h3>2. Noise Filtering</h3>
+        <h3>2. Signal Amplification</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Noisy Signal Input] --> B[Signal Detection]
-    B --> C[Noise Assessment]
-    C --> D{Signal-to-Noise Ratio?}
-    D -->|High| E[Signal Processing]
-    D -->|Low| F[Noise Filtering]
-    
-    E --> G[Direct Output]
-    F --> H[Filter Application]
+    A[Weak Input Signal] --> B[Signal Detection]
+    B --> C[Receptor Activation]
+    C --> D[Second Messenger Production]
+    D --> E[Enzyme Cascade]
     
-    H --> I[Filtered Signal]
-    I --> J[Signal Enhancement]
-    J --> K[Clean Output]
+    E --> F[Signal Amplification]
+    F --> G[Multiple Outputs]
+    G --> H[Response Amplification]
     
-    G --> L[Information Processing]
-    K --> L
+    H --> I[Enhanced Response]
+    I --> J[Signal Termination]
+    J --> K[System Reset]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>3. Pattern Recognition</h3>
+        <h3>3. Noise Filtering</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Pattern Input] --> B[Feature Extraction]
-    B --> C[Pattern Analysis]
-    C --> D{Pattern Match?}
-    D -->|Yes| E[Pattern Recognition]
-    D -->|No| F[Pattern Learning]
+    A[Noisy Input] --> B[Signal Processing]
+    B --> C[Noise Detection]
+    C --> D[Filter Application]
+    D --> E[Signal Extraction]
     
-    E --> G[Known Pattern Response]
-    F --> H[New Pattern Storage]
+    E --> F[Clean Signal]
+    F --> G[Threshold Check]
+    G --> H{Signal Valid?}
     
-    G --> I[Predictive Response]
-    H --> J[Pattern Database Update]
+    H -->|Yes| I[Signal Transmission]
+    H -->|No| J[Signal Rejection]
     
-    I --> K[Behavioral Output]
-    J --> L[Learning Enhancement]
+    I --> K[Response Generation]
+    J --> L[No Response]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>4. Signal Amplification</h3>
+        <h3>4. Cross-Talk Integration</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Weak Signal] --> B[Signal Detection]
-    B --> C[Amplification Cascade]
-    C --> D[Signal Multiplication]
-    D --> E[Amplified Output]
-    E --> F[Response Generation]
-    
-    F --> G{Amplification Sufficient?}
-    G -->|Yes| H[Response Execution]
-    G -->|No| I[Further Amplification]
+    A[Multiple Signals] --> B[Signal Convergence]
+    B --> C[Cross-Talk Detection]
+    C --> D[Signal Integration]
+    D --> E[Combined Response]
     
-    I --> C
-    H --> J[System Response]
+    E --> F[Response Modulation]
+    F --> G[Output Generation]
+    G --> H[System Response]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style D fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style E fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style H fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>5. Memory Storage</h3>
+        <h3>5. Feedback Regulation</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Information Input] --> B[Memory Encoding]
-    B --> C[Short-term Storage]
-    C --> D{Memory Consolidation?}
-    D -->|Yes| E[Long-term Storage]
-    D -->|No| F[Memory Decay]
-    
-    E --> G[Memory Retrieval]
-    F --> H[Information Loss]
-    
-    G --> I[Memory Access]
-    H --> I
-    
-    I --> J{Memory Available?}
-    J -->|Yes| K[Memory Recall]
-    J -->|No| L[Memory Reconstruction]
+    A[Input Signal] --> B[System Response]
+    B --> C[Output Generation]
+    C --> D[Feedback Signal]
+    D --> E[Response Modulation]
     
-    K --> M[Information Output]
-    L --> N[Partial Recall]
+    E --> F[System Adjustment]
+    F --> G[Homeostasis]
+    G --> H[Stable State]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style H fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>6. Error Detection</h3>
+        <h3>6. Signal Transduction</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Data Input] --> B[Error Checking]
-    B --> C{Error Detected?}
-    C -->|Yes| D[Error Correction]
-    C -->|No| E[Data Processing]
-    
-    D --> F[Error Repair]
-    E --> G[Data Validation]
+    A[Extracellular Signal] --> B[Receptor Binding]
+    B --> C[Conformational Change]
+    C --> D[Intracellular Signaling]
+    D --> E[Second Messengers]
     
-    F --> H[Corrected Data]
-    G --> I[Validated Data]
-    
-    H --> J[Data Output]
-    I --> J
-    
-    J --> K[System Continuation]
+    E --> F[Protein Kinases]
+    F --> G[Transcription Factors]
+    G --> H[Gene Expression]
+    H --> I[Cellular Response]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style G fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
+    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
         </div>
 
-        <h3>7. Adaptive Filtering</h3>
+        <h3>7. Information Processing</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Signal Input] --> B[Filter Assessment]
-    B --> C[Filter Performance]
-    C --> D{Filter Optimal?}
-    D -->|Yes| E[Current Filter]
-    D -->|No| F[Filter Adjustment]
-    
-    E --> G[Filtered Output]
-    F --> H[Filter Optimization]
-    
-    H --> I[New Filter Parameters]
-    I --> J[Filter Application]
-    J --> K[Improved Output]
+    A[Input Information] --> B[Information Processing]
+    B --> C[Decision Making]
+    C --> D[Response Selection]
+    D --> E[Output Generation]
     
-    G --> L[Information Processing]
-    K --> L
+    E --> F[System Response]
+    F --> G[Information Storage]
+    G --> H[Learning]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
+    style C fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style G fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
         </div>
 
-        <h3>8. Information Compression</h3>
+        <h3>8. Signal Integration</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Information Input] --> B[Redundancy Analysis]
-    B --> C[Pattern Identification]
-    C --> D[Compression Algorithm]
-    D --> E[Compressed Data]
-    E --> F[Storage Optimization]
+    A[Multiple Inputs] --> B[Signal Integration]
+    B --> C[Weighted Sum]
+    C --> D[Threshold Check]
+    D --> E{Threshold Exceeded?}
     
-    F --> G{Compression Efficient?}
-    G -->|Yes| H[Compressed Storage]
-    G -->|No| I[Algorithm Adjustment]
+    E -->|Yes| F[Response Generation]
+    E -->|No| G[No Response]
     
-    I --> D
-    H --> J[Information Retrieval]
-    J --> K[Decompression]
-    K --> L[Original Information]
+    F --> H[Output Signal]
+    G --> I[System Quiescence]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style H fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
+    style I fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
         </div>
 
         <div class="color-key">

metabolic_decision_systems_batch01_energy_balance.html

@@ -225,7 +225,7 @@
                     <span class="stat-label">Categories</span>
                 </div>
                 <div class="stat">
-                    <span class="stat-number">100%</span>
+                    <span class="stat-number">Complete</span>
                     <span class="stat-label">Complete</span>
                 </div>
             </div>

neural_decision_systems_batch01_winner_take_all.html

@@ -225,7 +225,7 @@
                     <span class="stat-label">Categories</span>
                 </div>
                 <div class="stat">
-                    <span class="stat-number">100%</span>
+                    <span class="stat-number">Complete</span>
                     <span class="stat-label">Complete</span>
                 </div>
             </div>

plant_decision_systems_batch01_photomorphogenesis.html

@@ -225,7 +225,7 @@
                     <span class="stat-label">Categories</span>
                 </div>
                 <div class="stat">
-                    <span class="stat-number">100%</span>
+                    <span class="stat-number">Complete</span>
                     <span class="stat-label">Complete</span>
                 </div>
             </div>

synthetic_biology_circuits_batch01_logic_gates.html

@@ -273,7 +273,6 @@ graph TD
         
         <h3>2. OR Logic Gate</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Input A Signal] --> B{Input A Present?}
     C[Input B Signal] --> D{Input B Present?}
@@ -320,7 +319,6 @@ graph TD
 
         <h3>3. NOT Logic Gate</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Input Signal] --> B{Input Present?}
     B -->|Yes| C[Repressor Active]
@@ -355,7 +353,6 @@ graph TD
 
         <h3>4. NAND Logic Gate</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Input A Signal] --> B{Input A Present?}
     C[Input B Signal] --> D{Input B Present?}
@@ -403,7 +400,6 @@ graph TD
 
         <h3>5. Toggle Switch</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Toggle Signal] --> B{Current State?}
     B -->|OFF| C[Repressor Inactive]
@@ -441,7 +437,6 @@ graph TD
 
         <h3>6. Oscillator Circuit</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Oscillator Initiation] --> B[Gene A Expression]
     B --> C[Protein A Synthesis]
@@ -483,7 +478,6 @@ graph TD
 
         <h3>7. Sensor Circuit</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Environmental Signal] --> B[Signal Detection]
     B --> C{Signal Threshold?}
@@ -512,7 +506,6 @@ graph TD
 
         <h3>8. Amplifier Circuit</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[Weak Input Signal] --> B[Signal Detection]
     B --> C[Transcription Factor]

temporal_programming_systems_batch01_cell_cycle.html

@@ -291,7 +291,6 @@ graph TD
         
         <h3>2. G2/M Checkpoint Decision</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
     A[G2 Phase Entry] --> B[DNA Replication Check]
     B --> C{Replication Complete?}
@@ -299,22 +298,23 @@ graph TD
     C -->|Yes| E[DNA Damage Check]
     
     D --> B
-    E --> F{DNA Damage Present?}
-    F -->|Yes| G[Damage Repair]
-    F -->|No| H[Chromosome Condensation]
+    E --> F{DNA Intact?}
+    F -->|No| G[DNA Repair Activation]
+    F -->|Yes| H[Spindle Assembly Check]
     
-    G --> I[Repair Completion]
-    I --> F
-    H --> J[Spindle Assembly Check]
+    G --> I[Repair Mechanisms]
+    I --> J{Repair Successful?}
+    J -->|No| K[Apoptosis Trigger]
+    J -->|Yes| E
     
-    J --> K{Spindle Ready?}
-    K -->|No| L[Spindle Formation]
-    K -->|Yes| M[Mitosis Initiation]
+    H --> L{Spindle Ready?}
+    L -->|No| M[Spindle Assembly]
+    L -->|Yes| N[Mitosis Entry]
     
-    L --> J
-    M --> N[Metaphase Entry]
-    N --> O[Chromosome Alignment]
-    O --> P[Anaphase Trigger]
+    M --> H
+    N --> O[Chromosome Condensation]
+    O --> P[Mitotic Spindle Formation]
+    P --> Q[Metaphase Alignment]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
@@ -324,85 +324,126 @@ graph TD
     style F fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style L fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style M fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style O fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style P fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
+    style O fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style P fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style Q fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
         </div>
 
-        <h3>3. Spindle Assembly Checkpoint</h3>
+        <h3>3. M Phase Progression</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Spindle Formation] --> B[Kinetochore Assembly]
-    B --> C[Microtubule Attachment]
-    C --> D{All Chromosomes Attached?}
-    D -->|No| E[Kinetochore Signaling]
-    D -->|Yes| F[Checkpoint Satisfaction]
-    
-    E --> G[Mad2 Activation]
-    G --> H[APC/C Inhibition]
-    H --> I[Anaphase Delay]
-    I --> C
-    
-    F --> J[Mad2 Inactivation]
-    J --> K[APC/C Activation]
-    K --> L[Securin Degradation]
-    L --> M[Separase Activation]
-    M --> N[Cohesin Cleavage]
-    N --> O[Anaphase Onset]
+    A[Mitosis Entry] --> B[Prophase]
+    B --> C[Chromosome Condensation]
+    C --> D[Nuclear Envelope Breakdown]
+    D --> E[Spindle Formation]
+    
+    E --> F[Metaphase]
+    F --> G[Chromosome Alignment]
+    G --> H{Alignment Complete?}
+    H -->|No| G
+    H -->|Yes| I[Anaphase]
+    
+    I --> J[Chromosome Separation]
+    J --> K[Telophase]
+    K --> L[Nuclear Reformation]
+    L --> M[Cytokinesis]
+    
+    M --> N{Division Complete?}
+    N -->|No| M
+    N -->|Yes| O[Two Daughter Cells]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
-    style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style B fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style K fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style N fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style N fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>4. DNA Damage Response Timing</h3>
+        <h3>4. Cell Cycle Exit Decision</h3>
+        <div class="mermaid">
+graph TD
+    A[G1 Phase] --> B{Cell Division Required?}
+    B -->|No| C[G0 Entry]
+    B -->|Yes| D[Growth Assessment]
+    
+    C --> E[Quiescent State]
+    E --> F{Stimulation Signal?}
+    F -->|Yes| G[G1 Re-entry]
+    F -->|No| E
+    
+    D --> H{Size Adequate?}
+    H -->|No| I[Growth Continuation]
+    H -->|Yes| J[Nutrient Check]
+    
+    I --> D
+    J --> K{Nutrients Sufficient?}
+    K -->|No| L[Starvation Response]
+    K -->|Yes| M[Cell Cycle Continuation]
+    
+    L --> N[Metabolic Adaptation]
+    N --> O{Environment Improved?}
+    O -->|Yes| J
+    O -->|No| P[Apoptosis]
+    
+    style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
+    style B fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style K fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style N fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style O fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style P fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+        </div>
+
+        <h3>5. DNA Damage Response</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[DNA Damage Detection] --> B[Damage Type Assessment]
-    B --> C{Double Strand Break?}
-    C -->|Yes| D[ATM Activation]
-    C -->|No| E[ATR Activation]
+    A[DNA Damage] --> B[Damage Detection]
+    B --> C{Damage Type?}
+    C -->|Single Strand| D[Base Excision Repair]
+    C -->|Double Strand| E[Double Strand Break Repair]
+    C -->|Crosslink| F[Crosslink Repair]
     
-    D --> F[Chk2 Phosphorylation]
-    E --> G[Chk1 Phosphorylation]
+    D --> G[Repair Completion]
+    E --> H{Repair Pathway?}
+    F --> I[Crosslink Resolution]
     
-    F --> H[Cell Cycle Arrest]
-    G --> H
+    H -->|NHEJ| J[Non-homologous End Joining]
+    H -->|HR| K[Homologous Recombination]
     
-    H --> I[DNA Repair Initiation]
-    I --> J{Repair Type?}
-    J -->|Homologous| K[HR Repair]
-    J -->|Non-homologous| L[NHEJ Repair]
+    J --> L[Repair Completion]
+    K --> L
+    I --> L
     
-    K --> M[Repair Completion]
+    G --> M{Repair Successful?}
     L --> M
-    M --> N[Damage Check]
-    N --> O{Repair Successful?}
     
-    O -->|No| P[Apoptosis]
-    O -->|Yes| Q[Checkpoint Release]
-    Q --> R[Cell Cycle Resumption]
+    M -->|Yes| N[Cell Cycle Continuation]
+    M -->|No| O[Apoptosis]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
@@ -410,172 +451,118 @@ graph TD
     style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style N fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style O fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style P fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style Q fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style R fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
+    style L fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style M fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
         </div>
 
-        <h3>5. Developmental Timing</h3>
+        <h3>6. Spindle Assembly Checkpoint</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Developmental Signal] --> B[Timing Gene Expression]
-    B --> C[Developmental Clock]
-    C --> D{Timing Threshold?}
-    D -->|No| E[Clock Continuation]
-    D -->|Yes| F[Stage Transition]
-    
-    E --> C
-    F --> G[New Gene Expression]
-    G --> H[Developmental Progress]
-    H --> I{Next Stage Ready?}
+    A[Metaphase] --> B[Kinetochore Attachment]
+    B --> C{All Chromosomes Attached?}
+    C -->|No| D[Unattached Kinetochores]
+    C -->|Yes| E[Tension Check]
+    
+    D --> F[SAC Activation]
+    F --> G[APC/C Inhibition]
+    G --> H[Metaphase Arrest]
+    H --> I[Re-attachment Attempt]
+    I --> B
     
-    I -->|No| J[Stage Maintenance]
-    I -->|Yes| K[Stage Completion]
+    E --> J{Tension Adequate?}
+    J -->|No| K[Tension Generation]
+    J -->|Yes| L[SAC Silencing]
     
-    J --> H
-    K --> L[Next Developmental Stage]
-    L --> M[New Timing Program]
-    M --> N[Developmental Continuation]
+    K --> E
+    L --> M[APC/C Activation]
+    M --> N[Anaphase Entry]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style C fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style D fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style J fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style M fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>6. Circadian Rhythm Integration</h3>
+        <h3>7. Cytokinesis Timing</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Light Signal] --> B[Clock Gene Expression]
-    B --> C[Circadian Oscillator]
-    C --> D[Clock Protein Synthesis]
-    D --> E[Protein Accumulation]
-    E --> F[Feedback Inhibition]
-    F --> G[Gene Repression]
-    G --> H[Protein Degradation]
-    H --> I[Repression Release]
-    I --> B
+    A[Anaphase Completion] --> B[Contractile Ring Assembly]
+    B --> C{Ring Formation Complete?}
+    C -->|No| D[Ring Assembly Continuation]
+    C -->|Yes| E[Actomyosin Contraction]
     
-    C --> J[Output Genes]
-    J --> K[Physiological Rhythms]
-    K --> L[Metabolic Timing]
-    L --> M[Behavioral Timing]
-    M --> N[Environmental Synchronization]
+    D --> B
+    E --> F{Membrane Cleavage?}
+    F -->|No| G[Contraction Continuation]
+    F -->|Yes| H[Cell Separation]
+    
+    G --> E
+    H --> I{Separation Complete?}
+    I -->|No| J[Final Cleavage]
+    I -->|Yes| K[Two Daughter Cells]
+    
+    J --> I
+    K --> L[Cell Cycle Completion]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
     style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style C fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style I fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style J fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
-        <h3>7. Aging Clock Mechanisms</h3>
+        <h3>8. Cell Cycle Synchronization</h3>
         <div class="mermaid">
-            <div class="mermaid">
 graph TD
-    A[Aging Signal] --> B[Telomere Shortening]
-    B --> C[DNA Damage Accumulation]
-    C --> D[Oxidative Stress]
-    D --> E[Metabolic Changes]
-    E --> F[Aging Clock Progression]
+    A[Population Signal] --> B{Synchronization Required?}
+    B -->|No| C[Independent Cycling]
+    B -->|Yes| D[Synchronization Signal]
     
-    F --> G{Clock Threshold?}
-    G -->|No| H[Clock Continuation]
-    G -->|Yes| I[Senescence Initiation]
+    C --> E[Random Phase Distribution]
+    D --> F[Phase Alignment]
+    F --> G{Alignment Complete?}
+    G -->|No| H[Phase Adjustment]
+    G -->|Yes| I[Synchronized Population]
     
     H --> F
-    I --> J[Cell Cycle Arrest]
-    J --> K[Senescence Program]
-    K --> L[Metabolic Reprogramming]
-    L --> M[Inflammatory Response]
-    M --> N[Tissue Dysfunction]
-    N --> O[Organismal Aging]
+    I --> J[Coordinated Division]
+    J --> K[Population Synchrony]
     
     style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
-    style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style B fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
+    style C fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
+    style D fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style E fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
+    style F fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
     style G fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
     style H fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style I fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style J fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style K fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style N fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style O fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
-        </div>
-
-        <h3>8. Synchronization Systems</h3>
-        <div class="mermaid">
-            <div class="mermaid">
-graph TD
-    A[Synchronization Signal] --> B[Phase Detection]
-    B --> C[Phase Comparison]
-    C --> D{Phase Aligned?}
-    D -->|No| E[Phase Adjustment]
-    D -->|Yes| F[Synchronized State]
-    
-    E --> G[Clock Speed Modulation]
-    G --> H[Phase Shift]
-    H --> I[New Phase]
-    I --> C
-    
-    F --> J[Coordinated Behavior]
-    J --> K[Population Synchrony]
-    K --> L[Collective Timing]
-    L --> M[Environmental Adaptation]
-    
-    style A fill:#ff6b6b,stroke:#333,stroke-width:2px,color:#fff
-    style B fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style C fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style D fill:#ffd43b,stroke:#333,stroke-width:2px,color:#000
-    style E fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style F fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
-    style G fill:#51cf66,stroke:#333,stroke-width:2px,color:#fff
-    style H fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style I fill:#74c0fc,stroke:#333,stroke-width:2px,color:#fff
     style J fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
     style K fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style L fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-    style M fill:#b197fc,stroke:#333,stroke-width:2px,color:#fff
-            </div>
         </div>
 
         <div class="color-key">

viral_decision_systems_batch01_phage_lysogeny.html

@@ -225,7 +225,7 @@
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                 </div>
                 <div class="stat">
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+                    <span class="stat-number">Complete</span>
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yeast_decision_systems_batch01_mating_type_switching.html

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                 </div>
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