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ecoli_batch01_dna_replication_repair.html

@@ -107,22 +107,26 @@
     <div class="container">
         <div class="header">
             <h1>🦠 E. coli Batch 01: DNA Replication & Repair</h1>
-            <p>Programming Framework Analysis - 4 DNA Processes</p>
+            <p>Programming Framework Analysis - 8 DNA Processes</p>
         </div>
         <div class="content">
             <div class="intro">
                 <h2>🦠 DNA Replication & Repair Systems</h2>
-                <p><strong>Batch Overview:</strong> This batch contains 4 fundamental E. coli processes responsible for DNA replication and repair. These processes represent the core computational systems that ensure genomic integrity and faithful inheritance of genetic information.</p>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental E. coli processes responsible for DNA replication and repair. These processes represent the core computational systems that ensure genomic integrity and faithful inheritance of genetic information.</p>
                 <p>Each process demonstrates sophisticated biological programming with error correction and quality control.</p>
             </div>
             
             <div class="toc">
-                <h2>📋 Table of Contents - 4 DNA Processes</h2>
+                <h2>📋 Table of Contents - 8 DNA Processes</h2>
                 <ul>
                     <li><a href="#dna-replication-initiation">1. DNA Replication Initiation</a></li>
                     <li><a href="#dna-replication-elongation">2. DNA Replication Elongation</a></li>
                     <li><a href="#dna-replication-termination">3. DNA Replication Termination</a></li>
                     <li><a href="#dna-repair">4. DNA Repair</a></li>
+                    <li><a href="#base-excision-repair">5. Base Excision Repair</a></li>
+                    <li><a href="#nucleotide-excision-repair">6. Nucleotide Excision Repair</a></li>
+                    <li><a href="#mismatch-repair">7. Mismatch Repair</a></li>
+                    <li><a href="#sos-response">8. SOS Response</a></li>
                 </ul>
             </div>
             
@@ -265,6 +269,257 @@ graph TD
                     </div>
                 </div>
             </div>
+
+            <!-- Process 5: Base Excision Repair -->
+            <div class="process-item" id="base-excision-repair">
+                <h3>5. Base Excision Repair</h3>
+                <p>Detailed analysis of E. coli Base Excision Repair using the Programming Framework, revealing computational logic and regulatory patterns for small DNA lesions.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% DNA Damage Detection
+    A[Damaged Base] --> B[DNA Glycosylase Recognition]
+    C[Oxidative Damage] --> B
+    D[Alkylation Damage] --> B
+    E[Deamination] --> B
+    
+    %% Base Removal
+    B --> F[Glycosylase Binding]
+    F --> G[Base Excision]
+    G --> H[AP Site Formation]
+    
+    %% AP Site Processing
+    H --> I[AP Endonuclease]
+    I --> J[5' Incision]
+    J --> K[3' Incision]
+    K --> L[Gap Formation]
+    
+    %% Gap Filling
+    L --> M[DNA Polymerase I]
+    M --> N[Single Nucleotide Insertion]
+    N --> O[DNA Ligase]
+    O --> P[Repair Complete]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    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:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Nucleotide Excision Repair -->
+            <div class="process-item" id="nucleotide-excision-repair">
+                <h3>6. Nucleotide Excision Repair</h3>
+                <p>Detailed analysis of E. coli Nucleotide Excision Repair using the Programming Framework, revealing computational logic and regulatory patterns for bulky DNA lesions.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Damage Recognition
+    A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition]
+    C[UV-Induced Damage] --> B
+    D[Chemical Adducts] --> B
+    E[Cross-links] --> B
+    
+    %% Damage Verification
+    B --> F[UvrA Release]
+    F --> G[UvrB-DNA Complex]
+    G --> H[UvrC Recruitment]
+    H --> I[UvrBC Complex]
+    
+    %% Dual Incision
+    I --> J[3' Incision]
+    I --> K[5' Incision]
+    J --> L[Oligonucleotide Release]
+    K --> L
+    L --> M[Gap Formation]
+    
+    %% Gap Filling
+    M --> N[DNA Polymerase I]
+    N --> O[Gap Filling]
+    O --> P[DNA Ligase]
+    P --> Q[Repair Complete]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#74c0fc,color:#fff
+    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:#74c0fc,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Mismatch Repair -->
+            <div class="process-item" id="mismatch-repair">
+                <h3>7. Mismatch Repair</h3>
+                <p>Detailed analysis of E. coli Mismatch Repair using the Programming Framework, revealing computational logic and regulatory patterns for replication errors.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Mismatch Detection
+    A[DNA Mismatch] --> B[MutS Recognition]
+    C[Replication Error] --> B
+    D[Insertion/Deletion] --> B
+    E[Base Mismatch] --> B
+    
+    %% Complex Formation
+    B --> F[MutS-DNA Complex]
+    F --> G[MutL Recruitment]
+    G --> H[MutS-MutL Complex]
+    H --> I[DNA Bending]
+    
+    %% Strand Discrimination
+    I --> J[GATC Site Recognition]
+    J --> K[MutH Activation]
+    K --> L[Strand Incision]
+    L --> M[Nick Formation]
+    
+    %% Excision and Repair
+    M --> N[Helicase II Loading]
+    N --> O[Exonuclease Activity]
+    O --> P[Gap Formation]
+    P --> Q[DNA Polymerase III]
+    Q --> R[Gap Filling]
+    R --> S[DNA Ligase]
+    S --> T[Repair Complete]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style F fill:#74c0fc,color:#fff
+    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:#ffd43b,color:#000
+    style M fill:#74c0fc,color:#fff
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#74c0fc,color:#fff
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: SOS Response -->
+            <div class="process-item" id="sos-response">
+                <h3>8. SOS Response</h3>
+                <p>Detailed analysis of E. coli SOS Response using the Programming Framework, revealing computational logic and regulatory patterns for emergency DNA repair.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% DNA Damage Detection
+    A[DNA Damage] --> B[Single-Strand DNA]
+    C[UV Radiation] --> A
+    D[Chemical Mutagens] --> A
+    E[Replication Stress] --> A
+    
+    %% RecA Activation
+    B --> F[RecA Protein Binding]
+    F --> G[RecA Nucleofilament]
+    G --> H[RecA Activation]
+    H --> I[LexA Cleavage]
+    
+    %% SOS Regulon Activation
+    I --> J[LexA Degradation]
+    J --> K[SOS Genes Derepressed]
+    K --> L[DNA Repair Genes]
+    L --> M[Error-Prone Repair]
+    
+    %% Repair Execution
+    M --> N[UmuC/UmuD Expression]
+    N --> O[Translesion Synthesis]
+    O --> P[Error-Prone Bypass]
+    P --> Q[Cell Survival]
+    
+    %% Recovery
+    Q --> R[Damage Cleared]
+    R --> S[RecA Inactivation]
+    S --> T[LexA Reformation]
+    T --> U[SOS Genes Repressed]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    style F fill:#ffd43b,color:#000
+    style G fill:#74c0fc,color:#fff
+    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:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#b197fc,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    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:#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>

ecoli_batch02_transcription_regulation.html

@@ -107,22 +107,26 @@
     <div class="container">
         <div class="header">
             <h1>🦠 E. coli Batch 02: Transcription Regulation</h1>
-            <p>Programming Framework Analysis - 4 Transcription Processes</p>
+            <p>Programming Framework Analysis - 8 Transcription Processes</p>
         </div>
         <div class="content">
             <div class="intro">
                 <h2>🦠 Transcription Regulation Systems</h2>
-                <p><strong>Batch Overview:</strong> This batch contains 4 fundamental E. coli processes responsible for transcription regulation and gene expression control. These processes represent the core computational systems that ensure proper gene expression timing and regulation.</p>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental E. coli processes responsible for transcription regulation and gene expression control. These processes represent the core computational systems that ensure proper gene expression timing and regulation.</p>
                 <p>Each process demonstrates sophisticated biological programming with promoter recognition and regulatory mechanisms.</p>
             </div>
             
             <div class="toc">
-                <h2>📋 Table of Contents - 4 Transcription Processes</h2>
+                <h2>📋 Table of Contents - 8 Transcription Processes</h2>
                 <ul>
                     <li><a href="#transcription-initiation">1. Transcription Initiation</a></li>
                     <li><a href="#sigma-factor-regulation">2. Sigma Factor Regulation</a></li>
                     <li><a href="#operon-regulation">3. Operon Regulation</a></li>
                     <li><a href="#transcription-termination">4. Transcription Termination</a></li>
+                    <li><a href="#attenuation-control">5. Attenuation Control</a></li>
+                    <li><a href="#antisense-regulation">6. Antisense Regulation</a></li>
+                    <li><a href="#riboswitch-regulation">7. Riboswitch Regulation</a></li>
+                    <li><a href="#global-regulation">8. Global Regulation</a></li>
                 </ul>
             </div>
             
@@ -265,6 +269,199 @@ graph TD
                     </div>
                 </div>
             </div>
+
+            <!-- Process 5: Attenuation Control -->
+            <div class="process-item" id="attenuation-control">
+                <h3>5. Attenuation Control</h3>
+                <p>Detailed analysis of E. coli Attenuation Control using the Programming Framework, revealing computational logic and regulatory patterns for premature transcription termination.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Leader Peptide Translation
+    A[Leader Peptide Synthesis] --> B[Ribosome Stalling]
+    C[High Amino Acid Levels] --> B
+    D[Low Amino Acid Levels] --> E[Ribosome Pausing]
+    
+    %% RNA Structure Formation
+    B --> F[Terminator Hairpin]
+    F --> G[Transcription Termination]
+    E --> H[Antiterminator Hairpin]
+    H --> I[Transcription Continuation]
+    
+    %% Regulatory Outcome
+    G --> J[Gene Expression Repressed]
+    I --> K[Gene Expression Activated]
+    J --> L[Metabolic Adaptation]
+    K --> L
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#74c0fc,color:#fff
+    style E fill:#74c0fc,color:#fff
+    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:#b197fc,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L 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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 6: Antisense Regulation -->
+            <div class="process-item" id="antisense-regulation">
+                <h3>6. Antisense Regulation</h3>
+                <p>Detailed analysis of E. coli Antisense Regulation using the Programming Framework, revealing computational logic and regulatory patterns for RNA interference.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Antisense RNA Production
+    A[Antisense Promoter] --> B[Antisense RNA Synthesis]
+    C[Environmental Signal] --> A
+    D[Stress Condition] --> A
+    
+    %% RNA-RNA Interaction
+    B --> E[Antisense RNA Binding]
+    E --> F[Target mRNA Recognition]
+    F --> G[RNA-RNA Duplex]
+    G --> H[Ribosome Binding Block]
+    
+    %% Regulatory Outcome
+    H --> I[Translation Inhibition]
+    I --> J[Protein Synthesis Repressed]
+    J --> K[Gene Expression Control]
+    K --> L[Cellular Response]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E fill:#ffd43b,color:#000
+    style F fill:#74c0fc,color:#fff
+    style G fill:#74c0fc,color:#fff
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#b197fc,color:#fff
+    style K fill:#b197fc,color:#fff
+    style L 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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Riboswitch Regulation -->
+            <div class="process-item" id="riboswitch-regulation">
+                <h3>7. Riboswitch Regulation</h3>
+                <p>Detailed analysis of E. coli Riboswitch Regulation using the Programming Framework, revealing computational logic and regulatory patterns for metabolite sensing.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Metabolite Binding
+    A[Metabolite Availability] --> B[Riboswitch Binding]
+    C[High Metabolite] --> B
+    D[Low Metabolite] --> E[No Binding]
+    
+    %% Conformational Change
+    B --> F[Riboswitch Folding]
+    F --> G[Terminator Formation]
+    E --> H[Antiterminator Formation]
+    H --> I[Transcription Continuation]
+    
+    %% Regulatory Outcome
+    G --> J[Transcription Termination]
+    J --> K[Gene Expression Repressed]
+    I --> L[Gene Expression Activated]
+    K --> M[Metabolic Balance]
+    L --> M
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E fill:#74c0fc,color:#fff
+    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:#ffd43b,color:#000
+    style K fill:#b197fc,color:#fff
+    style L fill:#b197fc,color:#fff
+    style M 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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Global Regulation -->
+            <div class="process-item" id="global-regulation">
+                <h3>8. Global Regulation</h3>
+                <p>Detailed analysis of E. coli Global Regulation using the Programming Framework, revealing computational logic and regulatory patterns for coordinated gene expression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Global Signal Detection
+    A[Environmental Change] --> B[Global Regulator Activation]
+    C[Stress Condition] --> B
+    D[Nutrient Availability] --> B
+    E[Growth Phase] --> B
+    
+    %% Regulator Network
+    B --> F[Regulon Activation]
+    F --> G[Multiple Operons]
+    G --> H[Coordinated Expression]
+    H --> I[Metabolic Shift]
+    
+    %% Cellular Response
+    I --> J[Stress Response]
+    J --> K[Adaptation Response]
+    K --> L[Cell Survival]
+    L --> M[Population Fitness]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#74c0fc,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:#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>

ecoli_batch03_translation_protein_synthesis.html

@@ -107,22 +107,26 @@
     <div class="container">
         <div class="header">
             <h1>🦠 E. coli Batch 03: Translation & Protein Synthesis</h1>
-            <p>Programming Framework Analysis - 4 Translation Processes</p>
+            <p>Programming Framework Analysis - 8 Translation Processes</p>
         </div>
         <div class="content">
             <div class="intro">
                 <h2>🦠 Translation & Protein Synthesis Systems</h2>
-                <p><strong>Batch Overview:</strong> This batch contains 4 fundamental E. coli processes responsible for translation and protein synthesis. These processes represent the core computational systems that ensure proper protein production and quality control.</p>
+                <p><strong>Batch Overview:</strong> This batch contains 8 fundamental E. coli processes responsible for translation and protein synthesis. These processes represent the core computational systems that ensure proper protein production and quality control.</p>
                 <p>Each process demonstrates sophisticated biological programming with ribosomal machinery and translational regulation.</p>
             </div>
             
             <div class="toc">
-                <h2>📋 Table of Contents - 4 Translation Processes</h2>
+                <h2>📋 Table of Contents - 8 Translation Processes</h2>
                 <ul>
                     <li><a href="#translation-initiation">1. Translation Initiation</a></li>
                     <li><a href="#translation-elongation">2. Translation Elongation</a></li>
                     <li><a href="#translation-termination">3. Translation Termination</a></li>
                     <li><a href="#protein-folding">4. Protein Folding</a></li>
+                    <li><a href="#ribosome-assembly">5. Ribosome Assembly</a></li>
+                    <li><a href="#tRNA-aminoacylation">6. tRNA Aminoacylation</a></li>
+                    <li><a href="#translation-regulation">7. Translation Regulation</a></li>
+                    <li><a href="#protein-targeting">8. Protein Targeting</a></li>
                 </ul>
             </div>
             
@@ -265,6 +269,201 @@ graph TD
                     </div>
                 </div>
             </div>
+
+            <!-- Process 5: Ribosome Assembly -->
+            <div class="process-item" id="ribosome-assembly">
+                <h3>5. Ribosome Assembly</h3>
+                <p>Detailed analysis of E. coli Ribosome Assembly using the Programming Framework, revealing computational logic and regulatory patterns for ribosomal biogenesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% rRNA Processing
+    A[rRNA Transcription] --> B[rRNA Processing]
+    C[RNase III Cleavage] --> B
+    D[RNase E Processing] --> B
+    B --> E[Mature rRNA]
+    
+    %% Ribosomal Protein Synthesis
+    F[Ribosomal Protein Genes] --> G[Protein Translation]
+    G --> H[Protein Folding]
+    H --> I[Assembly Factors]
+    
+    %% Assembly Process
+    E --> J[30S Assembly]
+    I --> J
+    J --> K[50S Assembly]
+    K --> L[70S Ribosome]
+    L --> M[Functional Ribosome]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E fill:#74c0fc,color:#fff
+    style F fill:#ff6b6b,color:#fff
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#74c0fc,color:#fff
+    style J fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style L fill:#74c0fc,color:#fff
+    style M 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: tRNA Aminoacylation -->
+            <div class="process-item" id="tRNA-aminoacylation">
+                <h3>6. tRNA Aminoacylation</h3>
+                <p>Detailed analysis of E. coli tRNA Aminoacylation using the Programming Framework, revealing computational logic and regulatory patterns for tRNA charging.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% tRNA Recognition
+    A[tRNA Recognition] --> B[Aminoacyl-tRNA Synthetase]
+    C[Anticodon Recognition] --> B
+    D[Acceptor Stem Binding] --> B
+    
+    %% Amino Acid Activation
+    E[Amino Acid] --> F[ATP Binding]
+    F --> G[Aminoacyl-AMP]
+    G --> H[Pyrophosphate Release]
+    
+    %% tRNA Charging
+    H --> I[tRNA Binding]
+    I --> J[Amino Acid Transfer]
+    J --> K[Aminoacyl-tRNA]
+    K --> L[AMP Release]
+    L --> M[Charged tRNA]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E fill:#ff6b6b,color:#fff
+    style F fill:#ffd43b,color:#000
+    style G fill:#74c0fc,color:#fff
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#74c0fc,color:#fff
+    style L fill:#ffd43b,color:#000
+    style M 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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 7: Translation Regulation -->
+            <div class="process-item" id="translation-regulation">
+                <h3>7. Translation Regulation</h3>
+                <p>Detailed analysis of E. coli Translation Regulation using the Programming Framework, revealing computational logic and regulatory patterns for translational control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Regulatory Signals
+    A[Environmental Stress] --> B[ppGpp Synthesis]
+    C[Nutrient Limitation] --> B
+    D[Growth Phase] --> E[Stringent Response]
+    
+    %% Translation Inhibition
+    B --> F[Stringent Factor]
+    F --> G[Translation Inhibition]
+    E --> G
+    G --> H[Ribosome Stalling]
+    
+    %% Regulatory Proteins
+    H --> I[RelA Activation]
+    I --> J[ppGpp Production]
+    J --> K[Gene Expression Shift]
+    K --> L[Stress Adaptation]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E 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:#51cf66,color:#fff
+    style L 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: Protein Targeting -->
+            <div class="process-item" id="protein-targeting">
+                <h3>8. Protein Targeting</h3>
+                <p>Detailed analysis of E. coli Protein Targeting using the Programming Framework, revealing computational logic and regulatory patterns for protein localization.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Signal Sequence Recognition
+    A[Signal Sequence] --> B[Signal Recognition Particle]
+    C[SecA Binding] --> B
+    D[Translocation Complex] --> E[SecYEG Channel]
+    
+    %% Membrane Targeting
+    B --> F[SRP Receptor]
+    F --> G[Translocation Complex]
+    G --> H[Protein Unfolding]
+    H --> I[Membrane Insertion]
+    
+    %% Protein Localization
+    I --> J[Signal Peptidase]
+    J --> K[Signal Cleavage]
+    K --> L[Protein Release]
+    L --> M[Final Localization]
+    
+    %% Styling - Programming Framework Colors
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style D fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style E fill:#74c0fc,color:#fff
+    style F fill:#ffd43b,color:#000
+    style G fill:#74c0fc,color:#fff
+    style H fill:#ffd43b,color:#000
+    style I fill:#51cf66,color:#fff
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#74c0fc,color:#fff
+    style M 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>

ecoli_batch08_motility_chemotaxis.html

@@ -120,13 +120,13 @@
         <div class="content">
             <div class="intro">
                 <h2>Motility & Chemotaxis: Bacterial Navigation, Propulsion, and Environmental Sensing</h2>
-                <p>This batch contains 6 fundamental E. coli processes responsible for bacterial motility, navigation, and environmental sensing. These processes represent the core computational systems that ensure proper bacterial movement, chemotaxis, and environmental adaptation.</p>
+                <p>This batch contains 8 fundamental E. coli processes responsible for bacterial motility, navigation, and environmental sensing. These processes represent the core computational systems that ensure proper bacterial movement, chemotaxis, and environmental adaptation.</p>
                 
                 <p>Each process demonstrates sophisticated biological programming with signal processing, motor control, adaptive behavior, and environmental navigation that functions as a biological guidance and propulsion platform.</p>
             </div>
             
             <div class="toc">
-                <h2>📋 Table of Contents - 6 Motility & Chemotaxis Processes</h2>
+                <h2>📋 Table of Contents - 8 Motility & Chemotaxis Processes</h2>
                 <ul>
                     <li><a href="#chemotaxis">1. Chemotaxis</a></li>
                     <li><a href="#flagellar-assembly">2. Flagellar Assembly</a></li>
@@ -134,6 +134,8 @@
                     <li><a href="#swimming-tumbling">4. Swimming vs Tumbling</a></li>
                     <li><a href="#aerotaxis">5. Aerotaxis</a></li>
                     <li><a href="#ph-taxis">6. pH Taxis</a></li>
+                    <li><a href="#phototaxis">7. Phototaxis</a></li>
+                    <li><a href="#magnetotaxis">8. Magnetotaxis</a></li>
                 </ul>
             </div>
 
@@ -629,6 +631,149 @@ graph TD
                 </div>
             </div>
 
+            <!-- Process 7: Phototaxis -->
+            <div class="process-item" id="phototaxis">
+                <h3>7. Phototaxis</h3>
+                <p>Analysis of bacterial phototaxis demonstrating light sensing, photopigment activation, and light gradient navigation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Light Sensing
+    A[Light Intensity] --> B[Photoreceptor Activation]
+    C[Blue Light] --> D[BLUF Domain]
+    E[Red Light] --> F[Phytochrome]
+    G[UV Light] --> H[UV Receptor]
+    
+    %% Signal Transduction
+    B --> I[Photopigment Conformation]
+    D --> I
+    F --> I
+    H --> I
+    I --> J[Signal Amplification]
+    J --> K[Response Regulator]
+    
+    %% Behavioral Response
+    K --> L{Light Intensity?}
+    L -->|High| M[Light Avoidance]
+    L -->|Low| N[Light Seeking]
+    M --> O[Swimming Away]
+    N --> P[Swimming Toward]
+    
+    %% Navigation
+    O --> Q[Dark Environment]
+    P --> R[Light Environment]
+    Q --> S[Photoprotection]
+    R --> T[Photosynthesis]
+    
+    %% Integration
+    S --> U[Phototaxis]
+    T --> U
+    U --> V[Light 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:#74c0fc,color:#fff
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#74c0fc,color:#fff
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#74c0fc,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style S fill:#b197fc,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:#74c0fc;"></span>Intermediates</span>
+                        <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Process 8: Magnetotaxis -->
+            <div class="process-item" id="magnetotaxis">
+                <h3>8. Magnetotaxis</h3>
+                <p>Analysis of bacterial magnetotaxis demonstrating magnetic field sensing, magnetosome formation, and magnetic navigation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Magnetic Field Detection
+    A[Earth's Magnetic Field] --> B[Magnetosome Chain]
+    C[Magnetic Field Lines] --> D[Magnetosome Alignment]
+    E[Field Strength] --> F[Magnetic Moment]
+    
+    %% Magnetosome Formation
+    G[Magnetosome Genes] --> H[Magnetosome Membrane]
+    H --> I[Iron Transport]
+    I --> J[Iron Oxide Crystallization]
+    J --> K[Magnetite Formation]
+    K --> L[Magnetosome Chain]
+    
+    %% Navigation System
+    L --> M[Magnetic Orientation]
+    M --> N[Swimming Direction]
+    N --> O[North-South Navigation]
+    O --> P[Vertical Migration]
+    
+    %% Environmental Response
+    P --> Q{Optimal Environment?}
+    Q -->|Yes| R[Maintain Position]
+    Q -->|No| S[Seek Better Environment]
+    R --> T[Stable Habitat]
+    S --> U[Environmental Migration]
+    
+    %% Integration
+    T --> V[Magnetotaxis]
+    U --> V
+    V --> W[Magnetic Navigation]
+    
+    %% 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:#74c0fc,color:#fff
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ff6b6b,color:#fff
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#74c0fc,color:#fff
+    style L fill:#74c0fc,color:#fff
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#74c0fc,color:#fff
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    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:#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 E. coli motility and chemotaxis systems</p>