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Yeast_Processes_110_Flowcharts_via_Canvas.html

@@ -119,44 +119,40 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Pyruvate from Glycolysis] --> B[Pyruvate Decarboxylase PDC1] B --> A[Acetaldehyde] A --> D[Alcohol Dehydrogenase ADH1] D --> B[Ethanol] B --> F[NAD+ Regeneration] F --> G[Glycolysis Continuation] G --> H[ATP Production] %% Feedback regulation H --> I[Energy Status Monitoring] I 
-
-    --> J{Energy Sufficient?} J 
-
-    -->|No| 
-K[Continue Fermentation] J 
-
-    -->|Yes| 
-L[Reduce Fermentation] %% Alternative pathways A --> M[Acetaldehyde Dehydrogenase] M --> N[Acetic Acid] N --> O[Acetate Production] %% Key proteins and regulation 
-C[PDC1] --> B 
-D[PDC5] --> B 
-E[ADH1] --> D 
-F[ADH2] --> D 
-G[NAD+] --> F 
-H[ATP] --> H %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
+    A[Pyruvate from Glycolysis] --> B[Pyruvate Decarboxylase PDC1] B --> A[Acetaldehyde] A --> D[Alcohol Dehydrogenase ADH1] D --> B[Ethanol] B --> F[NAD+ Regeneration] F --> G[Glycolysis Continuation] G --> H[ATP Production] %% Feedback regulation H --> I[Energy Status Monitoring] I
+    --> J{Energy Sufficient?} J
+    -->|No|
+    K[Continue Fermentation] J
+    -->|Yes|
+    L[Reduce Fermentation] %% Alternative pathways A --> M[Acetaldehyde Dehydrogenase] M --> N[Acetic Acid] N --> O[Acetate Production] %% Key proteins and regulation
+    C[PDC1] --> B
+    D[PDC5] --> B
+    E[ADH1] --> D
+    F[ADH2] --> D
+    G[NAD+] --> F
+    H[ATP] --> H %% Styling
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#ffd43b,color:#000
-
-    </div>
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+                    </div>
     </div>
     </div><!-- DNA Replication --> <div class="flowchart-item">
         <h4>🧬 DNA Replication Initiation</h4>
@@ -166,56 +162,52 @@ H[ATP] --> H %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Cell Cycle G1 Phase] --> B[Origin Recognition Complex ORC] G --> C[ORC Binding to Origins] H --> D[Cdc6 Recruitment] I --> E[Cdt1 Loading] E --> F[Pre-Replicative Complex Pre-RC] F --> G[Licensing Complete] G 
-
-    --> H{Cell Cycle Checkpoint?} H 
-
-    -->|No| 
-I[G1/S Transition] H 
-
-    -->|Yes| 
-J[G1 Arrest] I --> K[Cdc7-Dbf4 Activation] K --> L[S-Cdk Activation] L --> M[Pre-RC Phosphorylation] M --> N[Helicase Activation] N --> O[DNA Unwinding] O --> P[Replication Fork Formation] P --> Q[DNA Polymerase Loading] Q --> R[Replication Elongation] %% Feedback regulation R --> S[Replication Stress] S --> T[Checkpoint Activation] T --> U[Replication Slowdown] %% Key proteins 
-A[ORC1-6] --> G 
-B[Cdc6] --> I 
-C[Cdt1] --> E 
-D[Mcm2-7] --> F 
-E[Cdc7] --> K F 
-F[Dbf4] --> K G 
-G[S-Cdk] --> L H 
-H[Mcm10] --> N I 
-I[Cdc45] --> N %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
+    A[Cell Cycle G1 Phase] --> B[Origin Recognition Complex ORC] G --> C[ORC Binding to Origins] H --> D[Cdc6 Recruitment] I --> E[Cdt1 Loading] E --> F[Pre-Replicative Complex Pre-RC] F --> G[Licensing Complete] G
+    --> H{Cell Cycle Checkpoint?} H
+    -->|No|
+    I[G1/S Transition] H
+    -->|Yes|
+    J[G1 Arrest] I --> K[Cdc7-Dbf4 Activation] K --> L[S-Cdk Activation] L --> M[Pre-RC Phosphorylation] M --> N[Helicase Activation] N --> O[DNA Unwinding] O --> P[Replication Fork Formation] P --> Q[DNA Polymerase Loading] Q --> R[Replication Elongation] %% Feedback regulation R --> S[Replication Stress] S --> T[Checkpoint Activation] T --> U[Replication Slowdown] %% Key proteins
+    A[ORC1-6] --> G
+    B[Cdc6] --> I
+    C[Cdt1] --> E
+    D[Mcm2-7] --> F
+    E[Cdc7] --> K F
+    F[Dbf4] --> K G
+    G[S-Cdk] --> L H
+    H[Mcm10] --> N I
+    I[Cdc45] --> N %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
     style 
D fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Cell Cycle --> <div class="flowchart-item">
         <h4>🔄 G1/S Transition</h4>
@@ -225,15 +217,14 @@ I[Cdc45] --> N %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Growth Signals] --> B[Cyclin Synthesis] B --> C[CDK Activation] C --> D[Rb Phosphorylation] D --> E[E2F Release] E --> F[S-Phase Genes] F --> G[DNA Replication] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Growth Signals] --> B[Cyclin Synthesis] B --> C[CDK Activation] C --> D[Rb Phosphorylation] D --> E[E2F Release] E --> F[S-Phase Genes] F --> G[DNA Replication] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Translation --> <div class="flowchart-item">
         <h4>📝 Translation Initiation</h4>
@@ -243,15 +234,14 @@ I[Cdc45] --> N %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[mRNA] --> B[eIF4E Binding] B --> C[eIF4G Recruitment] C --> D[40S Ribosome Loading] D --> E[Start Codon Recognition] E --> F[60S Subunit Joining] F --> G[Translation Elongation] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
+    A[mRNA] --> B[eIF4E Binding] B --> C[eIF4G Recruitment] C --> D[40S Ribosome Loading] D --> E[Start Codon Recognition] E --> F[60S Subunit Joining] F --> G[Translation Elongation] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- TORC1 Nutrient Sensing --> <div class="flowchart-item">
         <h4>📡 TORC1 Nutrient Sensing (Detailed)</h4>
@@ -261,56 +251,47 @@ I[Cdc45] --> N %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Availability] --> B[TORC1 Complex] B 
-
-    --> C{High Nutrients?} C 
-
-    -->|Yes| 
-D[Activate TORC1] C 
-
-    -->|No| 
-E[Inhibit TORC1] D --> F[Phosphorylate S6K] D --> G[Phosphorylate 4E-BP] F --> H[Activate Protein Synthesis] G --> I[Release eIF4E] I 
-
-    --> H E --> J[Activate Autophagy] E --> K[Inhibit Protein Synthesis] %% Additional regulatory inputs 
-L[Amino Acids] --> B 
-A[Glucose] --> B 
-B[Oxygen] --> B 
-O[Rheb GTPase] --> D 
-C[AMPK] --> E %% Feedback loops H --> Q[Protein Levels] Q 
-
-    --> R{Protein Sufficient?} R 
-
-    -->|Yes| 
-S[Reduce Synthesis] R 
-
-    -->|No| 
-T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V 
-
-    --> B %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Nutrient Availability] --> B[TORC1 Complex] B
+    --> C{High Nutrients?} C
+    -->|Yes|
+    D[Activate TORC1] C
+    -->|No|
+    E[Inhibit TORC1] D --> F[Phosphorylate S6K] D --> G[Phosphorylate 4E-BP] F --> H[Activate Protein Synthesis] G --> I[Release eIF4E] I
+    --> H E --> J[Activate Autophagy] E --> K[Inhibit Protein Synthesis] %% Additional regulatory inputs
+    L[Amino Acids] --> B
+    A[Glucose] --> B
+    B[Oxygen] --> B
+    O[Rheb GTPase] --> D
+    C[AMPK] --> E %% Feedback loops H --> Q[Protein Levels] Q
+    --> R{Protein Sufficient?} R
+    -->|Yes|
+    S[Reduce Synthesis] R
+    -->|No|
+    T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V
+    --> B %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#74c0fc,color:#fff
-
-    </div>
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+                    </div>
     </div>
     </div><!-- Glycolysis --> <div class="flowchart-item">
         <h4>⚡ Glycolysis (Detailed)</h4>
@@ -320,54 +301,49 @@ T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Glucose] --> B[Hexokinase] B --> C[Glucose-6-Phosphate] K --> D[Phosphoglucose Isomerase] R --> D[Fructose-6-Phosphate] R --> E[Phosphofructokinase-1] E --> F[Fructose-1,6-Bisphosphate] F --> G[Aldolase] G --> H[Glyceraldehyde-3-Phosphate] G --> J[Dihydroxyacetone Phosphate] J --> K[Triose Phosphate Isomerase] K 
-
-    --> H H --> L[Glyceraldehyde-3-Phosphate Dehydrogenase] L --> I[1,3-Bisphosphoglycerate] I --> N[Phosphoglycerate Kinase] N --> J[3-Phosphoglycerate] J --> P[Phosphoglycerate Mutase] P --> K[2-Phosphoglycerate] K --> L[Enolase] L --> M[Phosphoenolpyruvate] M --> T[Pyruvate Kinase] T --> N[Pyruvate] %% Regulatory feedback N --> V[Energy Status] V 
-
-    --> W{Energy Sufficient?} W 
-
-    -->|No| 
-X[Continue Glycolysis] W 
-
-    -->|Yes| 
-Y[Inhibit Glycolysis] %% Key enzymes and regulation 
-O[Hexokinase] --> B P 
-P[PFK-1] --> E B 
-B[Pyruvate Kinase] --> T K 
-Q[ATP] --> V R 
-R[ADP] --> V %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
+    A[Glucose] --> B[Hexokinase] B --> C[Glucose-6-Phosphate] K --> D[Phosphoglucose Isomerase] R --> D[Fructose-6-Phosphate] R --> E[Phosphofructokinase-1] E --> F[Fructose-1,6-Bisphosphate] F --> G[Aldolase] G --> H[Glyceraldehyde-3-Phosphate] G --> J[Dihydroxyacetone Phosphate] J --> K[Triose Phosphate Isomerase] K
+    --> H H --> L[Glyceraldehyde-3-Phosphate Dehydrogenase] L --> I[1,3-Bisphosphoglycerate] I --> N[Phosphoglycerate Kinase] N --> J[3-Phosphoglycerate] J --> P[Phosphoglycerate Mutase] P --> K[2-Phosphoglycerate] K --> L[Enolase] L --> M[Phosphoenolpyruvate] M --> T[Pyruvate Kinase] T --> N[Pyruvate] %% Regulatory feedback N --> V[Energy Status] V
+    --> W{Energy Sufficient?} W
+    -->|No|
+    X[Continue Glycolysis] W
+    -->|Yes|
+    Y[Inhibit Glycolysis] %% Key enzymes and regulation
+    O[Hexokinase] --> B P
+    P[PFK-1] --> E B
+    B[Pyruvate Kinase] --> T K
+    Q[ATP] --> V R
+    R[ADP] --> V %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
     style 
D fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Fatty Acid Synthesis --> <div class="flowchart-item">
         <h4>🔄 Fatty Acid Synthesis (Detailed)</h4>
@@ -377,71 +353,65 @@ R[ADP] --> V %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Acetyl-CoA] --> B[Acetyl-CoA Carboxylase] I --> B[Malonyl-CoA] J --> D[Fatty Acid Synthase] K --> E[Fatty Acid Chain] L --> F[Fatty Acid] %% Additional regulatory mechanisms 
-G[Citrate Activation] --> I 
-H[Palmitoyl-CoA Inhibition] --> I 
-I[ACC Phosphorylation] --> I 
-J[AMPK Regulation] --> I 
-K[Insulin Signaling] --> I 
-L[FAS Complex] --> K 
-M[Acyl Carrier Protein] --> K 
-C[Thioesterase] --> L 
-O[Chain Elongation Cycles] --> L 
-P[Palmitic Acid] --> M 
-Q[Stearic Acid] --> M %% Feedback regulation M --> R[Fatty Acid Levels] R 
-
-    --> S{Sufficient Fatty Acids?} S 
-
-    -->|Yes| 
-T[Inhibit Synthesis] S 
-
-    -->|No| 
-U[Continue Synthesis] T 
-
-    --> H U --> V[Increase ACC Activity] %% Alternative pathways 
-D[Glucose] --> E[Glycolysis] L --> F[Pyruvate] M --> G[Acetyl-CoA] G 
-
-    --> H %% Key enzymes and regulation H 
-H[ACC1] --> I I 
-I[FAS] --> L J 
-J[ACP] --> M K 
-K[AMPK] --> J L 
-L[Insulin] --> K M 
-M[Citrate] --> G %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#ffd43b,color:#000 
-    style 
E fill:#ffd43b,color:#000 
+    A[Acetyl-CoA] --> B[Acetyl-CoA Carboxylase] I --> B[Malonyl-CoA] J --> D[Fatty Acid Synthase] K --> E[Fatty Acid Chain] L --> F[Fatty Acid] %% Additional regulatory mechanisms
+    G[Citrate Activation] --> I
+    H[Palmitoyl-CoA Inhibition] --> I
+    I[ACC Phosphorylation] --> I
+    J[AMPK Regulation] --> I
+    K[Insulin Signaling] --> I
+    L[FAS Complex] --> K
+    M[Acyl Carrier Protein] --> K
+    C[Thioesterase] --> L
+    O[Chain Elongation Cycles] --> L
+    P[Palmitic Acid] --> M
+    Q[Stearic Acid] --> M %% Feedback regulation M --> R[Fatty Acid Levels] R
+    --> S{Sufficient Fatty Acids?} S
+    -->|Yes|
+    T[Inhibit Synthesis] S
+    -->|No|
+    U[Continue Synthesis] T
+    --> H U --> V[Increase ACC Activity] %% Alternative pathways
+    D[Glucose] --> E[Glycolysis] L --> F[Pyruvate] M --> G[Acetyl-CoA] G
+    --> H %% Key enzymes and regulation H
+    H[ACC1] --> I I
+    I[FAS] --> L J
+    J[ACP] --> M K
+    K[AMPK] --> J L
+    L[Insulin] --> K M
+    M[Citrate] --> G %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
+    style 
D fill:#ffd43b,color:#000
+    style 
E fill:#ffd43b,color:#000
     style 
F fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Cell Wall Synthesis --> <div class="flowchart-item">
         <h4>🏗️ Cell Wall Synthesis (Detailed)</h4>
@@ -451,69 +421,60 @@ M[Citrate] --> G %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[UDP-Glucose] --> B[Cellulose Synthase] G --> B[Cellulose] H --> D[Cell Wall Assembly] I --> E[Cell Wall] %% Additional regulatory mechanisms 
-C[Glucose-6-Phosphate] --> G[UDP-Glucose Synthesis] G 
-
-    --> K 
-H[Cell Cycle Signals] --> G 
-I[Chitin Synthesis] --> J[Chitin Fibrils] K[β-Glucan Synthesis] --> L[β-Glucan Chains] D[Mannoproteins] --> N[Protein Glycosylation] N --> O[Mannoprotein Incorporation] J 
-
-    --> I L 
-
-    --> I O 
-
-    --> I %% Quality control mechanisms J --> P[Cell Wall Integrity Check] P 
-
-    --> Q{Wall Integrity OK?} Q 
-
-    -->|Yes| 
-R[Continue Growth] Q 
-
-    -->|No| 
-S[Activate CWI Pathway] S --> T[Repair Mechanisms] T --> U[Additional Synthesis] U 
-
-    --> I %% Cell cycle regulation R --> V[Cell Expansion] V --> W[Bud Formation] W --> X[Septum Formation] X --> Y[Cell Division] %% Key enzymes and regulation 
-E[Chs1] --> I K 
-F[Fks1] --> K G 
-G[Gsc2] --> G H 
-H[Cwp1] --> I I 
-I[Slt2] --> S J 
-J[Pkc1] --> S K 
-K[Rom2] --> S %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#ffd43b,color:#000 
-    style 
E fill:#ffd43b,color:#000 
+    A[UDP-Glucose] --> B[Cellulose Synthase] G --> B[Cellulose] H --> D[Cell Wall Assembly] I --> E[Cell Wall] %% Additional regulatory mechanisms
+    C[Glucose-6-Phosphate] --> G[UDP-Glucose Synthesis] G
+    --> K
+    H[Cell Cycle Signals] --> G
+    I[Chitin Synthesis] --> J[Chitin Fibrils] K[β-Glucan Synthesis] --> L[β-Glucan Chains] D[Mannoproteins] --> N[Protein Glycosylation] N --> O[Mannoprotein Incorporation] J
+    --> I L
+    --> I O
+    --> I %% Quality control mechanisms J --> P[Cell Wall Integrity Check] P
+    --> Q{Wall Integrity OK?} Q
+    -->|Yes|
+    R[Continue Growth] Q
+    -->|No|
+    S[Activate CWI Pathway] S --> T[Repair Mechanisms] T --> U[Additional Synthesis] U
+    --> I %% Cell cycle regulation R --> V[Cell Expansion] V --> W[Bud Formation] W --> X[Septum Formation] X --> Y[Cell Division] %% Key enzymes and regulation
+    E[Chs1] --> I K
+    F[Fks1] --> K G
+    G[Gsc2] --> G H
+    H[Cwp1] --> I I
+    I[Slt2] --> S J
+    J[Pkc1] --> S K
+    K[Rom2] --> S %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
+    style 
D fill:#ffd43b,color:#000
+    style 
E fill:#ffd43b,color:#000
     style 
F fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Transcription Initiation --> <div class="flowchart-item">
         <h4>📄 Transcription Initiation (Detailed)</h4>
@@ -523,77 +484,68 @@ K[Rom2] --> S %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Promoter] --> B[TFIID Binding] B --> C[RNA Polymerase II] C --> D[Transcription Initiation] D --> E[mRNA Synthesis] %% Additional regulatory mechanisms 
-F[TATA Box] --> B 
-G[Initiator Elements] --> B 
-H[CAAT Box] --> I[TFIIB Binding] H 
-
-    --> B 
-J[GC Box] --> K[Sp1 Binding] K 
-
-    --> B 
-B[Enhancers] --> M[Activator Proteins] M 
-
-    --> B 
-C[Silencers] --> O[Repressor Proteins] O --> P[Transcription Inhibition] %% Pre-initiation complex assembly B --> Q[TFIIA Recruitment] Q --> R[TFIIB Recruitment] R --> S[RNA Pol II Recruitment] S --> T[TFIIF Association] T --> U[TFIIE Recruitment] U --> V[TFIIH Recruitment] V --> W[Pre-initiation Complex] W --> X[Promoter Melting] X --> Y[Open Complex Formation] Y 
-
-    --> D %% Quality control mechanisms E --> Z[mRNA Processing] Z 
-
-    --> A 
-A[5' Capping] AA 
-
-    --> B 
-B[3' Polyadenylation] BB 
-
-    --> C 
-C[mRNA Export] CC 
-
-    --> D 
-D[Translation] %% Key proteins and regulation E 
-E[TBP] --> B F 
-F[TAFs] --> B G 
-G[Pol II] --> C G 
-G[CTD] --> GG H 
-H[Mediator] --> M J 
-J[Chromatin Remodeling] --> A %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#b197fc,color:#fff 
-    style 
E 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 
+    A[Promoter] --> B[TFIID Binding] B --> C[RNA Polymerase II] C --> D[Transcription Initiation] D --> E[mRNA Synthesis] %% Additional regulatory mechanisms
+    F[TATA Box] --> B
+    G[Initiator Elements] --> B
+    H[CAAT Box] --> I[TFIIB Binding] H
+    --> B
+    J[GC Box] --> K[Sp1 Binding] K
+    --> B
+    B[Enhancers] --> M[Activator Proteins] M
+    --> B
+    C[Silencers] --> O[Repressor Proteins] O --> P[Transcription Inhibition] %% Pre-initiation complex assembly B --> Q[TFIIA Recruitment] Q --> R[TFIIB Recruitment] R --> S[RNA Pol II Recruitment] S --> T[TFIIF Association] T --> U[TFIIE Recruitment] U --> V[TFIIH Recruitment] V --> W[Pre-initiation Complex] W --> X[Promoter Melting] X --> Y[Open Complex Formation] Y
+    --> D %% Quality control mechanisms E --> Z[mRNA Processing] Z
+    --> A
+    A[5' Capping] AA
+    --> B
+    B[3' Polyadenylation] BB
+    --> C
+    C[mRNA Export] CC
+    --> D
+    D[Translation] %% Key proteins and regulation E
+    E[TBP] --> B F
+    F[TAFs] --> B G
+    G[Pol II] --> C G
+    G[CTD] --> GG H
+    H[Mediator] --> M J
+    J[Chromatin Remodeling] --> A %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
+    style 
D fill:#b197fc,color:#fff
+    style 
E 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:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- RNA Splicing --> <div class="flowchart-item">
         <h4>✂️ RNA Splicing (Detailed)</h4>
@@ -603,104 +555,90 @@ J[Chromatin Remodeling] --> A %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Pre-mRNA] --> B[Spliceosome Assembly] B --> C[Intron Recognition] C --> D[Splicing Reaction] D --> E[Mature mRNA] %% Additional regulatory mechanisms 
-F[5' Splice Site] --> C 
-G[3' Splice Site] --> C 
-H[Branch Point] --> C 
-I[Polypyrimidine Tract] --> C 
-J[U1 snRNP] --> K[5' SS Recognition] E 
-
-    --> B 
-B[U2AF] --> M[3' SS Recognition] G 
-
-    --> B 
-N[U2 snRNP] --> O[Branch Point Recognition] I 
-
-    --> B 
-P[U4/U6•U5 snRNP] --> Q[Catalytic Core Assembly] J 
-
-    --> B 
-C[Prp8] --> J 
-D[Prp2] --> J %% Splicing reaction steps B --> T[Spliceosome Activation] T --> U[First Transesterification] U --> V[Lariat Formation] V --> W[Second Transesterification] W --> X[Exon Ligation] X --> Y[Intron Release] Y 
-
-    --> D %% Quality control mechanisms E --> Z[mRNA Quality Check] Z 
-
-    --> AA{Splicing Correct?} AA 
-
-    -->|Yes| B 
-B[mRNA Export] AA 
-
-    -->|No| C 
-C[Nonsense-Mediated Decay] %% Alternative splicing D 
-D[Splicing Regulators] --> E 
-E[Alternative 5' SS] EE 
-
-    --> F 
-F[Isoform 1] DD 
-
-    --> G 
-G[Alternative 3' SS] GG 
-
-    --> H 
-H[Isoform 2] DD 
-
-    --> I 
-I[Exon Skipping] II 
-
-    --> J 
-J[Isoform 3] %% Key proteins and regulation E 
-E[U1] --> J F 
-F[U2AF65] --> F G 
-G[U2AF35] --> F H 
-H[U2] --> H I 
-I[U4/U6•U5] --> P P 
-P[SR Proteins] --> DD J 
-J[hnRNPs] --> DD %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
A fill:#74c0fc,color:#fff 
-    style 
B fill:#b197fc,color:#fff 
-    style 
C fill:#b197fc,color:#fff 
-    style 
D fill:#ffd43b,color:#000 
-    style 
E fill:#ff6b6b,color:#fff 
-    style 
F fill:#b197fc,color:#fff 
-    style 
G fill:#ff6b6b,color:#fff 
-    style 
H fill:#b197fc,color:#fff 
-    style 
I fill:#ffd43b,color:#000 
-    style 
J fill:#b197fc,color:#fff 
-    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 
+    A[Pre-mRNA] --> B[Spliceosome Assembly] B --> C[Intron Recognition] C --> D[Splicing Reaction] D --> E[Mature mRNA] %% Additional regulatory mechanisms
+    F[5' Splice Site] --> C
+    G[3' Splice Site] --> C
+    H[Branch Point] --> C
+    I[Polypyrimidine Tract] --> C
+    J[U1 snRNP] --> K[5' SS Recognition] E
+    --> B
+    B[U2AF] --> M[3' SS Recognition] G
+    --> B
+    N[U2 snRNP] --> O[Branch Point Recognition] I
+    --> B
+    P[U4/U6•U5 snRNP] --> Q[Catalytic Core Assembly] J
+    --> B
+    C[Prp8] --> J
+    D[Prp2] --> J %% Splicing reaction steps B --> T[Spliceosome Activation] T --> U[First Transesterification] U --> V[Lariat Formation] V --> W[Second Transesterification] W --> X[Exon Ligation] X --> Y[Intron Release] Y
+    --> D %% Quality control mechanisms E --> Z[mRNA Quality Check] Z
+    --> AA{Splicing Correct?} AA
+    -->|Yes| B
+    B[mRNA Export] AA
+    -->|No| C
+    C[Nonsense-Mediated Decay] %% Alternative splicing D
+    D[Splicing Regulators] --> E
+    E[Alternative 5' SS] EE
+    --> F
+    F[Isoform 1] DD
+    --> G
+    G[Alternative 3' SS] GG
+    --> H
+    H[Isoform 2] DD
+    --> I
+    I[Exon Skipping] II
+    --> J
+    J[Isoform 3] %% Key proteins and regulation E
+    E[U1] --> J F
+    F[U2AF65] --> F G
+    G[U2AF35] --> F H
+    H[U2] --> H I
+    I[U4/U6•U5] --> P P
+    P[SR Proteins] --> DD J
+    J[hnRNPs] --> DD %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
A fill:#74c0fc,color:#fff
+    style 
B fill:#b197fc,color:#fff
+    style 
C fill:#b197fc,color:#fff
+    style 
D fill:#ffd43b,color:#000
+    style 
E fill:#ff6b6b,color:#fff
+    style 
F fill:#b197fc,color:#fff
+    style 
G fill:#ff6b6b,color:#fff
+    style 
H fill:#b197fc,color:#fff
+    style 
I fill:#ffd43b,color:#000
+    style 
J fill:#b197fc,color:#fff
+    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:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Heat Shock Response --> <div class="flowchart-item">
         <h4>🔥 Heat Shock Response (Detailed)</h4>
@@ -710,44 +648,40 @@ J[hnRNPs] --> DD %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Heat Stress] --> B[HSF1 Activation] B --> C[HSF1 Trimerization] C --> D[HSF1 Phosphorylation] D --> E[HSF1 Nuclear Localization] E --> F[HSF1 Binding to HSE] F --> G[HSP Gene Transcription] G --> H[HSP Protein Synthesis] H --> I[Protein Refolding] I --> J[Cell Survival] %% Additional regulatory mechanisms 
-K[Protein Misfolding] --> A 
-L[HSF1 Inhibitors] --> B 
-A[HSP90] --> D 
-B[HSP70] --> I 
-C[HSP60] --> I %% Feedback regulation I --> P[Protein Quality] P 
-
-    --> Q{Proteins Refolded?} Q 
-
-    -->|Yes| 
-R[Reduce HSP Synthesis] Q 
-
-    -->|No| 
-S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization] T --> U[HSF1 Deactivation] U --> V[Return to Normal State] %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
+    A[Heat Stress] --> B[HSF1 Activation] B --> C[HSF1 Trimerization] C --> D[HSF1 Phosphorylation] D --> E[HSF1 Nuclear Localization] E --> F[HSF1 Binding to HSE] F --> G[HSP Gene Transcription] G --> H[HSP Protein Synthesis] H --> I[Protein Refolding] I --> J[Cell Survival] %% Additional regulatory mechanisms
+    K[Protein Misfolding] --> A
+    L[HSF1 Inhibitors] --> B
+    A[HSP90] --> D
+    B[HSP70] --> I
+    C[HSP60] --> I %% Feedback regulation I --> P[Protein Quality] P
+    --> Q{Proteins Refolded?} Q
+    -->|Yes|
+    R[Reduce HSP Synthesis] Q
+    -->|No|
+    S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization] T --> U[HSF1 Deactivation] U --> V[Return to Normal State] %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+                    </div>
     </div>
     </div><!-- Autophagy Initiation --> <div class="flowchart-item">
         <h4>🔄 Autophagy Initiation (Detailed)</h4>
@@ -757,49 +691,45 @@ S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Deprivation] --> B[TORC1 Inhibition] B --> C[Atg1 Complex Activation] C --> D[Phosphorylation of Atg13] D --> E[Atg1-Atg13 Complex Formation] E --> F[Vps34 Complex Activation] F --> G[PI3P Production] G --> H[Phagophore Formation] H --> I[Atg8 Conjugation] I --> J[Autophagosome Formation] J --> K[Cargo Degradation] %% Additional regulatory inputs 
-L[Energy Status] --> A 
-M[Growth Factors] --> B 
-A[Atg1] --> C 
-B[Atg13] --> D 
-C[Vps34] --> F 
-D[Atg8] --> I %% Quality control mechanisms K --> R[Autophagosome Maturation] R --> S[Lysosome Fusion] S --> T[Content Degradation] T --> U[Nutrient Recycling] U --> V[Cell Survival] %% Feedback regulation V --> W[Nutrient Levels] W 
-
-    --> X{Sufficient Nutrients?} X 
-
-    -->|Yes| 
-Y[Inhibit Autophagy] X 
-
-    -->|No| 
-Z[Continue Autophagy] %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
+    A[Nutrient Deprivation] --> B[TORC1 Inhibition] B --> C[Atg1 Complex Activation] C --> D[Phosphorylation of Atg13] D --> E[Atg1-Atg13 Complex Formation] E --> F[Vps34 Complex Activation] F --> G[PI3P Production] G --> H[Phagophore Formation] H --> I[Atg8 Conjugation] I --> J[Autophagosome Formation] J --> K[Cargo Degradation] %% Additional regulatory inputs
+    L[Energy Status] --> A
+    M[Growth Factors] --> B
+    A[Atg1] --> C
+    B[Atg13] --> D
+    C[Vps34] --> F
+    D[Atg8] --> I %% Quality control mechanisms K --> R[Autophagosome Maturation] R --> S[Lysosome Fusion] S --> T[Content Degradation] T --> U[Nutrient Recycling] U --> V[Cell Survival] %% Feedback regulation V --> W[Nutrient Levels] W
+    --> X{Sufficient Nutrients?} X
+    -->|Yes|
+    Y[Inhibit Autophagy] X
+    -->|No|
+    Z[Continue Autophagy] %% Styling
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#ffd43b,color:#000
-
-    </div>
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+                    </div>
     </div>
     </div><!-- Histone Modification --> <div class="flowchart-item">
         <h4>🎛️ Histone Modification (Detailed)</h4>
@@ -809,62 +739,58 @@ Z[Continue Autophagy] %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[DNA Damage] --> B[Histone Kinases] G --> C[Histone Phosphorylation] C --> D[Chromatin Remodeling] D --> E[DNA Repair] %% Additional regulatory mechanisms 
-F[DNA Damage Sensors] --> F 
-G[ATM/ATR Kinases] --> G 
-H[Histone H2AX] --> C 
-I[γ-H2AX Formation] --> C 
-J[MDC1 Recruitment] --> I 
-K[53BP1 Binding] --> J 
-L[BRCA1 Recruitment] --> K 
-M[DNA Repair Complex Assembly] --> L 
-N[Double Strand Break Repair] --> M 
-O[Chromatin Restoration] --> N %% Quality control mechanisms O --> P[Repair Verification] P 
-
-    --> Q{Repair Successful?} Q 
-
-    -->|Yes| 
-R[Cell Survival] Q 
-
-    -->|No| 
-S[Additional Repair Attempts] S --> T[Alternative Repair Pathways] T --> U[Apoptosis if Failed] %% Key proteins and regulation 
-A[ATM] --> G 
-B[ATR] --> G 
-C[H2AX] --> H 
-D[MDC1] --> J 
-E[53BP1] --> K F 
-F[BRCA1] --> L G 
-G[Rad51] --> M %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
+    A[DNA Damage] --> B[Histone Kinases] G --> C[Histone Phosphorylation] C --> D[Chromatin Remodeling] D --> E[DNA Repair] %% Additional regulatory mechanisms
+    F[DNA Damage Sensors] --> F
+    G[ATM/ATR Kinases] --> G
+    H[Histone H2AX] --> C
+    I[γ-H2AX Formation] --> C
+    J[MDC1 Recruitment] --> I
+    K[53BP1 Binding] --> J
+    L[BRCA1 Recruitment] --> K
+    M[DNA Repair Complex Assembly] --> L
+    N[Double Strand Break Repair] --> M
+    O[Chromatin Restoration] --> N %% Quality control mechanisms O --> P[Repair Verification] P
+    --> Q{Repair Successful?} Q
+    -->|Yes|
+    R[Cell Survival] Q
+    -->|No|
+    S[Additional Repair Attempts] S --> T[Alternative Repair Pathways] T --> U[Apoptosis if Failed] %% Key proteins and regulation
+    A[ATM] --> G
+    B[ATR] --> G
+    C[H2AX] --> H
+    D[MDC1] --> J
+    E[53BP1] --> K F
+    F[BRCA1] --> L G
+    G[Rad51] --> M %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
     style 
B fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Osmotic Stress Adaptation --> <div class="flowchart-item">
         <h4>💧 Osmotic Stress Adaptation (Detailed)</h4>
@@ -874,67 +800,63 @@ G[Rad51] --> M %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[High Osmolarity] --> B[HOG1 MAPK Pathway] G --> C[Glycerol Biosynthesis] G --> D[Intracellular Glycerol] G --> E[Osmotic Balance] G --> F[Cell Survival] %% Additional regulatory mechanisms 
-G[Osmolarity Sensors] --> G 
-H[Sln1 Sensor] --> G 
-I[Msb2 Sensor] --> G 
-J[Ste20 PAK] --> G 
-K[Pbs2 MAPKK] --> G 
-L[Hog1 MAPK] --> G 
-M[Gpd1 Activation] --> G 
-N[Gpd2 Activation] --> G 
-O[Glycerol Transport] --> G 
-P[Glycerol Channels] --> O %% Feedback regulation G --> Q[Osmolarity Monitoring] Q 
-
-    --> R{Osmolarity Normal?} R 
-
-    -->|Yes| 
-S[Reduce Glycerol Production] R 
-
-    -->|No| 
-T[Continue Adaptation] %% Alternative pathways 
-U[Low Osmolarity] --> V[Hog1 Inactivation] V --> W[Glycerol Export] W --> X[Cell Shrinkage] X --> Y[Osmotic Balance] %% Key proteins and regulation 
-A[Sln1] --> H G 
-B[Msb2] --> I G 
-C[Ste20] --> J G 
-D[Pbs2] --> K G 
-E[Hog1] --> L G 
-F[Gpd1] --> M G 
-G[Gpd2] --> N %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#ffd43b,color:#000 
-    style 
E fill:#ffd43b,color:#000 
+    A[High Osmolarity] --> B[HOG1 MAPK Pathway] G --> C[Glycerol Biosynthesis] G --> D[Intracellular Glycerol] G --> E[Osmotic Balance] G --> F[Cell Survival] %% Additional regulatory mechanisms
+    G[Osmolarity Sensors] --> G
+    H[Sln1 Sensor] --> G
+    I[Msb2 Sensor] --> G
+    J[Ste20 PAK] --> G
+    K[Pbs2 MAPKK] --> G
+    L[Hog1 MAPK] --> G
+    M[Gpd1 Activation] --> G
+    N[Gpd2 Activation] --> G
+    O[Glycerol Transport] --> G
+    P[Glycerol Channels] --> O %% Feedback regulation G --> Q[Osmolarity Monitoring] Q
+    --> R{Osmolarity Normal?} R
+    -->|Yes|
+    S[Reduce Glycerol Production] R
+    -->|No|
+    T[Continue Adaptation] %% Alternative pathways
+    U[Low Osmolarity] --> V[Hog1 Inactivation] V --> W[Glycerol Export] W --> X[Cell Shrinkage] X --> Y[Osmotic Balance] %% Key proteins and regulation
+    A[Sln1] --> H G
+    B[Msb2] --> I G
+    C[Ste20] --> J G
+    D[Pbs2] --> K G
+    E[Hog1] --> L G
+    F[Gpd1] --> M G
+    G[Gpd2] --> N %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
+    style 
D fill:#ffd43b,color:#000
+    style 
E fill:#ffd43b,color:#000
     style 
F fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Sporulation --> <div class="flowchart-item">
         <h4>🌱 Sporulation (Detailed)</h4>
@@ -944,78 +866,72 @@ G[Gpd2] --> N %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Limitation] --> B[Meiosis Initiation] B --> C[Haploid Nuclei] A --> D[Spore Formation] B --> E[Mature Spores] E --> F[Spore Dormancy] %% Additional regulatory mechanisms 
-G[Glucose Depletion] --> A 
-H[Nitrogen Limitation] --> A 
-I[Ime1 Transcription Factor] --> B 
-J[Ime2 Kinase] --> B 
-K[Meiotic Genes Activation] --> B 
-L[DNA Replication] --> A 
-M[Meiotic Recombination] --> A 
-N[Chromosome Segregation] --> A 
-O[Spore Wall Assembly] --> B 
-P[Spore Coat Formation] --> B 
-Q[Trehalose Accumulation] --> E 
-R[Spore Maturation] --> E 
-S[Environmental Sensing] --> F 
-T[Germination Signals] --> F %% Quality control mechanisms F --> U[Spore Viability Check] U 
-
-    --> V{Spores Viable?} V 
-
-    -->|Yes| 
-W[Maintain Dormancy] V 
-
-    -->|No| 
-X[Spore Death] %% Alternative pathways 
-Y[Rich Medium] --> Z[Return to Vegetative Growth] Z 
-
-    --> A 
-A[Cell Division] AA 
-
-    --> B 
-B[Colony Formation] %% Key proteins and regulation A 
-A[Ime1] --> I B 
-B[Ime2] --> J E 
-E[Meiotic Genes] --> K F 
-F[Spore Wall Proteins] --> O G 
-G[Trehalose Synthase] --> Q H 
-H[Germination Factors] --> T %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#b197fc,color:#fff 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#ffd43b,color:#000 
-    style 
E fill:#ffd43b,color:#000 
-    style 
F fill:#ffd43b,color:#000 
-    style 
G fill:#ffd43b,color:#000 
+    A[Nutrient Limitation] --> B[Meiosis Initiation] B --> C[Haploid Nuclei] A --> D[Spore Formation] B --> E[Mature Spores] E --> F[Spore Dormancy] %% Additional regulatory mechanisms
+    G[Glucose Depletion] --> A
+    H[Nitrogen Limitation] --> A
+    I[Ime1 Transcription Factor] --> B
+    J[Ime2 Kinase] --> B
+    K[Meiotic Genes Activation] --> B
+    L[DNA Replication] --> A
+    M[Meiotic Recombination] --> A
+    N[Chromosome Segregation] --> A
+    O[Spore Wall Assembly] --> B
+    P[Spore Coat Formation] --> B
+    Q[Trehalose Accumulation] --> E
+    R[Spore Maturation] --> E
+    S[Environmental Sensing] --> F
+    T[Germination Signals] --> F %% Quality control mechanisms F --> U[Spore Viability Check] U
+    --> V{Spores Viable?} V
+    -->|Yes|
+    W[Maintain Dormancy] V
+    -->|No|
+    X[Spore Death] %% Alternative pathways
+    Y[Rich Medium] --> Z[Return to Vegetative Growth] Z
+    --> A
+    A[Cell Division] AA
+    --> B
+    B[Colony Formation] %% Key proteins and regulation A
+    A[Ime1] --> I B
+    B[Ime2] --> J E
+    E[Meiotic Genes] --> K F
+    F[Spore Wall Proteins] --> O G
+    G[Trehalose Synthase] --> Q H
+    H[Germination Factors] --> T %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#b197fc,color:#fff
+    style 
C fill:#ffd43b,color:#000
+    style 
D 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:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- Base Excision Repair --> <div class="flowchart-item">
         <h4>🔧 Base Excision Repair (Detailed)</h4>
@@ -1025,85 +941,78 @@ H[Germination Factors] --> T %% Styling
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Damaged Base] --> B[DNA Glycosylase] B --> C[AP Site] C --> D[DNA Polymerase] A --> E[DNA Ligase] B --> F[Repaired DNA] %% Additional regulatory mechanisms 
-G[Oxidative Damage] --> A 
-H[Alkylation Damage] --> A 
-I[Deamination Damage] --> A 
-J[Ung1 Glycosylase] --> B 
-K[Ogg1 Glycosylase] --> B 
-L[Mag1 Glycosylase] --> B 
-M[AP Endonuclease] --> C 
-N[AP Lyase] --> C 
-O[DNA Polymerase β] --> A 
-P[DNA Polymerase δ] --> A 
-Q[DNA Polymerase ε] --> A 
-R[DNA Ligase I] --> B 
-S[DNA Ligase III] --> B %% Quality control mechanisms C --> T[Repair Verification] T 
-
-    --> U{Repair Successful?} U 
-
-    -->|Yes| 
-V[Cell Survival] U 
-
-    -->|No| 
-W[Additional Repair Attempts] W --> X[Alternative Repair Pathways] X --> Y[Apoptosis if Failed] %% Feedback regulation V --> Z[DNA Damage Monitoring] Z 
-
-    --> AA{More Damage?} AA 
-
-    -->|Yes| B 
-B[Continue Repair] AA 
-
-    -->|No| C 
-C[Return to Normal] %% Key proteins and regulation A 
-A[Ung1] --> J B 
-B[Ogg1] --> E C 
-C[Mag1] --> F D 
-D[APE1] --> M H 
-H[Pol β] --> O I 
-I[Pol δ] --> P J 
-J[Pol ε] --> Q E 
-E[Lig1] --> R F 
-F[Lig3] --> S %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
A fill:#74c0fc,color:#fff 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#b197fc,color:#fff 
-    style 
D 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:#ffd43b,color:#000 
-    style 
I fill:#ffd43b,color:#000 
-    style 
J fill:#ffd43b,color:#000 
-    style 
K fill:#ffd43b,color:#000 
+    A[Damaged Base] --> B[DNA Glycosylase] B --> C[AP Site] C --> D[DNA Polymerase] A --> E[DNA Ligase] B --> F[Repaired DNA] %% Additional regulatory mechanisms
+    G[Oxidative Damage] --> A
+    H[Alkylation Damage] --> A
+    I[Deamination Damage] --> A
+    J[Ung1 Glycosylase] --> B
+    K[Ogg1 Glycosylase] --> B
+    L[Mag1 Glycosylase] --> B
+    M[AP Endonuclease] --> C
+    N[AP Lyase] --> C
+    O[DNA Polymerase β] --> A
+    P[DNA Polymerase δ] --> A
+    Q[DNA Polymerase ε] --> A
+    R[DNA Ligase I] --> B
+    S[DNA Ligase III] --> B %% Quality control mechanisms C --> T[Repair Verification] T
+    --> U{Repair Successful?} U
+    -->|Yes|
+    V[Cell Survival] U
+    -->|No|
+    W[Additional Repair Attempts] W --> X[Alternative Repair Pathways] X --> Y[Apoptosis if Failed] %% Feedback regulation V --> Z[DNA Damage Monitoring] Z
+    --> AA{More Damage?} AA
+    -->|Yes| B
+    B[Continue Repair] AA
+    -->|No| C
+    C[Return to Normal] %% Key proteins and regulation A
+    A[Ung1] --> J B
+    B[Ogg1] --> E C
+    C[Mag1] --> F D
+    D[APE1] --> M H
+    H[Pol β] --> O I
+    I[Pol δ] --> P J
+    J[Pol ε] --> Q E
+    E[Lig1] --> R F
+    F[Lig3] --> S %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
A fill:#74c0fc,color:#fff
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#b197fc,color:#fff
+    style 
D 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:#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
-
-    </div>
+                    </div>
     </div>
     </div>
     </div>

Yeast_Processes_as_Programs.html

@@ -73,44 +73,40 @@
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Pyruvate from Glycolysis] --> B[Pyruvate Decarboxylase PDC1] B --> A[Acetaldehyde] A --> D[Alcohol Dehydrogenase ADH1] D --> B[Ethanol] B --> F[NAD+ Regeneration] F --> G[Glycolysis Continuation] G --> H[ATP Production] %% Feedback regulation H --> I[Energy Status Monitoring] I 
-
-    --> J{Energy Sufficient?} J 
-
-    -->|No| 
-K[Continue Fermentation] J 
-
-    -->|Yes| 
-L[Reduce Fermentation] %% Alternative pathways A --> M[Acetaldehyde Dehydrogenase] M --> N[Acetic Acid] N --> O[Acetate Production] %% Key proteins and regulation 
-C[PDC1] --> B 
-D[PDC5] --> B 
-E[ADH1] --> D 
-F[ADH2] --> D 
-G[NAD+] --> F 
-H[ATP] --> H %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
+    A[Pyruvate from Glycolysis] --> B[Pyruvate Decarboxylase PDC1] B --> A[Acetaldehyde] A --> D[Alcohol Dehydrogenase ADH1] D --> B[Ethanol] B --> F[NAD+ Regeneration] F --> G[Glycolysis Continuation] G --> H[ATP Production] %% Feedback regulation H --> I[Energy Status Monitoring] I
+    --> J{Energy Sufficient?} J
+    -->|No|
+    K[Continue Fermentation] J
+    -->|Yes|
+    L[Reduce Fermentation] %% Alternative pathways A --> M[Acetaldehyde Dehydrogenase] M --> N[Acetic Acid] N --> O[Acetate Production] %% Key proteins and regulation
+    C[PDC1] --> B
+    D[PDC5] --> B
+    E[ADH1] --> D
+    F[ADH2] --> D
+    G[NAD+] --> F
+    H[ATP] --> H %% Styling
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#ffd43b,color:#000
-
-    </div>
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+                    </div>
     </div>
     </div><!-- DNA Replication --> <div class="process-showcase">
         <h3>
@@ -125,56 +121,52 @@ H[ATP] --> H %% Styling
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Cell Cycle G1 Phase] --> B[Origin Recognition Complex ORC] G --> C[ORC Binding to Origins] H --> D[Cdc6 Recruitment] I --> E[Cdt1 Loading] E --> F[Pre-Replicative Complex Pre-RC] F --> G[Licensing Complete] G 
-
-    --> H{Cell Cycle Checkpoint?} H 
-
-    -->|No| 
-I[G1/S Transition] H 
-
-    -->|Yes| 
-J[G1 Arrest] I --> K[Cdc7-Dbf4 Activation] K --> L[S-Cdk Activation] L --> M[Pre-RC Phosphorylation] M --> N[Helicase Activation] N --> O[DNA Unwinding] O --> P[Replication Fork Formation] P --> Q[DNA Polymerase Loading] Q --> R[Replication Elongation] %% Feedback regulation R --> S[Replication Stress] S --> T[Checkpoint Activation] T --> U[Replication Slowdown] %% Key proteins 
-A[ORC1-6] --> G 
-B[Cdc6] --> I 
-C[Cdt1] --> E 
-D[Mcm2-7] --> F 
-E[Cdc7] --> K F 
-F[Dbf4] --> K G 
-G[S-Cdk] --> L H 
-H[Mcm10] --> N I 
-I[Cdc45] --> N %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
+    A[Cell Cycle G1 Phase] --> B[Origin Recognition Complex ORC] G --> C[ORC Binding to Origins] H --> D[Cdc6 Recruitment] I --> E[Cdt1 Loading] E --> F[Pre-Replicative Complex Pre-RC] F --> G[Licensing Complete] G
+    --> H{Cell Cycle Checkpoint?} H
+    -->|No|
+    I[G1/S Transition] H
+    -->|Yes|
+    J[G1 Arrest] I --> K[Cdc7-Dbf4 Activation] K --> L[S-Cdk Activation] L --> M[Pre-RC Phosphorylation] M --> N[Helicase Activation] N --> O[DNA Unwinding] O --> P[Replication Fork Formation] P --> Q[DNA Polymerase Loading] Q --> R[Replication Elongation] %% Feedback regulation R --> S[Replication Stress] S --> T[Checkpoint Activation] T --> U[Replication Slowdown] %% Key proteins
+    A[ORC1-6] --> G
+    B[Cdc6] --> I
+    C[Cdt1] --> E
+    D[Mcm2-7] --> F
+    E[Cdc7] --> K F
+    F[Dbf4] --> K G
+    G[S-Cdk] --> L H
+    H[Mcm10] --> N I
+    I[Cdc45] --> N %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
     style 
D fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- G1/S Transition --> <div class="process-showcase">
         <h3>
@@ -189,58 +181,53 @@ I[Cdc45] --> N %% Styling
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Growth Signals] --> B[Cyclin D Synthesis] B --> C[CDK4/6 Activation] C --> D[Rb Phosphorylation] D --> E[E2F Release] E --> F[S-Phase Gene Expression] F --> G[Cyclin E Synthesis] G --> H[CDK2 Activation] H --> I[G1/S Transition] I --> J[DNA Replication Initiation] %% Checkpoint mechanisms 
-K[DNA Damage] --> L[p53 Activation] L --> M[p21 Induction] M --> N[CDK Inhibition] N --> O[G1 Arrest] %% Growth factor dependency 
-P[Growth Factor Withdrawal] --> Q[Cyclin D Degradation] Q --> R[CDK Inactivation] R --> S[Rb Hypophosphorylation] S --> T[E2F Sequestration] T --> U[Cell Cycle Exit] %% Quality control J --> V[Replication Licensing Check] V 
-
-    --> W{All Origins Licensed?} W 
-
-    -->|Yes| 
-X[Proceed to S Phase] W 
-
-    -->|No| 
-Y[Licensing Repair] Y 
-
-    --> V %% Key regulators 
-Z[Cyclin D] --> B A 
-A[CDK4/6] --> C B 
-B[Rb] --> D C 
-C[E2F] --> E D 
-D[p53] --> L E 
-E[p21] --> M %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
A fill:#ffd43b,color:#000 
-    style 
B fill:#ffd43b,color:#000 
-    style 
C fill:#ffd43b,color:#000 
-    style 
D fill:#ffd43b,color:#000 
+    A[Growth Signals] --> B[Cyclin D Synthesis] B --> C[CDK4/6 Activation] C --> D[Rb Phosphorylation] D --> E[E2F Release] E --> F[S-Phase Gene Expression] F --> G[Cyclin E Synthesis] G --> H[CDK2 Activation] H --> I[G1/S Transition] I --> J[DNA Replication Initiation] %% Checkpoint mechanisms
+    K[DNA Damage] --> L[p53 Activation] L --> M[p21 Induction] M --> N[CDK Inhibition] N --> O[G1 Arrest] %% Growth factor dependency
+    P[Growth Factor Withdrawal] --> Q[Cyclin D Degradation] Q --> R[CDK Inactivation] R --> S[Rb Hypophosphorylation] S --> T[E2F Sequestration] T --> U[Cell Cycle Exit] %% Quality control J --> V[Replication Licensing Check] V
+    --> W{All Origins Licensed?} W
+    -->|Yes|
+    X[Proceed to S Phase] W
+    -->|No|
+    Y[Licensing Repair] Y
+    --> V %% Key regulators
+    Z[Cyclin D] --> B A
+    A[CDK4/6] --> C B
+    B[Rb] --> D C
+    C[E2F] --> E D
+    D[p53] --> L E
+    E[p21] --> M %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
A fill:#ffd43b,color:#000
+    style 
B fill:#ffd43b,color:#000
+    style 
C fill:#ffd43b,color:#000
+    style 
D fill:#ffd43b,color:#000
     style 
E fill:#ffd43b,color:#000
-
-    </div>
+                    </div>
     </div>
     </div><!-- TORC1 Nutrient Sensing --> <div class="process-showcase">
         <h3>
@@ -255,56 +242,47 @@ E[p21] --> M %% Styling
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Availability] --> B[TORC1 Complex] B 
-
-    --> C{High Nutrients?} C 
-
-    -->|Yes| 
-D[Activate TORC1] C 
-
-    -->|No| 
-E[Inhibit TORC1] D --> F[Phosphorylate S6K] D --> G[Phosphorylate 4E-BP] F --> H[Activate Protein Synthesis] G --> I[Release eIF4E] I 
-
-    --> H E --> J[Activate Autophagy] E --> K[Inhibit Protein Synthesis] %% Additional regulatory inputs 
-L[Amino Acids] --> B 
-A[Glucose] --> B 
-B[Oxygen] --> B 
-O[Rheb GTPase] --> D 
-C[AMPK] --> E %% Feedback loops H --> Q[Protein Levels] Q 
-
-    --> R{Protein Sufficient?} R 
-
-    -->|Yes| 
-S[Reduce Synthesis] R 
-
-    -->|No| 
-T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V 
-
-    --> B %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Nutrient Availability] --> B[TORC1 Complex] B
+    --> C{High Nutrients?} C
+    -->|Yes|
+    D[Activate TORC1] C
+    -->|No|
+    E[Inhibit TORC1] D --> F[Phosphorylate S6K] D --> G[Phosphorylate 4E-BP] F --> H[Activate Protein Synthesis] G --> I[Release eIF4E] I
+    --> H E --> J[Activate Autophagy] E --> K[Inhibit Protein Synthesis] %% Additional regulatory inputs
+    L[Amino Acids] --> B
+    A[Glucose] --> B
+    B[Oxygen] --> B
+    O[Rheb GTPase] --> D
+    C[AMPK] --> E %% Feedback loops H --> Q[Protein Levels] Q
+    --> R{Protein Sufficient?} R
+    -->|Yes|
+    S[Reduce Synthesis] R
+    -->|No|
+    T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V
+    --> B %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#74c0fc,color:#fff
-
-    </div>
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+                    </div>
     </div>
     </div><!-- Heat Shock Response --> <div class="process-showcase">
         <h3>
@@ -319,44 +297,40 @@ T[Continue Synthesis] J --> U[Autophagy Products] U --> V[Nutrient Recycling] V
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Heat Stress] --> B[HSF1 Activation] B --> C[HSF1 Trimerization] C --> D[HSF1 Phosphorylation] D --> E[HSF1 Nuclear Localization] E --> F[HSF1 Binding to HSE] F --> G[HSP Gene Transcription] G --> H[HSP Protein Synthesis] H --> I[Protein Refolding] I --> J[Cell Survival] %% Additional regulatory mechanisms 
-K[Protein Misfolding] --> A 
-L[HSF1 Inhibitors] --> B 
-A[HSP90] --> D 
-B[HSP70] --> I 
-C[HSP60] --> I %% Feedback regulation I --> P[Protein Quality] P 
-
-    --> Q{Proteins Refolded?} Q 
-
-    -->|Yes| 
-R[Reduce HSP Synthesis] Q 
-
-    -->|No| 
-S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization] T --> U[HSF1 Deactivation] U --> V[Return to Normal State] %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
+    A[Heat Stress] --> B[HSF1 Activation] B --> C[HSF1 Trimerization] C --> D[HSF1 Phosphorylation] D --> E[HSF1 Nuclear Localization] E --> F[HSF1 Binding to HSE] F --> G[HSP Gene Transcription] G --> H[HSP Protein Synthesis] H --> I[Protein Refolding] I --> J[Cell Survival] %% Additional regulatory mechanisms
+    K[Protein Misfolding] --> A
+    L[HSF1 Inhibitors] --> B
+    A[HSP90] --> D
+    B[HSP70] --> I
+    C[HSP60] --> I %% Feedback regulation I --> P[Protein Quality] P
+    --> Q{Proteins Refolded?} Q
+    -->|Yes|
+    R[Reduce HSP Synthesis] Q
+    -->|No|
+    S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization] T --> U[HSF1 Deactivation] U --> V[Return to Normal State] %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+                    </div>
     </div>
     </div><!-- RNA Splicing --> <div class="process-showcase">
         <h3>
@@ -371,68 +345,58 @@ S[Continue HSP Synthesis] %% Stress resolution J --> T[Temperature Normalization
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Pre-mRNA] --> B[Spliceosome Assembly] B --> C[Intron Recognition] C --> D[Splicing Reaction] D --> E[Mature mRNA] %% Additional regulatory mechanisms 
-F[5' Splice Site] --> C 
-G[3' Splice Site] --> C 
-H[Branch Point] --> C 
-I[Polypyrimidine Tract] --> C 
-J[U1 snRNP] --> K[5' SS Recognition] K 
-
-    --> B 
-B[U2AF] --> M[3' SS Recognition] M 
-
-    --> B 
-N[U2 snRNP] --> O[Branch Point Recognition] O 
-
-    --> B 
-P[U4/U6•U5 snRNP] --> Q[Catalytic Core Assembly] Q 
-
-    --> B %% Quality control mechanisms E --> R[mRNA Quality Check] R 
-
-    --> S{Splicing Correct?} S 
-
-    -->|Yes| 
-T[mRNA Export] S 
-
-    -->|No| 
-U[Nonsense-Mediated Decay] %% Alternative splicing 
-V[Splicing Regulators] --> W[Alternative 5' SS] W --> X[Isoform 1] V --> Y[Alternative 3' SS] Y --> Z[Isoform 2] V 
-
-    --> A 
-A[Exon Skipping] AA 
-
-    --> B 
-B[Isoform 3] %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
A fill:#ffd43b,color:#000 
+    A[Pre-mRNA] --> B[Spliceosome Assembly] B --> C[Intron Recognition] C --> D[Splicing Reaction] D --> E[Mature mRNA] %% Additional regulatory mechanisms
+    F[5' Splice Site] --> C
+    G[3' Splice Site] --> C
+    H[Branch Point] --> C
+    I[Polypyrimidine Tract] --> C
+    J[U1 snRNP] --> K[5' SS Recognition] K
+    --> B
+    B[U2AF] --> M[3' SS Recognition] M
+    --> B
+    N[U2 snRNP] --> O[Branch Point Recognition] O
+    --> B
+    P[U4/U6•U5 snRNP] --> Q[Catalytic Core Assembly] Q
+    --> B %% Quality control mechanisms E --> R[mRNA Quality Check] R
+    --> S{Splicing Correct?} S
+    -->|Yes|
+    T[mRNA Export] S
+    -->|No|
+    U[Nonsense-Mediated Decay] %% Alternative splicing
+    V[Splicing Regulators] --> W[Alternative 5' SS] W --> X[Isoform 1] V --> Y[Alternative 3' SS] Y --> Z[Isoform 2] V
+    --> A
+    A[Exon Skipping] AA
+    --> B
+    B[Isoform 3] %% Styling
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
A fill:#ffd43b,color:#000
     style 
B fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Autophagy --> <div class="process-showcase">
         <h3>
@@ -447,37 +411,33 @@ B[Isoform 3] %% Styling
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Deprivation] --> B[TORC1 Inhibition] B --> C[Atg1 Complex Activation] C --> D[Phosphorylation of Atg13] D --> E[Atg1-Atg13 Complex Formation] E --> F[Vps34 Complex Activation] F --> G[PI3P Production] G --> H[Phagophore Formation] H --> I[Atg8 Conjugation] I --> J[Autophagosome Formation] J --> K[Cargo Degradation] %% Quality control mechanisms K --> L[Autophagosome Maturation] L --> M[Lysosome Fusion] M --> N[Content Degradation] N --> O[Nutrient Recycling] O --> P[Cell Survival] %% Feedback regulation P --> Q[Nutrient Levels] Q 
-
-    --> R{Sufficient Nutrients?} R 
-
-    -->|Yes| 
-S[Inhibit Autophagy] R 
-
-    -->|No| 
-T[Continue Autophagy] %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
+    A[Nutrient Deprivation] --> B[TORC1 Inhibition] B --> C[Atg1 Complex Activation] C --> D[Phosphorylation of Atg13] D --> E[Atg1-Atg13 Complex Formation] E --> F[Vps34 Complex Activation] F --> G[PI3P Production] G --> H[Phagophore Formation] H --> I[Atg8 Conjugation] I --> J[Autophagosome Formation] J --> K[Cargo Degradation] %% Quality control mechanisms K --> L[Autophagosome Maturation] L --> M[Lysosome Fusion] M --> N[Content Degradation] N --> O[Nutrient Recycling] O --> P[Cell Survival] %% Feedback regulation P --> Q[Nutrient Levels] Q
+    --> R{Sufficient Nutrients?} R
+    -->|Yes|
+    S[Inhibit Autophagy] R
+    -->|No|
+    T[Continue Autophagy] %% Styling
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#ffd43b,color:#000
-
-    </div>
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+                    </div>
     </div>
     </div><!-- Sporulation --> <div class="process-showcase">
         <h3>
@@ -492,50 +452,44 @@ T[Continue Autophagy] %% Styling
     </div><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Limitation] --> B[Meiosis Initiation] B --> C[Meiotic Gene Expression] C --> D[DNA Replication] D --> E[Chromosome Pairing] E --> F[Meiotic Divisions] F --> G[Haploid Nuclei] G --> H[Spore Formation] H --> I[Spore Wall Assembly] I --> J[Mature Spores] J --> K[Spore Dormancy] %% Quality control mechanisms K --> L[Spore Viability Check] L 
-
-    --> M{Spores Viable?} M 
-
-    -->|Yes| 
-N[Maintain Dormancy] M 
-
-    -->|No| 
-O[Spore Death] %% Environmental sensing 
-P[Environmental Conditions] --> Q{Favorable for Growth?} Q 
-
-    -->|Yes| 
-A[Germination] Q 
-
-    -->|No| 
-S[Continue Dormancy] A --> T[Vegetative Growth] %% Key regulators 
-B[Ime1] --> B 
-C[Ime2] --> C 
-W[Meiotic Genes] --> D %% Styling 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
+    A[Nutrient Limitation] --> B[Meiosis Initiation] B --> C[Meiotic Gene Expression] C --> D[DNA Replication] D --> E[Chromosome Pairing] E --> F[Meiotic Divisions] F --> G[Haploid Nuclei] G --> H[Spore Formation] H --> I[Spore Wall Assembly] I --> J[Mature Spores] J --> K[Spore Dormancy] %% Quality control mechanisms K --> L[Spore Viability Check] L
+    --> M{Spores Viable?} M
+    -->|Yes|
+    N[Maintain Dormancy] M
+    -->|No|
+    O[Spore Death] %% Environmental sensing
+    P[Environmental Conditions] --> Q{Favorable for Growth?} Q
+    -->|Yes|
+    A[Germination] Q
+    -->|No|
+    S[Continue Dormancy] A --> T[Vegetative Growth] %% Key regulators
+    B[Ime1] --> B
+    C[Ime2] --> C
+    W[Meiotic Genes] --> D %% Styling
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#ffd43b,color:#000
-
-    </div>
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#74c0fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#b197fc,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+                    </div>
     </div>
     </div>
     </div><div class="section">

yeast_batch01_dna_replication_repair.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[G1/S Checkpoint] --> B[Origin Recognition Complex ORC]
     B --> C[MCM2-7 Loading]
     C --> D[Pre-Replication Complex Assembly]
@@ -151,7 +152,7 @@ graph TD
     L --> M[Replication Fork Establishment]
     M --> N[Leading Strand Synthesis]
     N --> O[Lagging Strand Synthesis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -185,6 +186,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Replication Fork Progression] --> B[CMG Helicase Unwinding]
     B --> C[Single-Strand DNA Binding RPA]
     C --> D[Leading Strand Synthesis]
@@ -200,7 +202,7 @@ graph TD
     M --> N[DNA Polymerase Switch]
     N --> O[Proofreading Activity]
     O --> P[Continued Elongation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -235,6 +237,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Replication Fork Convergence] --> B[Replication Fork Meeting]
     B --> C[Topoisomerase II Activity]
     C --> D[DNA Decatenation]
@@ -252,7 +255,7 @@ graph TD
     O --> P[Fork Stabilization]
     P --> Q[Termination Recovery]
     Q --> F
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -288,6 +291,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[DNA Damage Detection] --> B[Base Excision Glycosylase]
     B --> C[AP Site Formation]
     C --> D[AP Endonuclease]
@@ -296,7 +300,7 @@ graph TD
     F --> G[Repair Completion]
     G --> H[DNA Integrity Check]
     H --> I[Cell Cycle Progression]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff
@@ -324,6 +328,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[DNA Lesion Recognition] --> B[XPC-RAD23B Complex]
     B --> C[TFIIH Recruitment]
     C --> D[DNA Unwinding]
@@ -334,7 +339,7 @@ graph TD
     H --> I[DNA Polymerase δ/ε]
     I --> J[DNA Ligase I]
     J --> K[Repair Completion]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -364,6 +369,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Mismatch Detection] --> B[MSH2-MSH6 Complex]
     B --> C[MLH1-PMS2 Recruitment]
     C --> D[Exonuclease 1]
@@ -371,7 +377,7 @@ graph TD
     E --> F[DNA Ligase I]
     F --> G[Repair Completion]
     G --> H[Cell Cycle Checkpoint]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -398,6 +404,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[DSB Detection] --> B[ATM/ATR Activation]
     B --> C[γ-H2AX Phosphorylation]
     C --> D[MDC1 Recruitment]
@@ -408,7 +415,7 @@ graph TD
     H --> I[DNA Synthesis]
     I --> J[Resolution]
     J --> K[Repair Completion]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -438,6 +445,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Telomere Shortening] --> B[Telomerase Recruitment]
     B --> C[TERT Expression]
     C --> D[TERC Binding]
@@ -446,7 +454,7 @@ graph TD
     F --> G[TRF1/TRF2 Binding]
     G --> H[Telomere Protection]
     H --> I[Cell Viability]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch02_cell_cycle_control.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Growth Signals] --> B[Cyclin D Expression]
     B --> C[CDK4/6 Activation]
     C --> D[Rb Phosphorylation]
@@ -145,7 +146,7 @@ graph TD
     F --> G[DNA Replication Prep]
     G --> H[G1/S Checkpoint]
     H --> I[Cell Cycle Progression]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -173,6 +174,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[S Phase Entry] --> B[Cyclin E Expression]
     B --> C[CDK2 Activation]
     C --> D[Origin Firing]
@@ -180,7 +182,7 @@ graph TD
     E --> F[Replication Checkpoint]
     F --> G[S Phase Completion]
     G --> H[G2 Phase Entry]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -207,6 +209,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[G2 Phase Entry] --> B[Cyclin A Expression]
     B --> C[CDK1 Activation]
     C --> D[DNA Damage Check]
@@ -214,7 +217,7 @@ graph TD
     E --> F[Spindle Assembly Prep]
     F --> G[G2/M Transition]
     G --> H[Mitosis Entry]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -241,6 +244,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Mitosis Entry] --> B[Prophase Initiation]
     B --> C[Chromosome Condensation]
     C --> D[Metaphase Alignment]
@@ -249,7 +253,7 @@ graph TD
     F --> G[Chromosome Segregation]
     G --> H[Telophase Completion]
     H --> I[Cytokinesis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -277,6 +281,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Kinetochore Attachment] --> B[Mad2 Recruitment]
     B --> C[Mad2-Cdc20 Complex]
     C --> D[APC/C Inhibition]
@@ -289,7 +294,7 @@ graph TD
     J -->|No| K[Kinetochore Correction]
     J -->|Yes| L[Mad2 Release]
     L --> M[Anaphase Onset]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff
@@ -321,6 +326,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Spindle Checkpoint Release] --> B[Cdc20 Activation]
     B --> C[APC/C Activation]
     C --> D[Securin Recognition]
@@ -333,7 +339,7 @@ graph TD
     J --> K[Chromosome Segregation]
     K --> L[Anaphase B]
     L --> M[Spindle Elongation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -365,6 +371,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Anaphase Completion] --> B[Contractile Ring Assembly]
     B --> C[Actin-Myosin Contraction]
     C --> D[Membrane Invagination]
@@ -372,7 +379,7 @@ graph TD
     E --> F[Cell Wall Synthesis]
     F --> G[Daughter Cell Separation]
     G --> H[Cell Division Complete]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -399,6 +406,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cytokinesis Complete] --> B[Cyclin Degradation]
     B --> C[CDK Inactivation]
     C --> D[Cell Cycle Exit]
@@ -409,7 +417,7 @@ graph TD
     H --> I{Continue Division?}
     I -->|Yes| J[G1 Phase Re-entry]
     I -->|No| K[Terminal Differentiation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#51cf66,color:#fff
     style C fill:#ffd43b,color:#000

yeast_batch03_protein_synthesis_degradation.html

@@ -133,6 +133,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[mRNA Recognition] --> B[eIF4E Binding]
     B --> C[eIF4G Recruitment]
     C --> D[43S Complex Loading]
@@ -140,7 +141,7 @@ graph TD
     E --> F[60S Subunit Joining]
     F --> G[Translation Initiation]
     G --> H[Protein Synthesis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -167,6 +168,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Peptidyl Transfer] --> B[tRNA Translocation]
     B --> C[mRNA Movement]
     C --> D[Next Codon Reading]
@@ -174,7 +176,7 @@ graph TD
     E --> F[Peptide Bond Formation]
     F --> G[Elongation Cycle]
     G --> H[Protein Chain Growth]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -201,6 +203,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Stop Codon Recognition] --> B[Release Factor Binding]
     B --> C[Peptide Release]
     C --> D[Ribosome Dissociation]
@@ -208,7 +211,7 @@ graph TD
     E --> F[Post-translational Modification]
     F --> G[Protein Maturation]
     G --> H[Functional Protein]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -235,6 +238,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Protein Damage] --> B[Ubiquitin Recognition]
     B --> C[E3 Ligase Activity]
     C --> D[Polyubiquitination]
@@ -242,7 +246,7 @@ graph TD
     E --> F[Protein Unfolding]
     F --> G[Peptide Cleavage]
     G --> H[Amino Acid Recycling]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000

yeast_batch04_signal_transduction.html

@@ -133,6 +133,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Ligand Binding] --> B[Receptor Dimerization]
     B --> C[Conformational Change]
     C --> D[Kinase Activation]
@@ -140,7 +141,7 @@ graph TD
     E --> F[Signal Amplification]
     F --> G[Downstream Activation]
     G --> H[Cellular Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -167,6 +168,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Signal Reception] --> B[Ras Activation]
     B --> C[Raf Phosphorylation]
     C --> D[MEK Activation]
@@ -174,7 +176,7 @@ graph TD
     E --> F[Transcription Factor Activation]
     F --> G[Gene Expression]
     G --> H[Cellular Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -201,6 +203,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[GPCR Activation] --> B[G Protein Exchange]
     B --> C[GTP Binding]
     C --> D[Effector Activation]
@@ -208,7 +211,7 @@ graph TD
     E --> F[Signal Transduction]
     F --> G[Cellular Response]
     G --> H[Signal Termination]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -235,6 +238,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Calcium Release] --> B[IP3 Receptor Activation]
     B --> C[ER Calcium Release]
     C --> D[Calcium Binding Proteins]
@@ -242,7 +246,7 @@ graph TD
     E --> F[Signal Amplification]
     F --> G[Cellular Response]
     G --> H[Calcium Reuptake]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch05_energy_metabolism.html

@@ -133,6 +133,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Glucose Uptake] --> B[Hexokinase Activity]
     B --> C[Glucose-6-Phosphate]
     C --> D[Phosphofructokinase]
@@ -140,7 +141,7 @@ graph TD
     E --> F[Pyruvate Production]
     F --> G[NADH Generation]
     G --> H[ATP Production]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff
@@ -167,6 +168,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Acetyl-CoA Entry] --> B[Citrate Synthase]
     B --> C[Citrate Formation]
     C --> D[Isocitrate Dehydrogenase]
@@ -175,7 +177,7 @@ graph TD
     F --> G[Fumarate Formation]
     G --> H[Malate Dehydrogenase]
     H --> I[Oxaloacetate Regeneration]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff
@@ -203,6 +205,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[NADH Oxidation] --> B[Complex I Activity]
     B --> C[Ubiquinone Reduction]
     C --> D[Complex III Activity]
@@ -211,7 +214,7 @@ graph TD
     F --> G[Oxygen Reduction]
     G --> H[ATP Synthase]
     H --> I[ATP Production]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Pyruvate Accumulation] --> B[Pyruvate Decarboxylase]
     B --> C[Acetaldehyde Formation]
     C --> D[Alcohol Dehydrogenase]
@@ -246,7 +250,7 @@ graph TD
     E --> F[NAD+ Regeneration]
     F --> G[Glycolysis Continuation]
     G --> H[Anaerobic ATP Production]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#74c0fc,color:#fff

yeast_batch06_cell_division.html

@@ -133,6 +133,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cell Cycle Checkpoint] --> B[CDK Activation]
     B --> C[Cyclin B Accumulation]
     C --> D[Nuclear Envelope Breakdown]
@@ -140,7 +141,7 @@ graph TD
     E --> F[Chromosome Condensation]
     F --> G[Metaphase Alignment]
     G --> H[Mitosis Progression]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -167,6 +168,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Kinetochore Attachment] --> B[Spindle Checkpoint]
     B --> C[Anaphase Promoting Complex]
     C --> D[Cohesin Cleavage]
@@ -174,7 +176,7 @@ graph TD
     E --> F[Poleward Movement]
     F --> G[Chromosome Segregation]
     G --> H[Daughter Cell Formation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#ffd43b,color:#000
@@ -201,6 +203,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Contractile Ring Assembly] --> B[Actin-Myosin Contraction]
     B --> C[Membrane Invagination]
     C --> D[Cell Plate Formation]
@@ -208,7 +211,7 @@ graph TD
     E --> F[Membrane Fusion]
     F --> G[Cell Division]
     G --> H[Daughter Cells]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -235,6 +238,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cell Wall Degradation] --> B[Chitinase Activity]
     B --> C[Cell Wall Breakdown]
     C --> D[Membrane Separation]
@@ -242,7 +246,7 @@ graph TD
     E --> F[Cell Wall Reformation]
     F --> G[Independent Growth]
     G --> H[Cell Cycle Restart]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch06_lipid_membrane_biology.html

@@ -2,147 +2,666 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 06: Lipid & Membrane Biology</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
-            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: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 06: Lipid & Membrane Biology - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 06
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 06: Lipid & Membrane Biology (6 processes)
-    </h
><p>
-        Membrane dynamics and lipid metabolism systems
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 6 Lipid & Membrane Processes
-    </h
><ul>
-        <li>
-            <a href="#fatty-acid-synthesis">1. Fatty Acid Synthesis</a></li><li>
-            <a href="#phospholipid-synthesis">2. Phospholipid Synthesis</a></li><li>
-            <a href="#ergosterol-synthesis">3. Ergosterol Synthesis</a></li><li>
-            <a href="#membrane-biogenesis">4. Membrane Biogenesis</a></li><li>
-            <a href="#vesicle-trafficking">5. Vesicle Trafficking</a></li><li>
-            <a href="#endocytosis">6. Endocytosis</a></li></ul></div><!-- Process 1: Fatty Acid Synthesis --> <div class="process-item" id="fatty-acid-synthesis">
-        <h3>
-        1. Fatty Acid Synthesis
-    </h
><p>
-        Detailed analysis of fatty acid synthesis using the Programming Framework, revealing computational logic for lipid biosynthesis and membrane formation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Acetyl-CoA] --> B[Acetyl-CoA Carboxylase] B --> B[Malonyl-CoA] B --> D[Fatty Acid Synthase] D --> C[Condensation] C --> D[Reduction] D --> E[Dehydration] E --> H[Second Reduction] H --> I[Chain Elongation] I 
-
-    --> J{Chain Length Complete?} J 
-
-    -->|No| 
-K[Add Malonyl-CoA] K 
-
-    --> C J 
-
-    -->|Yes| 
-L[Fatty Acid Release] L --> M[Palmitic Acid] M --> N[Membrane Incorporation] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 2: Phospholipid Synthesis --> <div class="process-item" id="phospholipid-synthesis">
-        <h3>
-        2. Phospholipid Synthesis
-    </h
><p>
-        Detailed analysis of phospholipid synthesis using the Programming Framework, revealing computational logic for membrane lipid production.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Fatty Acyl-CoA] --> A[Glycerol-3-Phosphate] A --> C[Lysophosphatidic Acid] C --> D[Phosphatidic Acid] D --> B[CDP-Diacylglycerol] B 
-
-    --> F{Phospholipid Type?} F 
-
-    -->|PC| 
-C[Phosphatidylcholine] F 
+            <h1>🧬 Yeast Batch 06: Lipid & Membrane Biology</h1>
+            <p>Programming Framework Analysis - Comprehensive Membrane Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Lipid & Membrane Biology: Cellular Architecture and Dynamics</h2>
+                <p>This batch contains 6 fundamental yeast processes responsible for lipid biosynthesis, membrane biogenesis, and membrane trafficking. These processes represent the core computational systems that ensure proper cellular architecture, membrane integrity, and dynamic membrane remodeling essential for cellular function and adaptation.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with regulatory feedback loops, quality control mechanisms, and coordinated membrane dynamics that function as a biological membrane engineering and trafficking platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 6 Lipid & Membrane Processes</h2>
+                <ul>
+                    <li><a href="#fatty-acid-synthesis">1. Fatty Acid Synthesis</a></li>
+                    <li><a href="#phospholipid-synthesis">2. Phospholipid Synthesis</a></li>
+                    <li><a href="#ergosterol-synthesis">3. Ergosterol Synthesis</a></li>
+                    <li><a href="#membrane-biogenesis">4. Membrane Biogenesis</a></li>
+                    <li><a href="#vesicle-trafficking">5. Vesicle Trafficking</a></li>
+                    <li><a href="#endocytosis">6. Endocytosis</a></li>
+                </ul>
+            </div>
 
-    -->|PE| 
-D[Phosphatidylethanolamine] F 
+            <!-- Process 1: Fatty Acid Synthesis -->
+            <div class="process-item" id="fatty-acid-synthesis">
+                <h3>1. Fatty Acid Synthesis</h3>
+                <p>Detailed analysis of fatty acid synthesis using the Programming Framework, revealing computational logic for lipid biosynthesis and membrane formation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Substrate Preparation
+    A[Glucose Metabolism] --> B[Pyruvate Formation]
+    B --> C[Pyruvate Dehydrogenase Complex]
+    C --> D[Acetyl-CoA Production]
+    D --> E[Citrate Synthase]
+    E --> F[Citrate Formation]
+    F --> G[Cytosolic Transport]
+    G --> H[ATP-Citrate Lyase]
+    H --> I[Cytosolic Acetyl-CoA]
+    
+    %% Acetyl-CoA Carboxylation
+    I --> J[Acetyl-CoA Carboxylase Activation]
+    J --> K[Biotin Carboxylation]
+    K --> L[Carboxybiotin Formation]
+    L --> M[Acetyl-CoA Carboxylation]
+    M --> N[Malonyl-CoA Production]
+    
+    %% Fatty Acid Synthase Complex
+    N --> O[Fatty Acid Synthase Assembly]
+    O --> P[ACP Loading]
+    P --> Q[Acetyl Transfer]
+    Q --> R[Malonyl Transfer]
+    R --> S[Condensation Reaction]
+    S --> T[β-Ketoacyl Formation]
+    T --> U[NADPH-Dependent Reduction]
+    U --> V[β-Hydroxyacyl Formation]
+    V --> W[Dehydration Reaction]
+    W --> X[Enoyl Formation]
+    X --> Y[NADPH-Dependent Reduction]
+    Y --> Z[Butyryl-ACP Formation]
+    
+    %% Chain Elongation Cycle
+    Z --> AA{Chain Length Check}
+    AA -->|Incomplete| BB[Malonyl-CoA Addition]
+    BB --> CC[Condensation]
+    CC --> DD[Reduction]
+    DD --> EE[Dehydration]
+    EE --> FF[Final Reduction]
+    FF --> AA
+    AA -->|Complete| GG[Thioesterase Activity]
+    GG --> HH[Fatty Acid Release]
+    HH --> II[Palmitic Acid]
+    
+    %% Product Processing
+    II --> JJ[Fatty Acyl-CoA Synthetase]
+    JJ --> KK[Fatty Acyl-CoA]
+    KK --> LL[Membrane Incorporation]
+    LL --> MM[Phospholipid Synthesis]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style GG fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    style MM fill:#ffd43b,color:#000
+    
+    style MM fill:#74c0fc,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>
 
-    -->|PS| 
-E[Phosphatidylserine] F 
+            <!-- Process 2: Phospholipid Synthesis -->
+            <div class="process-item" id="phospholipid-synthesis">
+                <h3>2. Phospholipid Synthesis</h3>
+                <p>Detailed analysis of phospholipid synthesis using the Programming Framework, revealing computational logic for membrane lipid production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Glycerol-3-Phosphate Pathway
+    A[Glycerol-3-Phosphate] --> B[Glycerol-3-Phosphate Acyltransferase]
+    B --> C[Lysophosphatidic Acid]
+    C --> D[Lysophosphatidic Acid Acyltransferase]
+    D --> E[Phosphatidic Acid]
+    E --> F[Phosphatidic Acid Phosphatase]
+    F --> G[Diacylglycerol]
+    
+    %% CDP-Diacylglycerol Pathway
+    E --> H[CDP-Diacylglycerol Synthase]
+    H --> I[CDP-Diacylglycerol]
+    
+    %% Phosphatidylcholine Synthesis
+    I --> J[Phosphatidylcholine Synthase]
+    J --> K[CDP-Choline]
+    K --> L[Choline Kinase]
+    L --> M[Phosphocholine]
+    M --> N[CTP:Phosphocholine Cytidylyltransferase]
+    N --> O[CDP-Choline]
+    O --> P[CDP-Choline:Diacylglycerol Cholinephosphotransferase]
+    P --> Q[Phosphatidylcholine]
+    
+    %% Phosphatidylethanolamine Synthesis
+    I --> R[Phosphatidylserine Synthase]
+    R --> S[Phosphatidylserine]
+    S --> T[Phosphatidylserine Decarboxylase]
+    T --> U[Phosphatidylethanolamine]
+    
+    %% Phosphatidylinositol Synthesis
+    I --> V[Phosphatidylinositol Synthase]
+    V --> W[CDP-Diacylglycerol:Inositol Phosphatidyltransferase]
+    W --> X[Phosphatidylinositol]
+    X --> Y[Phosphatidylinositol Kinases]
+    Y --> Z[Phosphatidylinositol Phosphates]
+    
+    %% Membrane Integration
+    Q --> AA[Membrane Integration]
+    U --> AA
+    Z --> AA
+    AA --> BB[Membrane Bilayer Formation]
+    BB --> CC[Membrane Fluidity Regulation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    
+    style CC fill:#74c0fc,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>
 
-    -->|PI| 
-F[Phosphatidylinositol] C --> K[Membrane Integration] D 
+            <!-- Process 3: Ergosterol Synthesis -->
+            <div class="process-item" id="ergosterol-synthesis">
+                <h3>3. Ergosterol Synthesis</h3>
+                <p>Detailed analysis of ergosterol synthesis using the Programming Framework, revealing computational logic for sterol metabolism and membrane fluidity control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Mevalonate Pathway
+    A[Acetyl-CoA] --> B[Acetoacetyl-CoA Thiolase]
+    B --> C[Acetoacetyl-CoA]
+    C --> D[HMG-CoA Synthase]
+    D --> E[HMG-CoA]
+    E --> F[HMG-CoA Reductase]
+    F --> G[Mevalonate]
+    G --> H[Mevalonate Kinase]
+    H --> I[5-Phosphomevalonate]
+    I --> J[Phosphomevalonate Kinase]
+    J --> K[5-Pyrophosphomevalonate]
+    K --> L[Mevalonate Pyrophosphate Decarboxylase]
+    L --> M[Isopentenyl Pyrophosphate]
+    
+    %% Isoprenoid Synthesis
+    M --> N[Isopentenyl Pyrophosphate Isomerase]
+    N --> O[Dimethylallyl Pyrophosphate]
+    O --> P[Farnesyl Pyrophosphate Synthase]
+    P --> Q[Geranyl Pyrophosphate]
+    Q --> R[Farnesyl Pyrophosphate]
+    
+    %% Squalene Synthesis
+    R --> S[Squalene Synthase]
+    S --> T[Squalene]
+    T --> U[Squalene Epoxidase]
+    U --> V[Squalene 2,3-Epoxide]
+    V --> W[Lanosterol Synthase]
+    W --> X[Lanosterol]
+    
+    %% Ergosterol Biosynthesis
+    X --> Y[Lanosterol 14α-Demethylase]
+    Y --> Z[4,4-Dimethylcholesta-8,14,24-trienol]
+    Z --> AA[4,4-Dimethylcholesta-8,24-dienol]
+    AA --> BB[4-Methylcholesta-8,24-dienol]
+    BB --> CC[4-Methylcholesta-8,14,24-trienol]
+    CC --> DD[4-Methylcholesta-8,24-dienol]
+    DD --> EE[Zymosterol]
+    EE --> FF[Feccosterol]
+    FF --> GG[Episterol]
+    GG --> HH[Ergosta-5,7,22,24(28)-tetraenol]
+    HH --> II[Ergosterol]
+    
+    %% Membrane Integration
+    II --> JJ[Membrane Integration]
+    JJ --> KK[Membrane Fluidity Control]
+    KK --> LL[Sterol Regulatory Functions]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style X fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    
+    style LL fill:#74c0fc,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>
 
-    --> K E 
+            <!-- Process 4: Membrane Biogenesis -->
+            <div class="process-item" id="membrane-biogenesis">
+                <h3>4. Membrane Biogenesis</h3>
+                <p>Detailed analysis of membrane biogenesis using the Programming Framework, revealing computational logic for membrane assembly and organization.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Lipid Assembly
+    A[Phospholipid Synthesis] --> B[Lipid Asymmetry Establishment]
+    B --> C[Flippase Activity]
+    C --> D[Lipid Translocase]
+    D --> E[Membrane Leaflet Organization]
+    
+    %% Protein Integration
+    F[Integral Membrane Proteins] --> G[Signal Recognition Particle]
+    G --> H[Endoplasmic Reticulum Targeting]
+    H --> I[Translocon Complex]
+    I --> J[Protein Insertion]
+    J --> K[Membrane Protein Folding]
+    K --> L[Protein Quality Control]
+    
+    %% Membrane Domain Formation
+    E --> M[Lipid Raft Formation]
+    L --> M
+    M --> N[Cholesterol-Rich Domains]
+    N --> O[Sphingolipid Clustering]
+    O --> P[Membrane Microdomains]
+    
+    %% Organelle Membrane Assembly
+    P --> Q[Golgi Apparatus Assembly]
+    Q --> R[Lysosome Membrane Formation]
+    R --> S[Vacuole Membrane Assembly]
+    S --> T[Mitochondrial Membrane Assembly]
+    T --> U[Plasma Membrane Assembly]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style F fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style E 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    
+    style U fill:#74c0fc,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>
 
-    --> K F 
-
-    --> K 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 3: Ergosterol Synthesis --> <div class="process-item" id="ergosterol-synthesis">
-        <h3>
-        3. Ergosterol Synthesis
-    </h
><p>
-        Detailed analysis of ergosterol synthesis using the Programming Framework, revealing computational logic for sterol metabolism and membrane fluidity control.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Acetyl-CoA] --> B[HMG-CoA Reductase] B --> B[Mevalonate] B --> C[Isopentenyl-PP] C --> D[Farnesyl-PP] D --> E[Squalene] E --> F[Lanosterol] F --> H[Ergosterol Biosynthesis] H --> G[Ergosterol] G --> J[Membrane Incorporation] J --> K[Membrane Fluidity Control] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 4: Vesicle Trafficking --> <div class="process-item" id="vesicle-trafficking">
-        <h3>
-        5. Vesicle Trafficking
-    </h
><p>
-        Detailed analysis of vesicle trafficking using the Programming Framework, revealing computational logic for intracellular transport and protein sorting.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Cargo Recognition] --> B[Vesicle Formation] B --> C[COPII Coating] C --> D[ER Exit] D --> E[Golgi Transport] E --> F[Vesicle Fusion] F --> G[SNARE Complex] G --> H[Membrane Fusion] H --> I[Cargo Delivery] J[Retrograde Transport] --> K[COPI Coating] K --> L[Golgi to ER] L --> A[Recycling] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 5: Vesicle Trafficking -->
+            <div class="process-item" id="vesicle-trafficking">
+                <h3>5. Vesicle Trafficking</h3>
+                <p>Detailed analysis of vesicle trafficking using the Programming Framework, revealing computational logic for membrane transport and cargo delivery.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Vesicle Formation
+    A[Cargo Recognition] --> B[Coat Protein Recruitment]
+    B --> C[Clathrin Assembly]
+    C --> D[Adaptor Protein Binding]
+    D --> E[Membrane Curvature]
+    E --> F[Vesicle Budding]
+    F --> G[Vesicle Scission]
+    G --> H[Free Vesicle]
+    
+    %% Vesicle Transport
+    H --> I[Motor Protein Binding]
+    I --> J[Microtubule Association]
+    J --> K[Vesicle Movement]
+    K --> L[Target Recognition]
+    L --> M[Vesicle Docking]
+    M --> N[SNARE Complex Formation]
+    N --> O[Vesicle Fusion]
+    O --> P[Cargo Delivery]
+    
+    %% Regulatory Control
+    P --> Q[Rab GTPase Activity]
+    Q --> R[GTP Hydrolysis]
+    R --> S[Vesicle Recycling]
+    S --> T[Endosome Formation]
+    T --> U[Lysosomal Targeting]
+    U --> V[Autophagosome Formation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    
+    style V fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast lipid metabolism and membrane dynamics systems
-    </p><p>
-        <em>Batch 06 of 15: Lipid & Membrane Biology</em>
+            <!-- Process 6: Endocytosis -->
+            <div class="process-item" id="endocytosis">
+                <h3>6. Endocytosis</h3>
+                <p>Detailed analysis of endocytosis using the Programming Framework, revealing computational logic for membrane internalization and cargo uptake.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Receptor-Mediated Endocytosis
+    A[Ligand Binding] --> B[Receptor Clustering]
+    B --> C[Clathrin Recruitment]
+    C --> D[Adaptor Protein Assembly]
+    D --> E[Pit Formation]
+    E --> F[Membrane Invagination]
+    F --> G[Vesicle Budding]
+    G --> H[Clathrin-Coated Vesicle]
+    H --> I[Clathrin Uncoating]
+    I --> J[Early Endosome]
+    
+    %% Endosomal Processing
+    J --> K[Endosomal Acidification]
+    K --> L[V-ATPase Activity]
+    L --> M[Ligand-Receptor Dissociation]
+    M --> N[Receptor Recycling]
+    N --> O[Plasma Membrane Return]
+    O --> P[Receptor Reutilization]
+    
+    %% Lysosomal Targeting
+    M --> Q[Late Endosome Formation]
+    Q --> R[Multivesicular Body]
+    R --> S[Lysosome Fusion]
+    S --> T[Cargo Degradation]
+    T --> U[Nutrient Release]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    
+    style U fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast lipid and membrane biology systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 06 of 15: Lipid & Membrane Biology</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch07_cell_wall_extracellular.html

@@ -41,18 +41,15 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[UDP-Glucose] --> B[Cellulose Synthase] B --> B[β-1,3-Glucan] B --> D[Cell Wall Assembly] D --> E[Structural Integrity] F[Chitin Precursors] --> G[Chitin Synthase] G --> H[Chitin Fibers] H --> I[Cell Wall Reinforcement] C[Mannoproteins] --> K[Protein Glycosylation] K --> L[Cell Wall Proteins] L --> M[Surface Properties] E --> N[Cell Wall Complete] I 
-
-    --> N M 
-
-    --> N 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
+    A[UDP-Glucose] --> B[Cellulose Synthase] B --> B[β-1,3-Glucan] B --> D[Cell Wall Assembly] D --> E[Structural Integrity] F[Chitin Precursors] --> G[Chitin Synthase] G --> H[Chitin Fibers] H --> I[Cell Wall Reinforcement] C[Mannoproteins] --> K[Protein Glycosylation] K --> L[Cell Wall Proteins] L --> M[Surface Properties] E --> N[Cell Wall Complete] I
+    --> N M
+    --> N
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Process 2: Chitin Synthesis --> <div class="process-item" id="chitin-synthesis">
         <h3>
@@ -62,18 +59,15 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[UDP-N-Acetylglucosamine] --> B[Chitin Synthase I] B --> C[Chitin Chain] C --> D[Septum Formation] E[Cell Division Signal] --> F[Chitin Synthase II] F --> G[Lateral Wall Chitin] G --> H[Wall Strengthening] I[Stress Response] --> J[Chitin Synthase III] J --> K[Remedial Chitin] K --> L[Wall Repair] D --> M[Structural Support] H 
-
-    --> M L 
-
-    --> M 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
+    A[UDP-N-Acetylglucosamine] --> B[Chitin Synthase I] B --> C[Chitin Chain] C --> D[Septum Formation] E[Cell Division Signal] --> F[Chitin Synthase II] F --> G[Lateral Wall Chitin] G --> H[Wall Strengthening] I[Stress Response] --> J[Chitin Synthase III] J --> K[Remedial Chitin] K --> L[Wall Repair] D --> M[Structural Support] H
+    --> M L
+    --> M
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><div class="footer">
         <p>

yeast_batch07_metabolic_regulation.html

@@ -133,6 +133,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Glucose Sensing] --> B[Snf1 Kinase Activation]
     B --> C[Catabolite Repression]
     C --> D[Gene Expression Changes]
@@ -140,7 +141,7 @@ graph TD
     E --> F[Energy Production]
     F --> G[Glucose Utilization]
     G --> H[Metabolic Balance]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -167,6 +168,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Nitrogen Availability] --> B[Gln3 Transcription Factor]
     B --> C[Nitrogen Catabolite Repression]
     C --> D[Amino Acid Biosynthesis]
@@ -174,7 +176,7 @@ graph TD
     E --> F[Nitrogen Assimilation]
     F --> G[Metabolic Integration]
     G --> H[Nitrogen Balance]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -201,6 +203,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Fatty Acid Availability] --> B[ACC Enzyme Activation]
     B --> C[Fatty Acid Synthesis]
     C --> D[Phospholipid Assembly]
@@ -208,7 +211,7 @@ graph TD
     E --> F[Lipid Storage]
     F --> G[Energy Storage]
     G --> H[Lipid Homeostasis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -235,6 +238,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Environmental Stress] --> B[Hog1 MAP Kinase]
     B --> C[Stress Response Genes]
     C --> D[Osmolyte Production]
@@ -242,7 +246,7 @@ graph TD
     E --> F[Stress Adaptation]
     F --> G[Homeostasis Restoration]
     G --> H[Cell Survival]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch08_chromatin_transcription.html

@@ -2,113 +2,804 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 08: Chromatin & Transcription</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
-            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: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 08: Chromatin & Transcription - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 08
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 08: Chromatin & Transcription (7 processes)
-    </h
><p>
-        Gene expression and chromatin regulation systems
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 7 Chromatin & Transcription Processes
-    </h
><ul>
-        <li>
-            <a href="#transcription-initiation">1. Transcription Initiation</a></li><li>
-            <a href="#chromatin-remodeling">2. Chromatin Remodeling</a></li><li>
-            <a href="#histone-modification">3. Histone Modification</a></li><li>
-            <a href="#transcription-elongation">4. Transcription Elongation</a></li><li>
-            <a href="#transcription-termination">5. Transcription Termination</a></li><li>
-            <a href="#gene-silencing">6. Gene Silencing</a></li><li>
-            <a href="#epigenetic-regulation">7. Epigenetic Regulation</a></li></ul></div><!-- Process 1: Transcription Initiation --> <div class="process-item" id="transcription-initiation">
-        <h3>
-        1. Transcription Initiation
-    </h
><p>
-        Detailed analysis of Transcription Initiation using the Programming Framework, revealing computational logic for gene expression control.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Promoter Recognition] --> B[TFIID Binding] B --> C[TFIIA Recruitment] C --> D[TFIIB Assembly] D --> E[RNA Polymerase II] E --> F[TFIIF Escort] F --> G[TFIIE/TFIIH Recruitment] G --> H[Promoter Melting] H --> I[Transcription Start] I --> J[Promoter Clearance] J --> K[mRNA Synthesis] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <h1>🧬 Yeast Batch 08: Chromatin & Transcription</h1>
+            <p>Programming Framework Analysis - Comprehensive Gene Expression Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Chromatin & Transcription: Gene Expression and Epigenetic Regulation</h2>
+                <p>This batch contains 7 fundamental yeast processes responsible for chromatin dynamics, transcription regulation, and epigenetic control. These processes represent the core computational systems that ensure proper gene expression, chromatin organization, and transcriptional regulation essential for cellular function and adaptation.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with regulatory feedback loops, chromatin remodeling complexes, and transcriptional machinery that function as a biological gene expression and epigenetic control platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 7 Chromatin & Transcription Processes</h2>
+                <ul>
+                    <li><a href="#transcription-initiation">1. Transcription Initiation</a></li>
+                    <li><a href="#chromatin-remodeling">2. Chromatin Remodeling</a></li>
+                    <li><a href="#histone-modification">3. Histone Modification</a></li>
+                    <li><a href="#transcription-elongation">4. Transcription Elongation</a></li>
+                    <li><a href="#transcription-termination">5. Transcription Termination</a></li>
+                    <li><a href="#gene-silencing">6. Gene Silencing</a></li>
+                    <li><a href="#epigenetic-regulation">7. Epigenetic Regulation</a></li>
+                </ul>
+            </div>
 
-    </div>
-    </div>
-    </div><!-- Process 2: Chromatin Remodeling --> <div class="process-item" id="chromatin-remodeling">
-        <h3>
-        2. Chromatin Remodeling
-    </h
><p>
-        Detailed analysis of Chromatin Remodeling using the Programming Framework, revealing computational logic for DNA accessibility control.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Chromatin Signal] --> B[SWI/SNF Complex] B --> C[ATP Hydrolysis] C --> D[Nucleosome Sliding] D --> E[DNA Accessibility] E --> F[Transcription Factor Binding] F --> G[Gene Activation] H[Repressive Signal] --> I[ISWI Complex] I --> J[Nucleosome Assembly] J --> K[Chromatin Compaction] K --> L[Gene Silencing] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 1: Transcription Initiation -->
+            <div class="process-item" id="transcription-initiation">
+                <h3>1. Transcription Initiation</h3>
+                <p>Detailed analysis of transcription initiation using the Programming Framework, revealing computational logic for gene expression control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Promoter Recognition
+    A[Transcription Factor Binding] --> B[Promoter Recognition]
+    B --> C[TATA Box Binding]
+    C --> D[TFIID Complex Assembly]
+    D --> E[TBP Binding]
+    E --> F[TFIIA Recruitment]
+    F --> G[TFIIA-TFIID Stabilization]
+    G --> H[TFIIB Assembly]
+    H --> I[TFIIB-DNA Interaction]
+    I --> J[RNA Polymerase II Recruitment]
+    J --> K[Pol II-CTD Phosphorylation]
+    K --> L[TFIIF Escort]
+    L --> M[TFIIE Recruitment]
+    M --> N[TFIIH Recruitment]
+    N --> O[TFIIH Helicase Activity]
+    O --> P[Promoter DNA Melting]
+    P --> Q[Transcription Bubble Formation]
+    Q --> R[First Phosphodiester Bond]
+    R --> S[Transcription Start]
+    S --> T[Promoter Clearance]
+    T --> U[TFIIB Release]
+    U --> V[TFIIE/TFIIH Release]
+    V --> W[Elongation Complex Formation]
+    W --> X[mRNA Synthesis Initiation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,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>
-    </div>
-    </div><!-- Process 3: Histone Modification --> <div class="process-item" id="histone-modification">
-        <h3>
-        3. Histone Modification
-    </h
><p>
-        Detailed analysis of Histone Modification using the Programming Framework, revealing computational logic for epigenetic regulation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Regulatory Signal] --> B{Modification Type?} B 
+            <!-- Process 2: Chromatin Remodeling -->
+            <div class="process-item" id="chromatin-remodeling">
+                <h3>2. Chromatin Remodeling</h3>
+                <p>Detailed analysis of chromatin remodeling using the Programming Framework, revealing computational logic for DNA accessibility control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% SWI/SNF Complex Activation
+    A[Transcriptional Activation Signal] --> B[SWI/SNF Complex Recruitment]
+    B --> C[Snf2 ATPase Activation]
+    C --> D[ATP Binding]
+    D --> E[ATP Hydrolysis]
+    E --> F[Chromatin Remodeling]
+    F --> G[Nucleosome Sliding]
+    G --> H[Nucleosome Ejection]
+    H --> I[DNA Accessibility Increase]
+    I --> J[Transcription Factor Binding Sites]
+    J --> K[Transcription Factor Recruitment]
+    K --> L[Gene Activation]
+    L --> M[Transcriptional Enhancement]
+    
+    %% ISWI Complex Repression
+    N[Repressive Signal] --> O[ISWI Complex Recruitment]
+    O --> P[Isw1 ATPase Activation]
+    P --> Q[ATP-Dependent Remodeling]
+    Q --> R[Nucleosome Assembly]
+    R --> S[Nucleosome Spacing]
+    S --> T[Chromatin Compaction]
+    T --> U[DNA Accessibility Decrease]
+    U --> V[Transcription Factor Exclusion]
+    V --> W[Gene Silencing]
+    W --> X[Transcriptional Repression]
+    
+    %% CHD Complex
+    Y[Chromatin Organization Signal] --> Z[CHD Complex Recruitment]
+    Z --> AA[Chd1 ATPase Activity]
+    AA --> BB[Nucleosome Positioning]
+    BB --> CC[Chromatin Structure]
+    CC --> DD[Gene Expression Regulation]
+    
+    %% Integration
+    M --> EE[Chromatin Remodeling]
+    X --> EE
+    DD --> EE
+    EE --> FF[DNA Accessibility Control]
+    FF --> GG[Gene Expression Regulation]
+    GG --> HH[Transcriptional Control]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    style Y fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    
+    style HH fill:#74c0fc,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>
 
-    -->|Acetylation| 
-C[HAT Complex] B 
+            <!-- Process 3: Histone Modification -->
+            <div class="process-item" id="histone-modification">
+                <h3>3. Histone Modification</h3>
+                <p>Detailed analysis of histone modification using the Programming Framework, revealing computational logic for epigenetic regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Histone Acetylation
+    A[Transcriptional Activation Signal] --> B[HAT Complex Recruitment]
+    B --> C[Gcn5 HAT Activity]
+    C --> D[Acetyl-CoA Binding]
+    D --> E[Histone H3 Acetylation]
+    E --> F[Histone H4 Acetylation]
+    F --> G[Lysine Acetylation]
+    G --> H[Positive Charge Neutralization]
+    H --> I[Histone-DNA Interaction Weakening]
+    I --> J[Chromatin Opening]
+    J --> K[Transcription Factor Access]
+    K --> L[Transcriptional Activation]
+    
+    %% Histone Methylation
+    M[Epigenetic Regulation Signal] --> N[HMT Complex Recruitment]
+    N --> O[Set1 HMT Activity]
+    O --> P[SAM Binding]
+    P --> Q[Histone H3 Methylation]
+    Q --> R[Lysine Methylation]
+    R --> S[Arginine Methylation]
+    S --> T[Histone Code Establishment]
+    T --> U[Chromatin State]
+    U --> V[Gene Expression Regulation]
+    V --> W[Epigenetic Memory]
+    
+    %% Histone Phosphorylation
+    X[Cell Cycle Signal] --> Y[Histone Kinase Activation]
+    Y --> Z[Aurora B Kinase]
+    Z --> AA[Histone H3 Phosphorylation]
+    AA --> BB[Serine Phosphorylation]
+    BB --> CC[Threonine Phosphorylation]
+    CC --> DD[Histone Charge Modification]
+    DD --> EE[Chromatin Condensation]
+    EE --> FF[Cell Cycle Regulation]
+    FF --> GG[Chromosome Segregation]
+    
+    %% Histone Ubiquitination
+    HH[DNA Damage Signal] --> II[E3 Ubiquitin Ligase]
+    II --> JJ[Histone H2B Ubiquitination]
+    JJ --> KK[Ubiquitin Conjugation]
+    KK --> LL[Histone Modification]
+    LL --> MM[DNA Repair Response]
+    MM --> NN[Genome Stability]
+    
+    %% Integration
+    L --> OO[Histone Modification]
+    W --> OO
+    GG --> OO
+    NN --> OO
+    OO --> PP[Epigenetic Regulation]
+    PP --> QQ[Gene Expression Control]
+    QQ --> RR[Chromatin State]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style X fill:#ff6b6b,color:#fff
+    style HH fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    style MM fill:#ffd43b,color:#000
+    style NN fill:#ffd43b,color:#000
+    style OO fill:#ffd43b,color:#000
+    style PP fill:#ffd43b,color:#000
+    style QQ fill:#ffd43b,color:#000
+    style RR fill:#ffd43b,color:#000
+    
+    style RR fill:#74c0fc,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>
 
-    -->|Methylation| 
-D[HMT Complex] B 
+            <!-- Process 4: Transcription Elongation -->
+            <div class="process-item" id="transcription-elongation">
+                <h3>4. Transcription Elongation</h3>
+                <p>Detailed analysis of transcription elongation using the Programming Framework, revealing computational logic for mRNA synthesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Elongation Complex Formation
+    A[Promoter Clearance] --> B[Elongation Complex Assembly]
+    B --> C[Pol II CTD Phosphorylation]
+    C --> D[P-TEFb Recruitment]
+    D --> E[CDK9 Activation]
+    E --> F[Ser2 Phosphorylation]
+    F --> G[Elongation Factor Recruitment]
+    G --> H[Spt4/Spt5 Complex]
+    H --> I[DSIF Complex]
+    I --> J[Elongation Complex]
+    
+    %% Nucleotide Addition
+    J --> K[Template DNA Reading]
+    K --> L[NTP Binding]
+    L --> M[NTP Selection]
+    M --> N[Phosphodiester Bond Formation]
+    N --> O[RNA Chain Elongation]
+    O --> P[Template DNA Unwinding]
+    P --> Q[DNA Reannealing]
+    Q --> R[Transcription Bubble Movement]
+    R --> S[mRNA Synthesis]
+    
+    %% Chromatin Navigation
+    S --> T[Nucleosome Encounter]
+    T --> U[FACT Complex]
+    U --> V[Histone H2A/H2B Dimer Removal]
+    V --> W[Nucleosome Disassembly]
+    W --> X[Pol II Passage]
+    X --> Y[Histone Reassembly]
+    Y --> Z[Nucleosome Restoration]
+    Z --> AA[Chromatin Integrity]
+    
+    %% Elongation Control
+    AA --> BB[Elongation Pausing]
+    BB --> CC[Pause Site Recognition]
+    CC --> DD[Elongation Factor Release]
+    DD --> EE[Pol II Stalling]
+    EE --> FF[Elongation Resumption]
+    FF --> GG[Processive Transcription]
+    GG --> HH[Gene Body Transcription]
+    
+    %% Integration
+    HH --> II[Transcription Elongation]
+    II --> JJ[mRNA Synthesis]
+    JJ --> KK[Gene Expression]
+    KK --> LL[Protein Synthesis]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    
+    style LL fill:#74c0fc,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>
 
-    -->|Phosphorylation| 
-E[Histone Kinase] C --> F[Histone Acetylation] D --> G[Histone Methylation] E --> H[Histone Phosphorylation] F --> I[Chromatin Opening] G --> J[Gene Expression Regulation] H --> K[Cell Cycle Regulation] I --> L[Transcriptional Activation] J --> M[Epigenetic Memory] K --> N[Chromosome Condensation] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 5: Transcription Termination -->
+            <div class="process-item" id="transcription-termination">
+                <h3>5. Transcription Termination</h3>
+                <p>Detailed analysis of transcription termination using the Programming Framework, revealing computational logic for transcription completion.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Termination Signal Recognition
+    A[Polyadenylation Signal] --> B[Cleavage and Polyadenylation Complex]
+    B --> C[CPSF Complex]
+    C --> D[AAUAAA Recognition]
+    D --> E[CstF Complex]
+    E --> F[G/U-Rich Element]
+    F --> G[Cleavage Site Recognition]
+    G --> H[Pre-mRNA Cleavage]
+    H --> I[3' End Formation]
+    I --> J[Poly(A) Polymerase]
+    J --> K[Poly(A) Tail Addition]
+    K --> L[mRNA Maturation]
+    
+    %% Pol II Termination
+    L --> M[Pol II Release Signal]
+    M --> N[Torpedo Model]
+    N --> O[Xrn2 Exonuclease]
+    O --> P[5' to 3' Degradation]
+    P --> Q[Pol II Displacement]
+    Q --> R[Transcription Termination]
+    R --> S[Pol II Recycling]
+    S --> T[Transcription Complex Disassembly]
+    
+    %% Chromatin Restoration
+    T --> U[Chromatin Remodeling]
+    U --> V[Nucleosome Repositioning]
+    V --> W[Histone Modification Reset]
+    W --> X[Chromatin State Restoration]
+    X --> Y[Gene Locus Reset]
+    Y --> Z[Transcription Readiness]
+    
+    %% Integration
+    Z --> AA[Transcription Termination]
+    AA --> BB[mRNA Release]
+    BB --> CC[Gene Expression Completion]
+    CC --> DD[Transcription Cycle]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    
+    style DD fill:#74c0fc,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>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 6: Gene Silencing -->
+            <div class="process-item" id="gene-silencing">
+                <h3>6. Gene Silencing</h3>
+                <p>Detailed analysis of gene silencing using the Programming Framework, revealing computational logic for transcriptional repression.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Heterochromatin Formation
+    A[Silencing Signal] --> B[Sir Complex Recruitment]
+    B --> C[Sir2 Deacetylase]
+    C --> D[Sir3/Sir4 Binding]
+    D --> E[Histone Deacetylation]
+    E --> F[Chromatin Compaction]
+    F --> G[Heterochromatin Formation]
+    G --> H[Gene Silencing]
+    H --> I[Transcriptional Repression]
+    
+    %% RNAi Silencing
+    J[Double-Stranded RNA] --> K[Dicer Processing]
+    K --> L[Small Interfering RNA]
+    L --> M[RISC Complex]
+    M --> N[Target mRNA Recognition]
+    N --> O[mRNA Degradation]
+    O --> P[Gene Silencing]
+    P --> Q[Post-Transcriptional Silencing]
+    
+    %% Polycomb Silencing
+    R[Developmental Signal] --> S[Polycomb Complex]
+    S --> T[PRC1 Complex]
+    T --> U[PRC2 Complex]
+    U --> V[Histone Methylation]
+    V --> W[Chromatin Modification]
+    W --> X[Gene Repression]
+    X --> Y[Developmental Control]
+    
+    %% Integration
+    I --> Z[Gene Silencing]
+    Q --> Z
+    Y --> Z
+    Z --> AA[Transcriptional Control]
+    AA --> BB[Gene Expression Regulation]
+    BB --> CC[Epigenetic Memory]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style R fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    
+    style CC fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast chromatin regulation and transcription systems
-    </p><p>
-        <em>Batch 08 of 15: Chromatin & Transcription</em>
+            <!-- Process 7: Epigenetic Regulation -->
+            <div class="process-item" id="epigenetic-regulation">
+                <h3>7. Epigenetic Regulation</h3>
+                <p>Detailed analysis of epigenetic regulation using the Programming Framework, revealing computational logic for heritable gene expression control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% DNA Methylation
+    A[Epigenetic Signal] --> B[DNA Methyltransferase]
+    B --> C[Dnmt1 Maintenance]
+    C --> D[Dnmt3a/3b De Novo]
+    D --> E[CpG Methylation]
+    E --> F[DNA Methylation Pattern]
+    F --> G[Gene Expression Regulation]
+    G --> H[Epigenetic Memory]
+    
+    %% Histone Code
+    I[Regulatory Signal] --> J[Histone Modifying Enzymes]
+    J --> K[Histone Acetyltransferases]
+    K --> L[Histone Methyltransferases]
+    L --> M[Histone Phosphatases]
+    M --> N[Histone Code]
+    N --> O[Chromatin State]
+    O --> P[Gene Expression Control]
+    
+    %% Chromatin Remodeling
+    Q[Developmental Signal] --> R[Chromatin Remodeling Complexes]
+    R --> S[SWI/SNF Complex]
+    S --> T[ISWI Complex]
+    T --> U[CHD Complex]
+    U --> V[Chromatin Structure]
+    V --> W[DNA Accessibility]
+    W --> X[Transcription Regulation]
+    
+    %% Integration
+    H --> Y[Epigenetic Regulation]
+    P --> Y
+    X --> Y
+    Y --> Z[Heritable Gene Expression]
+    Z --> AA[Developmental Control]
+    AA --> BB[Cellular Memory]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style Q fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    
+    style BB fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast chromatin and transcription systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 08 of 15: Chromatin & Transcription</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch08_membrane_transport.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Glucose Concentration Gradient] --> B[Glucose Transporter Activation]
     B --> C[Glucose Binding]
     C --> D[Conformational Change]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Transporter Reset]
     F --> G[Glucose Uptake]
     G --> H[Metabolic Processing]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Amino Acid Availability] --> B[Amino Acid Transporter]
     B --> C[Substrate Recognition]
     C --> D[Transporter Activation]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Intracellular Release]
     F --> G[Protein Synthesis]
     G --> H[Cellular Growth]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Ion Concentration Gradient] --> B[Ion Channel Activation]
     B --> C[Ion Binding]
     C --> D[Channel Opening]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Channel Closing]
     F --> G[Ion Homeostasis]
     G --> H[Cellular Function]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cargo Loading] --> B[Vesicle Formation]
     B --> C[Coating Assembly]
     C --> D[Vesicle Budding]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Target Recognition]
     F --> G[Vesicle Fusion]
     G --> H[Cargo Delivery]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Protein Synthesis] --> B[Signal Peptide Recognition]
     B --> C[ER Targeting]
     C --> D[Protein Folding]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Golgi Transport]
     F --> G[Secretion Vesicle]
     G --> H[Extracellular Release]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Ligand Binding] --> B[Clathrin Assembly]
     B --> C[Membrane Invagination]
     C --> D[Vesicle Formation]
@@ -314,7 +320,7 @@ graph TD
     E --> F[Early Endosome]
     F --> G[Sorting Decision]
     G --> H[Intracellular Processing]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Vesicle Formation] --> B[Vesicle Transport]
     B --> C[Target Membrane Recognition]
     C --> D[SNARE Complex Assembly]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Fusion Pore Formation]
     F --> G[Content Release]
     G --> H[Extracellular Delivery]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Membrane Recognition] --> B[SNARE Protein Binding]
     B --> C[Zippering Process]
     C --> D[Membrane Deformation]
@@ -382,7 +390,7 @@ graph TD
     E --> F[Content Mixing]
     F --> G[Membrane Integration]
     G --> H[Fusion Complete]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch09_cell_communication.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Pheromone Secretion] --> B[Receptor Binding]
     B --> C[G Protein Activation]
     C --> D[Signal Transduction]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Mating Response]
     F --> G[Cell Fusion]
     G --> H[Diploid Formation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Population Density] --> B[Autoinducer Production]
     B --> C[Signal Accumulation]
     C --> D[Threshold Detection]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Collective Behavior]
     F --> G[Biofilm Formation]
     G --> H[Population Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cell Recognition] --> B[Adhesion Molecule Expression]
     B --> C[Ligand-Receptor Binding]
     C --> D[Cell Contact Formation]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Cell Aggregation]
     F --> G[Tissue Formation]
     G --> H[Multicellular Structure]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cell Contact] --> B[Connexin Expression]
     B --> C[Gap Junction Assembly]
     C --> D[Channel Formation]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Metabolic Coupling]
     F --> G[Signal Propagation]
     G --> H[Coordinated Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Ligand Binding] --> B[Receptor Activation]
     B --> C[Conformational Change]
     C --> D[Kinase Activity]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Signal Amplification]
     F --> G[Target Activation]
     G --> H[Cellular Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Primary Signal] --> B[Second Messenger Production]
     B --> C[Signal Amplification]
     C --> D[Target Protein Activation]
@@ -314,7 +320,7 @@ graph TD
     E --> F[Metabolic Changes]
     F --> G[Gene Expression]
     G --> H[Cellular Adaptation]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Signal Reception] --> B[Transcription Factor Activation]
     B --> C[DNA Binding]
     C --> D[Promoter Recognition]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Gene Transcription]
     F --> G[mRNA Production]
     G --> H[Protein Synthesis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Multiple Signals] --> B[Signal Integration]
     B --> C[Response Decision]
     C --> D[Pathway Coordination]
@@ -382,7 +390,7 @@ graph TD
     E --> F[Response Execution]
     F --> G[Feedback Regulation]
     G --> H[Coordinated Response]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch09_rna_processing_transport.html

@@ -2,101 +2,446 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 09: RNA Processing & Transport</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
-            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: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 09: RNA Processing & Transport - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 09
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 09: RNA Processing & Transport (4 processes)
-    </h
><p>
-        RNA maturation and nucleocytoplasmic transport systems
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 4 RNA Processing Processes
-    </h
><ul>
-        <li>
-            <a href="#rna-splicing">1. RNA Splicing</a></li><li>
-            <a href="#rna-capping">2. RNA Capping</a></li><li>
-            <a href="#polya-addition">3. Poly(A) Addition</a></li><li>
-            <a href="#mrna-export">4. mRNA Export</a></li></ul></div><!-- Process 1: RNA Splicing --> <div class="process-item" id="rna-splicing">
-        <h3>
-        1. RNA Splicing
-    </h
><p>
-        Detailed analysis of RNA Splicing using the Programming Framework, revealing computational logic for intron removal and exon joining.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Pre-mRNA] --> B[5' Splice Site Recognition] B --> C[U1 snRNP Binding] C --> D[Branch Point Recognition] D --> E[U2 snRNP Assembly] E --> F[3' Splice Site Recognition] F --> G[U4/U6•U5 tri-snRNP] G --> H[Spliceosome Assembly] H --> I[First Transesterification] I --> J[Lariat Formation] J --> K[Second Transesterification] K --> L[Exon Ligation] L --> M[Intron Release] M --> N[Mature mRNA] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <h1>🧬 Yeast Batch 09: RNA Processing & Transport</h1>
+            <p>Programming Framework Analysis - Comprehensive RNA Maturation Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>RNA Processing & Transport: mRNA Maturation and Nucleocytoplasmic Transport</h2>
+                <p>This batch contains 4 fundamental yeast processes responsible for RNA processing, maturation, and nucleocytoplasmic transport. These processes represent the core computational systems that ensure proper mRNA maturation, quality control, and delivery to the cytoplasm for translation.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with splicing machinery, capping enzymes, polyadenylation complexes, and transport systems that function as a biological RNA processing and delivery platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 4 RNA Processing & Transport Processes</h2>
+                <ul>
+                    <li><a href="#rna-splicing">1. RNA Splicing</a></li>
+                    <li><a href="#rna-capping">2. RNA Capping</a></li>
+                    <li><a href="#polya-addition">3. Poly(A) Addition</a></li>
+                    <li><a href="#mrna-export">4. mRNA Export</a></li>
+                </ul>
+            </div>
 
-    </div>
-    </div>
-    </div><!-- Process 2: RNA Capping --> <div class="process-item" id="rna-capping">
-        <h3>
-        2. RNA Capping
-    </h
><p>
-        Detailed analysis of RNA Capping using the Programming Framework, revealing computational logic for mRNA 5' end modification.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Nascent mRNA] --> B[Phosphatase Activity] B --> C[5'-Triphosphate Removal] C --> D[Capping Enzyme] D --> E[GMP Addition] E --> A[Methyltransferase] A --> B[N7-Methylguanosine] B --> C[2'-O-Methyltransferase] C --> I[Cap 1 Structure] I --> J[Cap-Binding Complex] J --> K[mRNA Stability] K --> L[Translation Enhancement] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 1: RNA Splicing -->
+            <div class="process-item" id="rna-splicing">
+                <h3>1. RNA Splicing</h3>
+                <p>Detailed analysis of RNA splicing using the Programming Framework, revealing computational logic for intron removal and exon joining.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Splice Site Recognition
+    A[Pre-mRNA Transcription] --> B[5' Splice Site Recognition]
+    B --> C[U1 snRNP Binding]
+    C --> D[5' Splice Site Scanning]
+    D --> E[Branch Point Recognition]
+    E --> F[U2 snRNP Assembly]
+    F --> G[U2 snRNP Binding]
+    G --> H[3' Splice Site Recognition]
+    H --> I[U4/U6•U5 tri-snRNP]
+    I --> J[U4/U6•U5 Recruitment]
+    J --> K[Spliceosome Assembly]
+    K --> L[U4/U6 Dissociation]
+    L --> M[U6-U2 Interaction]
+    M --> N[Catalytic Core Formation]
+    N --> O[First Transesterification]
+    O --> P[5' Exon Release]
+    P --> Q[Lariat Formation]
+    Q --> R[Branch Point Adenosine]
+    R --> S[Second Transesterification]
+    S --> T[3' Exon Attack]
+    T --> U[Exon Ligation]
+    U --> V[Intron Release]
+    V --> W[Lariat Intron]
+    W --> X[Mature mRNA]
+    X --> Y[Spliceosome Disassembly]
+    Y --> Z[snRNP Recycling]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,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>
-    </div>
-    </div><!-- Process 3: mRNA Export --> <div class="process-item" id="mrna-export">
-        <h3>
-        4. mRNA Export
-    </h
><p>
-        Detailed analysis of mRNA Export using the Programming Framework, revealing computational logic for nucleocytoplasmic transport.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Mature mRNA] --> B[mRNA-Protein Complex] B --> C[Nuclear Export Signal] C --> D[Exportin Recognition] D --> E[Nuclear Pore Complex] E --> A[Translocation] A --> G[Cytoplasmic Release] G --> H[mRNA Localization] H --> I[Translation Initiation] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 2: RNA Capping -->
+            <div class="process-item" id="rna-capping">
+                <h3>2. RNA Capping</h3>
+                <p>Detailed analysis of RNA capping using the Programming Framework, revealing computational logic for mRNA 5' end modification.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Capping Initiation
+    A[Nascent mRNA Synthesis] --> B[5' Triphosphate Recognition]
+    B --> C[Phosphatase Activity]
+    C --> D[5'-Triphosphate Removal]
+    D --> E[5' Diphosphate Formation]
+    E --> F[Capping Enzyme Recognition]
+    F --> G[Capping Enzyme Binding]
+    G --> H[GMP Transfer]
+    H --> I[5' GMP Addition]
+    I --> J[5'-5' Triphosphate Linkage]
+    J --> K[Guanylyltransferase Activity]
+    K --> L[Cap 0 Structure]
+    L --> M[N7-Methyltransferase]
+    M --> N[SAM Binding]
+    N --> O[N7-Methylation]
+    O --> P[N7-Methylguanosine]
+    P --> Q[Cap 1 Methyltransferase]
+    Q --> R[2'-O-Methyltransferase]
+    R --> S[2'-O-Methylation]
+    S --> T[Cap 1 Structure]
+    T --> U[Cap-Binding Complex]
+    U --> V[CBP20/CBP80 Binding]
+    V --> W[mRNA Stability]
+    W --> X[Translation Enhancement]
+    X --> Y[Nuclear Export Signal]
+    Y --> Z[mRNA Processing]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    
+    style Z fill:#74c0fc,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>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 3: Poly(A) Addition -->
+            <div class="process-item" id="polya-addition">
+                <h3>3. Poly(A) Addition</h3>
+                <p>Detailed analysis of poly(A) addition using the Programming Framework, revealing computational logic for mRNA 3' end processing.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Polyadenylation Signal Recognition
+    A[Transcription Termination] --> B[Polyadenylation Signal Recognition]
+    B --> C[AAUAAA Sequence]
+    C --> D[CPSF Complex]
+    D --> E[CPSF Binding]
+    E --> F[Cleavage Site Recognition]
+    F --> G[G/U-Rich Element]
+    G --> H[CstF Complex]
+    H --> I[CstF Binding]
+    I --> J[Cleavage and Polyadenylation Complex]
+    J --> K[Pre-mRNA Cleavage]
+    K --> L[3' End Formation]
+    L --> M[Poly(A) Polymerase]
+    M --> N[Poly(A) Polymerase Binding]
+    N --> O[ATP Binding]
+    O --> P[Poly(A) Tail Synthesis]
+    P --> Q[Adenosine Addition]
+    Q --> R[Poly(A) Tail Elongation]
+    R --> S[Poly(A) Binding Protein]
+    S --> T[PABP Binding]
+    T --> U[mRNA Stabilization]
+    U --> V[Translation Enhancement]
+    V --> W[Nuclear Export Signal]
+    W --> X[mRNA Maturation]
+    X --> Y[3' End Processing]
+    Y --> Z[Mature mRNA]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    
+    style Z fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast RNA processing and transport systems
-    </p><p>
-        <em>Batch 09 of 15: RNA Processing & Transport</em>
+            <!-- Process 4: mRNA Export -->
+            <div class="process-item" id="mrna-export">
+                <h3>4. mRNA Export</h3>
+                <p>Detailed analysis of mRNA export using the Programming Framework, revealing computational logic for nucleocytoplasmic transport.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% mRNA Export Preparation
+    A[Mature mRNA Formation] --> B[mRNA-Protein Complex Assembly]
+    B --> C[SR Protein Binding]
+    C --> D[SR Protein Phosphorylation]
+    D --> E[Nuclear Export Signal Recognition]
+    E --> F[NXF1/NXT1 Complex]
+    F --> G[Exportin Recognition]
+    G --> H[TAP/p15 Complex]
+    H --> I[Nuclear Export Signal Binding]
+    I --> J[Export Complex Formation]
+    J --> K[Nuclear Pore Complex]
+    K --> L[NPC Recognition]
+    L --> M[NPC Docking]
+    M --> N[Nuclear Basket]
+    N --> O[Central Channel]
+    O --> P[Translocation]
+    P --> Q[Cytoplasmic Filaments]
+    Q --> R[Cytoplasmic Release]
+    R --> S[Export Complex Disassembly]
+    S --> T[mRNA Release]
+    T --> U[mRNA Localization]
+    U --> V[Translation Initiation]
+    V --> W[Protein Synthesis]
+    W --> X[Cytoplasmic Function]
+    X --> Y[mRNA Processing]
+    Y --> Z[Nucleocytoplasmic Transport]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    
+    style Z fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast RNA processing and transport systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 09 of 15: RNA Processing & Transport</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch10_developmental_biology.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Nutrient Depletion] --> B[Spo0A Activation]
     B --> C[Developmental Switch]
     C --> D[Meiotic Division]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Spore Maturation]
     F --> G[Dormancy Establishment]
     G --> H[Spore Survival]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Pheromone Detection] --> B[Mating Response]
     B --> C[Cell Cycle Arrest]
     C --> D[Polarized Growth]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Nuclear Fusion]
     F --> G[Diploid Formation]
     G --> H[Zygote Development]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Nitrogen Limitation] --> B[Flo11 Expression]
     B --> C[Cell Elongation]
     C --> D[Polarized Growth]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Cell-Cell Adhesion]
     F --> G[Multicellular Structure]
     G --> H[Invasive Growth]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Environmental Cues] --> B[Gene Expression Changes]
     B --> C[Protein Synthesis]
     C --> D[Metabolic Reprogramming]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Specialized Functions]
     F --> G[Differentiated State]
     G --> H[Cell Specialization]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Temporal Signals] --> B[Clock Gene Expression]
     B --> C[Circadian Rhythm]
     C --> D[Developmental Clock]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Temporal Coordination]
     F --> G[Developmental Progression]
     G --> H[Maturation Complete]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Developmental Signals] --> B[Cytoskeletal Reorganization]
     B --> C[Cell Shape Changes]
     C --> D[Membrane Remodeling]
@@ -314,7 +320,7 @@ graph TD
     E --> F[Cell Wall Modification]
     F --> G[Structural Assembly]
     G --> H[Morphological Pattern]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Fate Signals] --> B[Transcription Factor Expression]
     B --> C[Gene Regulatory Network]
     C --> D[Fate Commitment]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Differentiation Program]
     F --> G[Fate Stabilization]
     G --> H[Cell Identity]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Environmental Inputs] --> B[Developmental Checkpoints]
     B --> C[Regulatory Networks]
     C --> D[Feedback Control]
@@ -382,7 +390,7 @@ graph TD
     E --> F[Quality Control]
     F --> G[Developmental Completion]
     G --> H[Developmental Success]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch10_stress_response_adaptation.html

@@ -2,100 +2,496 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 10: Stress Response & Adaptation</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
-            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: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 10: Stress Response & Adaptation - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 10
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 10: Stress Response & Adaptation (4 processes)
-    </h
><p>
-        Environmental stress sensing and adaptive response systems
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 4 Stress Response Processes
-    </h
><ul>
-        <li>
-            <a href="#heat-shock">1. Heat Shock Response</a></li><li>
-            <a href="#osmotic-stress">2. Osmotic Stress Response</a></li><li>
-            <a href="#oxidative-stress">3. Oxidative Stress Response</a></li><li>
-            <a href="#general-stress">4. General Stress Response</a></li></ul></div><!-- Process 1: Heat Shock Response --> <div class="process-item" id="heat-shock">
-        <h3>
-        1. Heat Shock Response
-    </h
><p>
-        Detailed analysis of Heat Shock Response using the Programming Framework, revealing computational logic for temperature stress adaptation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Temperature Stress] --> B[Protein Misfolding] B --> C[HSF1 Activation] C --> D[Heat Shock Element Binding] D --> E[HSP Gene Expression] E --> F[Heat Shock Proteins] F --> G[Protein Refolding] G --> H[Cellular Protection] H --> I[Stress Adaptation] J[Severe Stress] --> K[Protein Aggregation] K --> L[Autophagy Activation] L --> M[Aggregate Clearance] M --> N[Cell Survival] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <h1>🧬 Yeast Batch 10: Stress Response & Adaptation</h1>
+            <p>Programming Framework Analysis - Comprehensive Stress Management Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Stress Response & Adaptation: Environmental Sensing and Survival Systems</h2>
+                <p>This batch contains 4 fundamental yeast processes responsible for stress sensing, response activation, and adaptive survival mechanisms. These processes represent the core computational systems that ensure cellular survival under diverse environmental challenges and stress conditions.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with stress sensors, signal transduction pathways, and adaptive responses that function as a biological stress management and survival platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 4 Stress Response & Adaptation Processes</h2>
+                <ul>
+                    <li><a href="#heat-shock">1. Heat Shock Response</a></li>
+                    <li><a href="#osmotic-stress">2. Osmotic Stress Response</a></li>
+                    <li><a href="#oxidative-stress">3. Oxidative Stress Response</a></li>
+                    <li><a href="#general-stress">4. General Stress Response</a></li>
+                </ul>
+            </div>
 
-    </div>
-    </div>
-    </div><!-- Process 2: Osmotic Stress Response --> <div class="process-item" id="osmotic-stress">
-        <h3>
-        2. Osmotic Stress Response
-    </h
><p>
-        Detailed analysis of Osmotic Stress Response using the Programming Framework, revealing computational logic for water balance regulation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Osmotic Stress] --> B[Cell Wall Stress] B --> C[Sln1 Sensor] C --> D[HOG Pathway] D --> E[Hog1 MAPK] E --> F[Transcription Factor Activation] F --> G[Osmoprotectant Synthesis] G --> H[Glycerol Accumulation] H --> I[Osmotic Balance] I --> J[Cell Volume Recovery] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 1: Heat Shock Response -->
+            <div class="process-item" id="heat-shock">
+                <h3>1. Heat Shock Response</h3>
+                <p>Detailed analysis of heat shock response using the Programming Framework, revealing computational logic for temperature stress adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Heat Stress Detection
+    A[Temperature Increase] --> B[Protein Misfolding]
+    B --> C[Misfolded Protein Accumulation]
+    C --> D[Chaperone Saturation]
+    D --> E[HSF1 Monomer Release]
+    E --> F[HSF1 Trimerization]
+    F --> G[HSF1 Nuclear Localization]
+    G --> H[HSF1 Phosphorylation]
+    H --> I[HSF1 DNA Binding]
+    I --> J[Heat Shock Element Recognition]
+    J --> K[HSP Gene Transcription]
+    K --> L[HSP70 mRNA Synthesis]
+    L --> M[HSP90 mRNA Synthesis]
+    M --> N[HSP104 mRNA Synthesis]
+    N --> O[HSP Protein Translation]
+    O --> P[Heat Shock Protein Assembly]
+    P --> Q[Protein Refolding Activity]
+    Q --> R[Misfolded Protein Recognition]
+    R --> S[Protein Refolding]
+    S --> T[Cellular Protection]
+    T --> U[Stress Adaptation]
+    
+    %% Severe Stress Response
+    V[Severe Heat Stress] --> W[Protein Aggregation]
+    W --> X[Aggregate Formation]
+    X --> Y[Autophagy Activation]
+    Y --> Z[Atg1 Kinase]
+    Z --> AA[Autophagosome Formation]
+    AA --> BB[Aggregate Sequestration]
+    BB --> CC[Lysosomal Degradation]
+    CC --> DD[Aggregate Clearance]
+    DD --> EE[Cell Survival]
+    
+    %% Integration
+    U --> FF[Heat Shock Response]
+    EE --> FF
+    FF --> GG[Temperature Adaptation]
+    GG --> HH[Cellular Protection]
+    HH --> II[Stress Resistance]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style V fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    
+    style II fill:#74c0fc,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>
-    </div>
-    </div><!-- Process 3: Oxidative Stress Response --> <div class="process-item" id="oxidative-stress">
-        <h3>
-        3. Oxidative Stress Response
-    </h
><p>
-        Detailed analysis of Oxidative Stress Response using the Programming Framework, revealing computational logic for ROS detoxification.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Reactive Oxygen Species] --> B[Oxidative Damage] B --> C[Yap1 Activation] C --> D[Nuclear Translocation] D --> E[Antioxidant Gene Expression] E --> F[Catalase/SOD Production] F --> G[ROS Detoxification] G --> H[Cellular Protection] I[DNA Damage] --> J[Repair Mechanisms] J --> K[Genomic Stability] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 2: Osmotic Stress Response -->
+            <div class="process-item" id="osmotic-stress">
+                <h3>2. Osmotic Stress Response</h3>
+                <p>Detailed analysis of osmotic stress response using the Programming Framework, revealing computational logic for water balance regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Osmotic Stress Detection
+    A[Osmotic Stress] --> B[Cell Wall Stress]
+    B --> C[Membrane Tension]
+    C --> D[Sln1 Sensor Activation]
+    D --> E[Sln1 Phosphorylation]
+    E --> F[Ypd1 Phosphotransfer]
+    F --> G[Ssk1 Phosphorylation]
+    G --> H[Ssk2/Ssk22 MAPKKK]
+    H --> I[Pbs2 MAPKK]
+    I --> J[Hog1 MAPK]
+    J --> K[Hog1 Phosphorylation]
+    K --> L[Hog1 Nuclear Localization]
+    L --> M[Transcription Factor Activation]
+    M --> N[Hot1 Activation]
+    N --> O[Sko1 Activation]
+    O --> P[Msn2/Msn4 Activation]
+    P --> Q[Osmoprotectant Gene Expression]
+    Q --> R[Glycerol-3-Phosphate Dehydrogenase]
+    R --> S[Glycerol Synthesis]
+    S --> T[Glycerol Accumulation]
+    T --> U[Intracellular Osmolarity]
+    U --> V[Osmotic Balance]
+    V --> W[Cell Volume Recovery]
+    W --> X[Osmotic Adaptation]
+    
+    %% Integration
+    X --> Y[Osmotic Stress Response]
+    Y --> Z[Water Balance Regulation]
+    Z --> AA[Cell Volume Control]
+    AA --> BB[Osmotic Homeostasis]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    
+    style BB fill:#74c0fc,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>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 3: Oxidative Stress Response -->
+            <div class="process-item" id="oxidative-stress">
+                <h3>3. Oxidative Stress Response</h3>
+                <p>Detailed analysis of oxidative stress response using the Programming Framework, revealing computational logic for ROS detoxification.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Oxidative Stress Detection
+    A[Reactive Oxygen Species] --> B[ROS Accumulation]
+    B --> C[Oxidative Damage]
+    C --> D[Lipid Peroxidation]
+    D --> E[Protein Oxidation]
+    E --> F[DNA Damage]
+    F --> G[Yap1 Activation]
+    G --> H[Yap1 Phosphorylation]
+    H --> I[Yap1 Nuclear Localization]
+    I --> J[Yap1 DNA Binding]
+    J --> K[Antioxidant Gene Expression]
+    K --> L[Catalase Expression]
+    L --> M[Superoxide Dismutase]
+    M --> N[Glutathione Peroxidase]
+    N --> O[Antioxidant Enzyme Production]
+    O --> P[ROS Detoxification]
+    P --> Q[Superoxide Scavenging]
+    Q --> R[Hydrogen Peroxide Breakdown]
+    R --> S[Oxidative Damage Repair]
+    S --> T[Cellular Protection]
+    T --> U[Oxidative Stress Adaptation]
+    
+    %% DNA Damage Response
+    V[DNA Damage] --> W[DNA Repair Mechanisms]
+    W --> X[Base Excision Repair]
+    X --> Y[Nucleotide Excision Repair]
+    Y --> Z[DNA Polymerase Activity]
+    Z --> AA[DNA Ligase Activity]
+    AA --> BB[DNA Repair Completion]
+    BB --> CC[Genomic Stability]
+    CC --> DD[Cell Survival]
+    
+    %% Integration
+    U --> EE[Oxidative Stress Response]
+    DD --> EE
+    EE --> FF[ROS Detoxification]
+    FF --> GG[Cellular Protection]
+    GG --> HH[Oxidative Stress Resistance]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style V fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    
+    style HH fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast stress response and environmental adaptation systems
-    </p><p>
-        <em>Batch 10 of 15: Stress Response & Adaptation</em>
+            <!-- Process 4: General Stress Response -->
+            <div class="process-item" id="general-stress">
+                <h3>4. General Stress Response</h3>
+                <p>Detailed analysis of general stress response using the Programming Framework, revealing computational logic for broad stress adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% General Stress Detection
+    A[Environmental Stress] --> B[Stress Signal Integration]
+    B --> C[Msn2/Msn4 Activation]
+    C --> D[Msn2/Msn4 Dephosphorylation]
+    D --> E[Msn2/Msn4 Nuclear Localization]
+    E --> F[Stress Response Element Binding]
+    F --> G[General Stress Gene Expression]
+    G --> H[Trehalose Synthesis]
+    H --> I[Trehalose-6-Phosphate Synthase]
+    I --> J[Trehalose Accumulation]
+    J --> K[Stress Protection]
+    K --> L[Cell Survival]
+    L --> M[Stress Adaptation]
+    
+    %% RpoS Response
+    N[Multiple Stress Signals] --> O[RpoS Activation]
+    O --> P[RpoS Expression]
+    P --> Q[RpoS Accumulation]
+    Q --> R[Stationary Phase Genes]
+    R --> S[Stress Resistance Proteins]
+    S --> T[General Stress Protection]
+    T --> U[Stress Survival]
+    
+    %% Integration
+    M --> V[General Stress Response]
+    U --> V
+    V --> W[Stress Adaptation]
+    W --> X[Environmental Resistance]
+    X --> Y[Cell Survival]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style N fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    
+    style Y fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast stress response and adaptation systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 10 of 15: Stress Response & Adaptation</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch11_advanced_metabolic_pathways.html

@@ -2,132 +2,761 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 11: Advanced Metabolic Pathways</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
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-        } line-height: 1.6; margin: 0; padding: 0; background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); min-height: 100vh; } .container { max-width: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 11: Advanced Metabolic Pathways - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 11
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 11: Advanced Metabolic Pathways (8 processes)
-    </h
><p>
-        Specialized biosynthetic and catabolic pathways
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 8 Advanced Metabolic Processes
-    </h
><ul>
-        <li>
-            <a href="#amino-acid-biosynthesis">1. Amino Acid Biosynthesis</a></li><li>
-            <a href="#nucleotide-synthesis">2. Nucleotide Synthesis</a></li><li>
-            <a href="#vitamin-cofactor">3. Vitamin/Cofactor Synthesis</a></li><li>
-            <a href="#secondary-metabolism">4. Secondary Metabolism</a></li><li>
-            <a href="#polyamine-synthesis">5. Polyamine Synthesis</a></li><li>
-            <a href="#sulfur-metabolism">6. Sulfur Metabolism</a></li><li>
-            <a href="#one-carbon-metabolism">7. One-Carbon Metabolism</a></li><li>
-            <a href="#glyoxylate-cycle">8. Glyoxylate Cycle</a></li></ul></div><!-- Process 1: Amino Acid Biosynthesis --> <div class="process-item" id="amino-acid-biosynthesis">
-        <h3>
-        1. Amino Acid Biosynthesis
-    </h
><p>
-        Detailed analysis of Amino Acid Biosynthesis using the Programming Framework, revealing computational logic for protein building block production.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Carbon Skeletons] --> B{Amino Acid Family?} B 
-
-    -->|Aromatic| 
-C[Shikimate Pathway] B 
-
-    -->|Branched| 
-D[Pyruvate Family] B 
-
-    -->|Aspartate| 
-E[Aspartate Family] B 
+            <h1>🧬 Yeast Batch 11: Advanced Metabolic Pathways</h1>
+            <p>Programming Framework Analysis - Comprehensive Biosynthetic Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Advanced Metabolic Pathways: Specialized Biosynthetic and Catabolic Systems</h2>
+                <p>This batch contains 8 fundamental yeast processes responsible for specialized biosynthetic pathways, cofactor synthesis, and advanced metabolic regulation. These processes represent the core computational systems that ensure proper biosynthesis of essential cellular components and specialized metabolites.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with multi-step biosynthetic pathways, regulatory feedback loops, and metabolic integration that function as a biological chemical synthesis and regulation platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Advanced Metabolic Processes</h2>
+                <ul>
+                    <li><a href="#amino-acid-biosynthesis">1. Amino Acid Biosynthesis</a></li>
+                    <li><a href="#nucleotide-synthesis">2. Nucleotide Synthesis</a></li>
+                    <li><a href="#vitamin-cofactor">3. Vitamin/Cofactor Synthesis</a></li>
+                    <li><a href="#secondary-metabolism">4. Secondary Metabolism</a></li>
+                    <li><a href="#polyamine-synthesis">5. Polyamine Synthesis</a></li>
+                    <li><a href="#sulfur-metabolism">6. Sulfur Metabolism</a></li>
+                    <li><a href="#one-carbon-metabolism">7. One-Carbon Metabolism</a></li>
+                    <li><a href="#glyoxylate-cycle">8. Glyoxylate Cycle</a></li>
+                </ul>
+            </div>
 
-    -->|Glutamate| 
-F[Glutamate Family] C --> A[Phenylalanine/Tyrosine/Tryptophan] D --> B[Valine/Leucine/Isoleucine] E --> C[Lysine/Threonine/Methionine] F --> D[Proline/Arginine/Glutamine] A --> K[Protein Synthesis] B 
+            <!-- Process 1: Amino Acid Biosynthesis -->
+            <div class="process-item" id="amino-acid-biosynthesis">
+                <h3>1. Amino Acid Biosynthesis</h3>
+                <p>Detailed analysis of amino acid biosynthesis using the Programming Framework, revealing computational logic for protein building block production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Aromatic Amino Acid Biosynthesis
+    A[Phosphoenolpyruvate] --> B[Shikimate Pathway]
+    B --> C[3-Deoxy-D-arabino-heptulosonate-7-phosphate]
+    C --> D[3-Dehydroquinate]
+    D --> E[3-Dehydroshikimate]
+    E --> F[Shikimate]
+    F --> G[Shikimate-3-phosphate]
+    G --> H[5-Enolpyruvylshikimate-3-phosphate]
+    H --> I[Chorismate]
+    I --> J[Prephenate]
+    J --> K[Phenylpyruvate]
+    K --> L[Phenylalanine]
+    I --> M[4-Hydroxyphenylpyruvate]
+    M --> N[Tyrosine]
+    I --> O[Anthranilate]
+    O --> P[Indole-3-glycerol-phosphate]
+    P --> Q[Tryptophan]
+    
+    %% Branched Chain Amino Acids
+    R[Pyruvate] --> S[Acetolactate Synthase]
+    S --> T[Acetolactate]
+    T --> U[Acetohydroxy Acid Isomeroreductase]
+    U --> V[2,3-Dihydroxy-3-methylvalerate]
+    V --> W[Dihydroxy Acid Dehydratase]
+    W --> X[2-Keto-3-methylvalerate]
+    X --> Y[Valine]
+    X --> Z[2-Keto-4-methylvalerate]
+    Z --> AA[Leucine]
+    
+    %% Aspartate Family
+    BB[Oxaloacetate] --> CC[Aspartate Aminotransferase]
+    CC --> DD[Aspartate]
+    DD --> EE[Aspartate Kinase]
+    EE --> FF[Aspartate-β-semialdehyde]
+    FF --> GG[Homoserine]
+    GG --> HH[Threonine]
+    GG --> II[Methionine]
+    DD --> JJ[Lysine]
+    
+    %% Glutamate Family
+    KK[α-Ketoglutarate] --> LL[Glutamate Dehydrogenase]
+    LL --> MM[Glutamate]
+    MM --> NN[Glutamate Kinase]
+    NN --> OO[Glutamate-5-semialdehyde]
+    OO --> PP[Proline]
+    MM --> QQ[Glutamine Synthetase]
+    QQ --> RR[Glutamine]
+    MM --> SS[Arginine]
+    
+    %% Integration
+    L --> TT[Amino Acid Biosynthesis]
+    N --> TT
+    Q --> TT
+    Y --> TT
+    AA --> TT
+    HH --> TT
+    II --> TT
+    JJ --> TT
+    PP --> TT
+    RR --> TT
+    SS --> TT
+    TT --> UU[Protein Synthesis]
+    UU --> VV[Cellular Function]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style R fill:#ff6b6b,color:#fff
+    style BB fill:#ff6b6b,color:#fff
+    style KK fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    style MM fill:#ffd43b,color:#000
+    style NN fill:#ffd43b,color:#000
+    style OO fill:#ffd43b,color:#000
+    style PP fill:#ffd43b,color:#000
+    style QQ fill:#ffd43b,color:#000
+    style RR fill:#ffd43b,color:#000
+    style SS fill:#ffd43b,color:#000
+    style TT fill:#ffd43b,color:#000
+    style UU fill:#ffd43b,color:#000
+    style VV fill:#ffd43b,color:#000
+    
+    style VV fill:#74c0fc,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>
 
-    --> K C 
+            <!-- Process 2: Nucleotide Synthesis -->
+            <div class="process-item" id="nucleotide-synthesis">
+                <h3>2. Nucleotide Synthesis</h3>
+                <p>Detailed analysis of nucleotide synthesis using the Programming Framework, revealing computational logic for DNA/RNA precursor production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Purine Biosynthesis
+    A[Ribose-5-Phosphate] --> B[PRPP Synthetase]
+    B --> C[5-Phosphoribosyl-1-pyrophosphate]
+    C --> D[Glutamine-PRPP Amidotransferase]
+    D --> E[5-Phosphoribosylamine]
+    E --> F[Glycinamide Ribonucleotide]
+    F --> G[Formylglycinamide Ribonucleotide]
+    G --> H[Formylglycinamidine]
+    H --> I[5-Aminoimidazole Ribonucleotide]
+    I --> J[5-Aminoimidazole-4-carboxylate]
+    J --> K[5-Aminoimidazole-4-N-succinocarboxamide]
+    K --> L[AICAR]
+    L --> M[FAICAR]
+    M --> N[IMP]
+    N --> O[AMP Formation]
+    N --> P[GMP Formation]
+    
+    %% Pyrimidine Biosynthesis
+    Q[Carbamoyl Phosphate] --> R[Aspartate Transcarbamoylase]
+    R --> S[Carbamoyl Aspartate]
+    S --> T[Dihydroorotase]
+    T --> U[Dihydroorotate]
+    U --> V[Dihydroorotate Dehydrogenase]
+    V --> W[Orotate]
+    W --> X[Orotate Phosphoribosyltransferase]
+    X --> Y[OMP]
+    Y --> Z[UMP]
+    Z --> AA[UTP]
+    AA --> BB[CTP]
+    Z --> CC[TMP]
+    
+    %% Deoxyribonucleotide Synthesis
+    DD[NDP] --> EE[Ribonucleotide Reductase]
+    EE --> FF[dNDP]
+    FF --> GG[NDP Kinase]
+    GG --> HH[dNTP]
+    HH --> II[DNA Synthesis]
+    
+    %% Integration
+    O --> JJ[Nucleotide Synthesis]
+    P --> JJ
+    BB --> JJ
+    CC --> JJ
+    II --> JJ
+    JJ --> KK[Nucleic Acid Synthesis]
+    KK --> LL[Genetic Information]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style Q fill:#ff6b6b,color:#fff
+    style DD fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    style LL fill:#ffd43b,color:#000
+    
+    style LL fill:#74c0fc,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>
 
-    --> K D 
+            <!-- Process 3: Vitamin/Cofactor Synthesis -->
+            <div class="process-item" id="vitamin-cofactor">
+                <h3>3. Vitamin/Cofactor Synthesis</h3>
+                <p>Detailed analysis of vitamin and cofactor synthesis using the Programming Framework, revealing computational logic for essential cofactor production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Thiamine Biosynthesis
+    A[Pyruvate] --> B[Thiamine Biosynthesis]
+    B --> C[Thiazole Formation]
+    C --> D[Pyrimidine Formation]
+    D --> E[Thiamine Monophosphate]
+    E --> F[Thiamine Pyrophosphate]
+    F --> G[Coenzyme Function]
+    
+    %% Riboflavin Biosynthesis
+    H[GTP] --> I[Riboflavin Biosynthesis]
+    I --> J[6,7-Dimethyl-8-ribityllumazine]
+    J --> K[Riboflavin Synthase]
+    K --> L[Riboflavin]
+    L --> M[FMN]
+    M --> N[FAD]
+    N --> O[Electron Transfer]
+    
+    %% Biotin Biosynthesis
+    P[Pimeloyl-CoA] --> Q[Biotin Biosynthesis]
+    Q --> R[7-Keto-8-aminopelargonic Acid]
+    R --> S[7,8-Diaminopelargonic Acid]
+    S --> T[Dethiobiotin]
+    T --> U[Biotin]
+    U --> V[Carboxylation Reactions]
+    
+    %% Integration
+    G --> W[Vitamin/Cofactor Synthesis]
+    O --> W
+    V --> W
+    W --> X[Enzyme Function]
+    X --> Y[Metabolic Reactions]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style H fill:#ff6b6b,color:#fff
+    style P fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style E fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G 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 Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    
+    style Y fill:#74c0fc,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>
 
-    --> K 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 2: Nucleotide Synthesis --> <div class="process-item" id="nucleotide-synthesis">
-        <h3>
-        2. Nucleotide Synthesis
-    </h
><p>
-        Detailed analysis of Nucleotide Synthesis using the Programming Framework, revealing computational logic for DNA/RNA precursor production.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Ribose-5-Phosphate] --> B{Nucleotide Type?} B 
+            <!-- Process 4: Secondary Metabolism -->
+            <div class="process-item" id="secondary-metabolism">
+                <h3>4. Secondary Metabolism</h3>
+                <p>Detailed analysis of secondary metabolism using the Programming Framework, revealing computational logic for specialized metabolite production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Terpenoid Biosynthesis
+    A[Acetyl-CoA] --> B[Mevalonate Pathway]
+    B --> C[Isopentenyl Pyrophosphate]
+    C --> D[Geranyl Pyrophosphate]
+    D --> E[Farnesyl Pyrophosphate]
+    E --> F[Squalene]
+    F --> G[Lanosterol]
+    G --> H[Ergosterol]
+    H --> I[Membrane Function]
+    
+    %% Polyketide Biosynthesis
+    J[Malonyl-CoA] --> K[Polyketide Synthase]
+    K --> L[Polyketide Chain]
+    L --> M[Polyketide Products]
+    M --> N[Antimicrobial Activity]
+    
+    %% Alkaloid Biosynthesis
+    O[Amino Acids] --> P[Alkaloid Biosynthesis]
+    P --> Q[Alkaloid Precursors]
+    Q --> R[Alkaloid Products]
+    R --> S[Defense Compounds]
+    
+    %% Integration
+    I --> T[Secondary Metabolism]
+    N --> T
+    S --> T
+    T --> U[Specialized Functions]
+    U --> V[Environmental Adaptation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style O fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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 P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    
+    style V fill:#74c0fc,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>
 
-    -->|Purine| 
-C[IMP Synthesis] B 
+            <!-- Process 5: Polyamine Synthesis -->
+            <div class="process-item" id="polyamine-synthesis">
+                <h3>5. Polyamine Synthesis</h3>
+                <p>Detailed analysis of polyamine synthesis using the Programming Framework, revealing computational logic for polyamine production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Ornithine Decarboxylation
+    A[Ornithine] --> B[Ornithine Decarboxylase]
+    B --> C[Putrescine]
+    C --> D[Spermidine Synthase]
+    D --> E[Spermidine]
+    E --> F[Spermine Synthase]
+    F --> G[Spermine]
+    G --> H[DNA Binding]
+    H --> I[Gene Regulation]
+    
+    %% Integration
+    I --> J[Polyamine Synthesis]
+    J --> K[Cellular Growth]
+    K --> L[Cell Division]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 L fill:#74c0fc,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>
 
-    -->|Pyrimidine| 
-D[UMP Synthesis] C --> E[AMP/GMP Formation] D --> F[CMP/TMP Formation] E --> G[Ribonucleoside Diphosphates] F 
+            <!-- Process 6: Sulfur Metabolism -->
+            <div class="process-item" id="sulfur-metabolism">
+                <h3>6. Sulfur Metabolism</h3>
+                <p>Detailed analysis of sulfur metabolism using the Programming Framework, revealing computational logic for sulfur compound production.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Sulfate Assimilation
+    A[Sulfate] --> B[Sulfate Transporter]
+    B --> C[Sulfate Activation]
+    C --> D[Adenosine 5'-Phosphosulfate]
+    D --> E[3'-Phosphoadenosine 5'-Phosphosulfate]
+    E --> F[Sulfite Reductase]
+    F --> G[Sulfide]
+    G --> H[Cysteine Synthesis]
+    H --> I[Methionine Synthesis]
+    I --> J[Protein Synthesis]
+    
+    %% Integration
+    J --> K[Sulfur Metabolism]
+    K --> L[Amino Acid Production]
+    L --> M[Cellular Function]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 M fill:#74c0fc,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>
 
-    --> G G --> H[Ribonucleoside Triphosphates] H --> I[RNA Synthesis] G --> J[Ribonucleotide Reductase] J --> K[Deoxyribonucleoside Diphosphates] K --> L[Deoxyribonucleoside Triphosphates] L --> M[DNA Synthesis] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 3: One-Carbon Metabolism --> <div class="process-item" id="one-carbon-metabolism">
-        <h3>
-        7. One-Carbon Metabolism
-    </h
><p>
-        Detailed analysis of One-Carbon Metabolism using the Programming Framework, revealing computational logic for methylation and biosynthesis.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Serine] --> B[Serine Hydroxymethyltransferase] B --> C[Glycine + N5,N10-methylene-THF] C --> B[N5-methyl-THF] B --> E[Methionine Synthase] E --> C[Methionine] C --> D[S-Adenosylmethionine] D --> H[Methylation Reactions] H --> E[S-Adenosylhomocysteine] E --> F[Homocysteine] F --> K[Methionine Regeneration] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 7: One-Carbon Metabolism -->
+            <div class="process-item" id="one-carbon-metabolism">
+                <h3>7. One-Carbon Metabolism</h3>
+                <p>Detailed analysis of one-carbon metabolism using the Programming Framework, revealing computational logic for methylation and biosynthesis.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Serine to Glycine Conversion
+    A[Serine] --> B[Serine Hydroxymethyltransferase]
+    B --> C[Glycine + N5,N10-methylene-THF]
+    C --> D[N5,N10-methylene-THF Reductase]
+    D --> E[N5-methyl-THF]
+    E --> F[Methionine Synthase]
+    F --> G[Methionine]
+    G --> H[S-Adenosylmethionine Synthase]
+    H --> I[S-Adenosylmethionine]
+    I --> J[Methyltransferase]
+    J --> K[Methylation Reactions]
+    K --> L[S-Adenosylhomocysteine]
+    L --> M[S-Adenosylhomocysteine Hydrolase]
+    M --> N[Homocysteine]
+    N --> O[Methionine Regeneration]
+    
+    %% Integration
+    O --> P[One-Carbon Metabolism]
+    P --> Q[Methylation]
+    Q --> R[Epigenetic Regulation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    
+    style R fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast advanced metabolic and biosynthetic pathway systems
-    </p><p>
-        <em>Batch 11 of 15: Advanced Metabolic Pathways</em>
+            <!-- Process 8: Glyoxylate Cycle -->
+            <div class="process-item" id="glyoxylate-cycle">
+                <h3>8. Glyoxylate Cycle</h3>
+                <p>Detailed analysis of the glyoxylate cycle using the Programming Framework, revealing computational logic for acetate utilization.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Glyoxylate Cycle
+    A[Acetyl-CoA] --> B[Citrate Synthase]
+    B --> C[Citrate]
+    C --> D[Aconitase]
+    D --> E[Isocitrate]
+    E --> F[Isocitrate Lyase]
+    F --> G[Glyoxylate + Succinate]
+    G --> H[Malate Synthase]
+    H --> I[Malate]
+    I --> J[Malate Dehydrogenase]
+    J --> K[Oxaloacetate]
+    K --> L[Gluconeogenesis]
+    L --> M[Carbohydrate Synthesis]
+    
+    %% Integration
+    M --> N[Glyoxylate Cycle]
+    N --> O[Acetate Utilization]
+    O --> P[Energy Production]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 P fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast advanced metabolic pathway systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 11 of 15: Advanced Metabolic Pathways</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch11_stress_response.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[ROS Production] --> B[Oxidative Damage]
     B --> C[Stress Sensor Activation]
     C --> D[Transcription Factor Induction]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Antioxidant Production]
     F --> G[ROS Scavenging]
     G --> H[Oxidative Balance]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Temperature Increase] --> B[Protein Denaturation]
     B --> C[Heat Shock Factor Activation]
     C --> D[HSP Gene Expression]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Protein Refolding]
     F --> G[Chaperone Activity]
     G --> H[Protein Homeostasis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Osmotic Pressure] --> B[Cell Volume Changes]
     B --> C[Osmosensor Activation]
     C --> D[Signaling Cascade]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Osmolyte Accumulation]
     F --> G[Osmotic Balance]
     G --> H[Cell Survival]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Nutrient Depletion] --> B[Starvation Detection]
     B --> C[Metabolic Reprogramming]
     C --> D[Autophagy Induction]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Energy Conservation]
     F --> G[Survival Mode]
     G --> H[Cell Dormancy]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[DNA Damage] --> B[Damage Sensor Activation]
     B --> C[Checkpoint Activation]
     C --> D[Cell Cycle Arrest]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Repair Protein Synthesis]
     F --> G[DNA Repair]
     G --> H[Genomic Integrity]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Protein Misfolding] --> B[ER Stress Detection]
     B --> C[Unfolded Protein Response]
     C --> D[Chaperone Induction]
@@ -314,7 +320,7 @@ graph TD
     E --> F[ERAD Activation]
     F --> G[Protein Degradation]
     G --> H[Protein Homeostasis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Metabolic Imbalance] --> B[Energy Sensor Activation]
     B --> C[Metabolic Reprogramming]
     C --> D[Alternative Pathways]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Metabolic Adaptation]
     F --> G[Stress Tolerance]
     G --> H[Metabolic Homeostasis]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Multiple Stresses] --> B[Stress Integration]
     B --> C[Adaptive Response]
     C --> D[Gene Expression Changes]
@@ -382,7 +390,7 @@ graph TD
     E --> F[Physiological Adaptation]
     F --> G[Stress Tolerance]
     G --> H[Adapted State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch12_advanced_regulatory_networks.html

@@ -2,123 +2,577 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 12: Advanced Regulatory Networks</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, sans-serif; /* Ensure proper rendering of Greek characters */
-        h1, h2, h3, p, li, a {
-            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: 1200px; 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; } .batch-header { background: #f8f9fa; padding: 1.5rem; 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; } 
-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 12: Advanced Regulatory Networks - 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: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 12
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 12: Advanced Regulatory Networks (7 processes)
-    </h
><p>
-        Complex regulatory circuits and network control systems
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 7 Advanced Regulatory Processes
-    </h
><ul>
-        <li>
-            <a href="#circadian-regulation">1. Circadian Regulation</a></li><li>
-            <a href="#metabolic-oscillations">2. Metabolic Oscillations</a></li><li>
-            <a href="#feedback-loops">3. Feedback Loops</a></li><li>
-            <a href="#feedforward-circuits">4. Feedforward Circuits</a></li><li>
-            <a href="#bistable-switches">5. Bistable Switches</a></li><li>
-            <a href="#noise-filtering">6. Noise Filtering</a></li><li>
-            <a href="#adaptive-networks">7. Adaptive Networks</a></li></ul></div><!-- Process 1: Circadian Regulation --> <div class="process-item" id="circadian-regulation">
-        <h3>
-        1. Circadian Regulation
-    </h
><p>
-        Detailed analysis of Circadian Regulation using the Programming Framework, revealing computational logic for biological timing control.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Light Input] --> B[Clock Gene Expression] B --> C[Clock Protein Synthesis] C --> D[Protein Complex Formation] D --> E[Nuclear Translocation] E --> F[Transcriptional Repression] F --> G[Clock Gene Inhibition] G --> H[Protein Degradation] H --> I[Repression Release] I --> J[Cycle Reset] J 
-
-    --> B 
-K[Environmental Cues] --> L[Phase Adjustment] L --> M[Clock Synchronization] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><!-- Process 2: Metabolic Oscillations --> <div class="process-item" id="metabolic-oscillations">
-        <h3>
-        2. Metabolic Oscillations
-    </h
><p>
-        Detailed analysis of Metabolic Oscillations using the Programming Framework, revealing computational logic for rhythmic metabolism.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Glucose Pulse] --> B[Glycolytic Flux] B --> C[ATP Production] C --> D[Phosphofructokinase Inhibition] D --> E[Glycolytic Slowdown] E --> F[ATP Depletion] F --> G[PFK Activation] G --> H[Glycolytic Restart] H 
-
-    --> B 
-I[NADH Oscillations] --> J[Respiratory Chain] J --> K[Oxygen Consumption] K --> L[Metabolic Cycling] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <h1>🧬 Yeast Batch 12: Advanced Regulatory Networks</h1>
+            <p>Programming Framework Analysis - Comprehensive Regulatory Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Advanced Regulatory Networks: Complex Control Circuits and Network Systems</h2>
+                <p>This batch contains 7 fundamental yeast processes responsible for advanced regulatory networks, including circadian rhythms, metabolic oscillations, feedback loops, and bistable switches. These processes represent the core computational systems that ensure proper timing, coordination, and decision-making in cellular processes.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with complex regulatory circuits, oscillatory dynamics, and network control systems that function as a biological computational and control platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 7 Advanced Regulatory Network Processes</h2>
+                <ul>
+                    <li><a href="#circadian-regulation">1. Circadian Regulation</a></li>
+                    <li><a href="#metabolic-oscillations">2. Metabolic Oscillations</a></li>
+                    <li><a href="#feedback-loops">3. Feedback Loops</a></li>
+                    <li><a href="#feedforward-circuits">4. Feedforward Circuits</a></li>
+                    <li><a href="#bistable-switches">5. Bistable Switches</a></li>
+                    <li><a href="#noise-filtering">6. Noise Filtering</a></li>
+                    <li><a href="#adaptive-networks">7. Adaptive Networks</a></li>
+                </ul>
+            </div>
 
-    </div>
-    </div>
-    </div><!-- Process 3: Bistable Switches --> <div class="process-item" id="bistable-switches">
-        <h3>
-        5. Bistable Switches
-    </h
><p>
-        Detailed analysis of Bistable Switches using the Programming Framework, revealing computational logic for cellular decision-making.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Input Signal] --> B{Signal Threshold?} B 
-
-    -->|Low| 
-C[State A Maintenance] B 
+            <!-- Process 1: Circadian Regulation -->
+            <div class="process-item" id="circadian-regulation">
+                <h3>1. Circadian Regulation</h3>
+                <p>Detailed analysis of circadian regulation using the Programming Framework, revealing computational logic for biological timing control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Light Input and Signal Transduction
+    A[Light Input] --> B[Photoreceptor Activation]
+    B --> C[Signal Transduction]
+    C --> D[Clock Gene Expression]
+    D --> E[Clock Protein Synthesis]
+    E --> F[Protein Complex Formation]
+    F --> G[Protein Phosphorylation]
+    G --> H[Nuclear Translocation]
+    H --> I[DNA Binding]
+    I --> J[Transcriptional Repression]
+    J --> K[Clock Gene Inhibition]
+    K --> L[Protein Degradation]
+    L --> M[Repression Release]
+    M --> N[Cycle Reset]
+    N --> O[Next Cycle Initiation]
+    O --> D
+    
+    %% Environmental Synchronization
+    P[Environmental Cues] --> Q[Phase Adjustment]
+    Q --> R[Clock Synchronization]
+    R --> S[Circadian Entrainment]
+    S --> T[Biological Timing]
+    T --> U[Metabolic Coordination]
+    U --> V[Behavioral Rhythms]
+    
+    %% Integration
+    V --> W[Circadian Regulation]
+    W --> X[Biological Clock]
+    X --> Y[Temporal Organization]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style P fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    
+    style Y fill:#74c0fc,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>
 
-    -->|High| 
-D[Switch Trigger] D --> E[Positive Feedback] E --> F[State B Activation] F --> G[State B Maintenance] G 
+            <!-- Process 2: Metabolic Oscillations -->
+            <div class="process-item" id="metabolic-oscillations">
+                <h3>2. Metabolic Oscillations</h3>
+                <p>Detailed analysis of metabolic oscillations using the Programming Framework, revealing computational logic for rhythmic metabolism.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Glycolytic Oscillations
+    A[Glucose Pulse] --> B[Glucose Transport]
+    B --> C[Hexokinase Activity]
+    C --> D[Glucose-6-Phosphate]
+    D --> E[Phosphofructokinase]
+    E --> F[Fructose-1,6-Bisphosphate]
+    F --> G[Glycolytic Flux]
+    G --> H[ATP Production]
+    H --> I[ATP Inhibition of PFK]
+    I --> J[Glycolytic Slowdown]
+    J --> K[ATP Depletion]
+    K --> L[PFK Activation]
+    L --> M[Glycolytic Restart]
+    M --> N[Next Oscillation]
+    N --> G
+    
+    %% NADH Oscillations
+    O[NADH Production] --> P[NADH Oscillations]
+    P --> Q[Respiratory Chain]
+    Q --> R[Oxygen Consumption]
+    R --> S[Metabolic Cycling]
+    S --> T[Energy Balance]
+    T --> U[Metabolic Coordination]
+    
+    %% Integration
+    U --> V[Metabolic Oscillations]
+    V --> W[Rhythmic Metabolism]
+    W --> X[Energy Homeostasis]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style O fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,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>
 
-    --> H{Counter Signal?} H 
+            <!-- Process 3: Feedback Loops -->
+            <div class="process-item" id="feedback-loops">
+                <h3>3. Feedback Loops</h3>
+                <p>Detailed analysis of feedback loops using the Programming Framework, revealing computational logic for regulatory control.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Negative Feedback Loop
+    A[Input Signal] --> B[Signal Transduction]
+    B --> C[Transcription Factor Activation]
+    C --> D[Target Gene Expression]
+    D --> E[Protein Synthesis]
+    E --> F[Protein Function]
+    F --> G[Output Response]
+    G --> H[Feedback Inhibition]
+    H --> I[Signal Attenuation]
+    I --> J[System Stabilization]
+    J --> K[Homeostasis]
+    
+    %% Positive Feedback Loop
+    L[Stimulus] --> M[Receptor Activation]
+    M --> N[Signal Amplification]
+    N --> O[Positive Feedback]
+    O --> P[System Activation]
+    P --> Q[Response Amplification]
+    Q --> R[Threshold Crossing]
+    R --> S[State Transition]
+    
+    %% Integration
+    K --> T[Feedback Loops]
+    S --> T
+    T --> U[Regulatory Control]
+    U --> V[System Stability]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K 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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    
+    style V fill:#74c0fc,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>
 
-    -->|Yes| 
-I[Switch Reset] H 
+            <!-- Process 4: Feedforward Circuits -->
+            <div class="process-item" id="feedforward-circuits">
+                <h3>4. Feedforward Circuits</h3>
+                <p>Detailed analysis of feedforward circuits using the Programming Framework, revealing computational logic for anticipatory regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Feedforward Circuit
+    A[Primary Input] --> B[Direct Pathway]
+    B --> C[Immediate Response]
+    C --> D[Primary Output]
+    
+    A --> E[Feedforward Branch]
+    E --> F[Anticipatory Signal]
+    F --> G[Regulatory Protein]
+    G --> H[Modulatory Effect]
+    H --> I[Response Modulation]
+    I --> J[Optimized Output]
+    
+    %% Integration
+    D --> K[Feedforward Circuits]
+    J --> K
+    K --> L[Anticipatory Control]
+    L --> M[System Optimization]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 M fill:#74c0fc,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>
 
-    -->|No| 
-J[State B Stability] I --> K[State A Recovery] K 
+            <!-- Process 5: Bistable Switches -->
+            <div class="process-item" id="bistable-switches">
+                <h3>5. Bistable Switches</h3>
+                <p>Detailed analysis of bistable switches using the Programming Framework, revealing computational logic for cellular decision-making.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Bistable Switch Logic
+    A[Input Signal] --> B{Signal Threshold?}
+    B -->|Low| C[State A Maintenance]
+    B -->|High| D[Switch Trigger]
+    D --> E[Positive Feedback]
+    E --> F[State B Activation]
+    F --> G[State B Maintenance]
+    G --> H{Counter Signal?}
+    H -->|Yes| I[Switch Reset]
+    H -->|No| J[State B Stability]
+    I --> K[State A Recovery]
+    K --> C
+    
+    %% Integration
+    J --> L[Bistable Switches]
+    L --> M[Cellular Decision-Making]
+    M --> N[State Transitions]
+    
+    %% Styling - Biological Color Scheme
+    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:#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:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    
+    style N fill:#74c0fc,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>
 
-    --> C 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
-
-    </div>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 6: Noise Filtering -->
+            <div class="process-item" id="noise-filtering">
+                <h3>6. Noise Filtering</h3>
+                <p>Detailed analysis of noise filtering using the Programming Framework, revealing computational logic for signal processing.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Noise Filtering
+    A[Noisy Input] --> B[Signal Detection]
+    B --> C[Noise Identification]
+    C --> D[Filtering Mechanism]
+    D --> E[Signal Amplification]
+    E --> F[Noise Suppression]
+    F --> G[Filtered Signal]
+    G --> H[Signal Processing]
+    H --> I[Reliable Output]
+    
+    %% Integration
+    I --> J[Noise Filtering]
+    J --> K[Signal Reliability]
+    K --> L[System Robustness]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 L fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast advanced regulatory networks and control systems
-    </p><p>
-        <em>Batch 12 of 15: Advanced Regulatory Networks</em>
+            <!-- Process 7: Adaptive Networks -->
+            <div class="process-item" id="adaptive-networks">
+                <h3>7. Adaptive Networks</h3>
+                <p>Detailed analysis of adaptive networks using the Programming Framework, revealing computational logic for network plasticity.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Adaptive Network
+    A[Environmental Change] --> B[Network Sensing]
+    B --> C[Adaptation Signal]
+    C --> D[Network Reconfiguration]
+    D --> E[Connection Strength Changes]
+    E --> F[New Network Topology]
+    F --> G[Adaptive Response]
+    G --> H[Network Learning]
+    H --> I[Enhanced Function]
+    
+    %% Integration
+    I --> J[Adaptive Networks]
+    J --> K[Network Plasticity]
+    K --> L[System Adaptation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 L fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast advanced regulatory network systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 12 of 15: Advanced Regulatory Networks</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch12_aging_senescence.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Cell Division] --> B[Budding Process]
     B --> C[Asymmetric Division]
     C --> D[Replicative Clock]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Division Limit]
     F --> G[Replicative Senescence]
     G --> H[Cell Death]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Time Passage] --> B[Metabolic Changes]
     B --> C[Stress Accumulation]
     C --> D[Damage Buildup]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Chronological Clock]
     F --> G[Chronological Senescence]
     G --> H[Cell Death]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[DNA Replication] --> B[End Replication Problem]
     B --> C[Telomere Shortening]
     C --> D[Telomerase Activity]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Critical Length]
     F --> G[DNA Damage Response]
     G --> H[Senescence Trigger]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[ROS Production] --> B[Oxidative Stress]
     B --> C[Damage Accumulation]
     C --> D[Antioxidant Decline]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Cellular Dysfunction]
     F --> G[Aging Acceleration]
     G --> H[Senescence]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Protein Misfolding] --> B[Chaperone Decline]
     B --> C[Aggregate Formation]
     C --> D[Proteasome Dysfunction]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Cellular Toxicity]
     F --> G[Function Impairment]
     G --> H[Aging Phenotype]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Mitochondrial Damage] --> B[ROS Production]
     B --> C[mtDNA Mutations]
     C --> D[Respiratory Decline]
@@ -314,7 +320,7 @@ graph TD
     E --> F[Metabolic Dysfunction]
     F --> G[Cellular Decline]
     G --> H[Aging Acceleration]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Aging Signals] --> B[Senescence Factors]
     B --> C[Cell Cycle Arrest]
     C --> D[Senescence Program]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Senescence Phenotype]
     F --> G[Irreversible Arrest]
     G --> H[Senescent State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Death Signals] --> B[Apoptosis Induction]
     B --> C[Caspase Activation]
     C --> D[Programmed Death]
@@ -382,7 +390,7 @@ graph TD
     E --> F[DNA Fragmentation]
     F --> G[Phagocytosis]
     G --> H[Cell Elimination]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch13_environmental_adaptation.html

@@ -2,111 +2,884 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Yeast Batch 13: Environmental Adaptation</title>
-<script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js">
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-    </style></head>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Yeast Batch 13: Environmental Adaptation - 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;
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+            font-weight: 300;
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+            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 {
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+        }
+        .toc li {
+            margin: 0.5rem 0;
+        }
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+            font-weight: 500;
+        }
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+            margin: 2rem 0;
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+            border: 1px solid #dee2e6;
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+    </style>
+</head>
 <body>
     <div class="container">
         <div class="header">
-        <h1>
-        🧬 Yeast Cellular Processes
-    </h
><p>
-        Programming Framework Analysis - Batch 13
-    </p></div>    <div class="content">
-        <div class="batch-header">
-        <h2>
-        Batch 13: Environmental Adaptation (8 processes)
-    </h
><p>
-        Environmental sensing and long-term adaptive responses
-    </p></div><div class="toc">
-        <h2>
-        📋 Table of Contents - 8 Environmental Adaptation Processes
-    </h
><ul>
-        <li>
-            <a href="#pH-homeostasis">1. pH Homeostasis</a></li><li>
-            <a href="#metal-ion-homeostasis">2. Metal Ion Homeostasis</a></li><li>
-            <a href="#nutrient-limitation">3. Nutrient Limitation Response</a></li><li>
-            <a href="#temperature-adaptation">4. Temperature Adaptation</a></li><li>
-            <a href="#oxygen-sensing">5. Oxygen Sensing</a></li><li>
-            <a href="#carbon-source-adaptation">6. Carbon Source Adaptation</a></li><li>
-            <a href="#nitrogen-sensing">7. Nitrogen Sensing</a></li><li>
-            <a href="#phosphate-sensing">8. Phosphate Sensing</a></li></ul></div><!-- Process 1: pH Homeostasis --> <div class="process-item" id="pH-homeostasis">
-        <h3>
-        1. pH Homeostasis
-    </h
><p>
-        Detailed analysis of pH Homeostasis using the Programming Framework, revealing computational logic for cellular pH regulation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[pH Stress] --> B[Plasma Membrane H+-ATPase] B --> C[Proton Extrusion] C --> D[Cytoplasmic pH Regulation] E[Vacuolar pH] --> A[V-ATPase] A --> G[Vacuolar Acidification] G --> H[Ion Compartmentalization] I[Alkaline Stress] --> J[Potassium Uptake] J --> K[Cation Exchange] K --> L[pH Buffering] D --> M[pH Homeostasis] H 
+            <h1>🧬 Yeast Batch 13: Environmental Adaptation</h1>
+            <p>Programming Framework Analysis - Comprehensive Adaptation Systems</p>
+        </div>
+        
+        <div class="content">
+            <div class="intro">
+                <h2>Environmental Adaptation: Cellular Response and Survival Systems</h2>
+                <p>This batch contains 8 fundamental yeast processes responsible for environmental sensing, adaptation, and survival responses. These processes represent the core computational systems that ensure cellular homeostasis and survival under diverse environmental challenges.</p>
+                
+                <p>Each process demonstrates sophisticated biological programming with signal transduction pathways, regulatory feedback loops, and adaptive responses that function as a biological environmental monitoring and response platform.</p>
+            </div>
+            
+            <div class="toc">
+                <h2>📋 Table of Contents - 8 Environmental Adaptation Processes</h2>
+                <ul>
+                    <li><a href="#pH-homeostasis">1. pH Homeostasis</a></li>
+                    <li><a href="#metal-ion-homeostasis">2. Metal Ion Homeostasis</a></li>
+                    <li><a href="#nutrient-limitation">3. Nutrient Limitation Response</a></li>
+                    <li><a href="#temperature-adaptation">4. Temperature Adaptation</a></li>
+                    <li><a href="#oxygen-sensing">5. Oxygen Sensing</a></li>
+                    <li><a href="#carbon-source-adaptation">6. Carbon Source Adaptation</a></li>
+                    <li><a href="#nitrogen-sensing">7. Nitrogen Sensing</a></li>
+                    <li><a href="#phosphate-sensing">8. Phosphate Sensing</a></li>
+                </ul>
+            </div>
 
-    --> M L 
+            <!-- Process 1: pH Homeostasis -->
+            <div class="process-item" id="pH-homeostasis">
+                <h3>1. pH Homeostasis</h3>
+                <p>Detailed analysis of pH homeostasis using the Programming Framework, revealing computational logic for cellular pH regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Acid Stress Response
+    A[Extracellular Acid Stress] --> B[Plasma Membrane H+-ATPase Activation]
+    B --> C[Pma1 Phosphorylation]
+    C --> D[Proton Extrusion]
+    D --> E[Cytoplasmic pH Regulation]
+    E --> F[Vacuolar H+-ATPase Activation]
+    F --> G[V-ATPase Assembly]
+    G --> H[Vacuolar Acidification]
+    H --> I[Ion Compartmentalization]
+    I --> J[Proton Sequestration]
+    
+    %% Alkaline Stress Response
+    K[Extracellular Alkaline Stress] --> L[Potassium Uptake Activation]
+    L --> M[Trk1/Trk2 Transporters]
+    M --> N[K+ Influx]
+    N --> O[Cation Exchange]
+    O --> P[Proton Release]
+    P --> Q[Intracellular pH Buffering]
+    Q --> R[Organic Acid Production]
+    R --> S[Malate Synthesis]
+    S --> T[Citrate Accumulation]
+    
+    %% pH Sensing and Regulation
+    E --> U[Intracellular pH Sensing]
+    Q --> U
+    U --> V[Rim101 Pathway Activation]
+    V --> W[Rim101 Proteolytic Processing]
+    W --> X[Rim101 Nuclear Localization]
+    X --> Y[Target Gene Expression]
+    Y --> Z[pH-Responsive Proteins]
+    
+    %% Integration and Homeostasis
+    J --> AA[pH Homeostasis]
+    T --> AA
+    Z --> AA
+    AA --> BB[Cellular pH Balance]
+    BB --> CC[Metabolic Adaptation]
+    CC --> DD[Growth Optimization]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style K fill:#ff6b6b,color:#fff
+    style U fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    
+    style DD fill:#74c0fc,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>
 
-    --> M 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 2: Metal Ion Homeostasis -->
+            <div class="process-item" id="metal-ion-homeostasis">
+                <h3>2. Metal Ion Homeostasis</h3>
+                <p>Detailed analysis of metal ion homeostasis using the Programming Framework, revealing computational logic for essential metal regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Copper Homeostasis
+    A[Copper Excess] --> B[Cup1 Metallothionein Expression]
+    B --> C[Cup1 Transcription Activation]
+    C --> D[Ace1 Transcription Factor]
+    D --> E[Copper Binding]
+    E --> F[Copper Sequestration]
+    F --> G[Cytoplasmic Protection]
+    G --> H[Copper Detoxification]
+    
+    %% Iron Homeostasis
+    I[Iron Deficiency] --> J[Aft1/Aft2 Activation]
+    J --> K[Aft1 Nuclear Localization]
+    K --> L[Iron-Responsive Gene Expression]
+    L --> M[Fet3 High-Affinity Iron Transporter]
+    M --> N[Fet4 Low-Affinity Iron Transporter]
+    N --> O[Enhanced Iron Uptake]
+    O --> P[Cellular Iron Supply]
+    P --> Q[Iron-Sulfur Cluster Assembly]
+    Q --> R[Iron-Dependent Enzymes]
+    
+    %% Zinc Homeostasis
+    S[Zinc Excess] --> T[Zrc1 Vacuolar Transporter]
+    T --> U[Zinc Vacuolar Sequestration]
+    U --> V[Cytoplasmic Zinc Reduction]
+    V --> W[Zap1 Transcription Factor]
+    W --> X[Zinc-Responsive Gene Expression]
+    X --> Y[Zinc Homeostasis]
+    
+    %% Manganese Homeostasis
+    Z[Manganese Deficiency] --> AA[Smf1 Manganese Transporter]
+    AA --> BB[Smf2 Manganese Transporter]
+    BB --> CC[Manganese Uptake]
+    CC --> DD[Manganese-Dependent Enzymes]
+    DD --> EE[Superoxide Dismutase Activity]
+    EE --> FF[Oxidative Stress Protection]
+    
+    %% Integration
+    H --> GG[Metal Ion Homeostasis]
+    R --> GG
+    Y --> GG
+    FF --> GG
+    GG --> HH[Cellular Metal Balance]
+    HH --> II[Metabolic Function]
+    II --> JJ[Growth and Survival]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style I fill:#ff6b6b,color:#fff
+    style S fill:#ff6b6b,color:#fff
+    style Z fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    
+    style JJ fill:#74c0fc,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>
-    </div>
-    </div><!-- Process 2: Metal Ion Homeostasis --> <div class="process-item" id="metal-ion-homeostasis">
-        <h3>
-        2. Metal Ion Homeostasis
-    </h
><p>
-        Detailed analysis of Metal Ion Homeostasis using the Programming Framework, revealing computational logic for essential metal regulation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Metal Ion Excess] --> B[Metallothionein Expression] B --> C[Metal Sequestration] C --> D[Cytoplasmic Protection] E[Metal Ion Deficiency] --> F[High-Affinity Transporters] F --> G[Enhanced Uptake] G --> H[Cellular Metal Supply] I[Copper Homeostasis] --> A[Cox17/Sco1/Cox11] A --> K[Cytochrome Oxidase Assembly] L[Iron Homeostasis] --> M[Aft1/Aft2 Regulation] M --> N[Iron-Sulfur Cluster Assembly] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 3: Nutrient Limitation Response -->
+            <div class="process-item" id="nutrient-limitation">
+                <h3>3. Nutrient Limitation Response</h3>
+                <p>Detailed analysis of nutrient limitation response using the Programming Framework, revealing computational logic for resource scarcity adaptation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Amino Acid Limitation
+    A[Amino Acid Depletion] --> B[Uncharged tRNA Accumulation]
+    B --> C[Gcn2 Kinase Activation]
+    C --> D[eIF2α Phosphorylation]
+    D --> E[Translation Inhibition]
+    E --> F[Gcn4 Translation]
+    F --> G[Gcn4 Transcription Factor]
+    G --> H[Amino Acid Biosynthesis Genes]
+    H --> I[Arginine Biosynthesis]
+    I --> J[Lysine Biosynthesis]
+    J --> K[Leucine Biosynthesis]
+    K --> L[Amino Acid Supply]
+    
+    %% Glucose Limitation
+    M[Glucose Limitation] --> N[Snf1 Kinase Activation]
+    N --> O[Snf1 Complex Assembly]
+    O --> P[Snf1 Phosphorylation]
+    P --> Q[Catabolite Repression Relief]
+    Q --> R[Alternative Carbon Source Utilization]
+    R --> S[Ethanol Metabolism]
+    S --> T[Glycerol Utilization]
+    T --> U[Fatty Acid β-Oxidation]
+    U --> V[Energy Production]
+    
+    %% Phosphate Limitation
+    W[Phosphate Limitation] --> X[Pho4 Transcription Factor]
+    X --> Y[Pho4 Nuclear Localization]
+    Y --> Z[Pho4-Pho2 Complex]
+    Z --> AA[Phosphate-Responsive Genes]
+    AA --> BB[Phosphate Transporters]
+    BB --> CC[Phosphate Scavenging]
+    CC --> DD[Phosphatase Expression]
+    DD --> EE[Organic Phosphate Hydrolysis]
+    EE --> FF[Inorganic Phosphate Release]
+    FF --> GG[Phosphate Supply]
+    
+    %% Integration
+    L --> HH[Metabolic Adjustment]
+    V --> HH
+    GG --> HH
+    HH --> II[Resource Optimization]
+    II --> JJ[Growth Adaptation]
+    JJ --> KK[Survival Under Limitation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style W fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    style FF fill:#ffd43b,color:#000
+    style GG fill:#ffd43b,color:#000
+    style HH fill:#ffd43b,color:#000
+    style II fill:#ffd43b,color:#000
+    style JJ fill:#ffd43b,color:#000
+    style KK fill:#ffd43b,color:#000
+    
+    style KK fill:#74c0fc,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>
-    </div>
-    </div><!-- Process 3: Nutrient Limitation Response --> <div class="process-item" id="nutrient-limitation">
-        <h3>
-        3. Nutrient Limitation Response
-    </h
><p>
-        Detailed analysis of Nutrient Limitation Response using the Programming Framework, revealing computational logic for resource scarcity adaptation.
-    </p><div class="mermaid-container">
-        <div class="mermaid">
-        graph TD
-    A[Nutrient Depletion] --> B[General Amino Acid Control] B --> C[Gcn4 Activation] C --> D[Amino Acid Biosynthesis] E[Glucose Limitation] --> F[Snf1 Kinase Activation] F --> G[Alternative Carbon Source Utilization] H[Phosphate Limitation] --> I[Pho4 Activation] I --> J[Phosphatase Expression] J --> K[Phosphate Scavenging] D --> L[Metabolic Adjustment] G 
+            <!-- Process 4: Temperature Adaptation -->
+            <div class="process-item" id="temperature-adaptation">
+                <h3>4. Temperature Adaptation</h3>
+                <p>Detailed analysis of temperature adaptation using the Programming Framework, revealing computational logic for thermal stress response.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Heat Shock Response
+    A[Heat Stress] --> B[Heat Shock Protein Expression]
+    B --> C[Hsf1 Transcription Factor]
+    C --> D[Hsf1 Trimerization]
+    D --> E[Hsf1 Nuclear Localization]
+    E --> F[Heat Shock Element Binding]
+    F --> G[Hsp70 Expression]
+    G --> H[Hsp90 Expression]
+    H --> I[Hsp104 Expression]
+    I --> J[Protein Folding Assistance]
+    J --> K[Denatured Protein Refolding]
+    K --> L[Protein Aggregation Prevention]
+    
+    %% Cold Shock Response
+    M[Cold Stress] --> N[Cold Shock Protein Expression]
+    N --> O[Csp1 Expression]
+    O --> P[Csp2 Expression]
+    P --> Q[RNA Chaperone Activity]
+    Q --> R[RNA Secondary Structure Maintenance]
+    R --> S[Translation Efficiency]
+    S --> T[Cold Adaptation]
+    
+    %% Membrane Adaptation
+    U[Temperature Change] --> V[Membrane Fluidity Sensing]
+    V --> W[Fatty Acid Desaturase Expression]
+    W --> X[Ole1 Desaturase]
+    X --> Y[Unsaturated Fatty Acid Synthesis]
+    Y --> Z[Membrane Fluidity Regulation]
+    Z --> AA[Membrane Function Maintenance]
+    
+    %% Integration
+    L --> BB[Heat Adaptation]
+    T --> BB
+    AA --> BB
+    BB --> CC[Temperature Homeostasis]
+    CC --> DD[Growth Optimization]
+    DD --> EE[Stress Resistance]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style M fill:#ff6b6b,color:#fff
+    style U fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#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 N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    style EE fill:#ffd43b,color:#000
+    
+    style EE fill:#74c0fc,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>
 
-    --> L K 
+            <!-- Process 5: Oxygen Sensing -->
+            <div class="process-item" id="oxygen-sensing">
+                <h3>5. Oxygen Sensing</h3>
+                <p>Detailed analysis of oxygen sensing using the Programming Framework, revealing computational logic for oxygen-dependent gene regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Hypoxic Response
+    A[Low Oxygen] --> B[Hap1 Transcription Factor]
+    B --> C[Hap1 Activation]
+    C --> D[Hap1 DNA Binding]
+    D --> E[Oxygen-Responsive Gene Expression]
+    E --> F[Cytochrome c Expression]
+    F --> G[Cytochrome c Oxidase]
+    G --> H[Respiratory Chain Optimization]
+    H --> I[Oxygen Utilization Efficiency]
+    
+    %% Rox1 Repression
+    J[High Oxygen] --> K[Rox1 Repressor]
+    K --> L[Rox1 DNA Binding]
+    L --> M[Anaerobic Gene Repression]
+    M --> N[Fermentation Gene Downregulation]
+    N --> O[Respiratory Gene Upregulation]
+    O --> P[Aerobic Metabolism]
+    
+    %% Hap2/3/4/5 Complex
+    Q[Oxygen Availability] --> R[Hap2/3/4/5 Complex]
+    R --> S[Hap Complex Assembly]
+    S --> T[Respiratory Gene Expression]
+    T --> U[Citric Acid Cycle Genes]
+    U --> V[Electron Transport Chain]
+    V --> W[ATP Production]
+    
+    %% Integration
+    I --> X[Oxygen Adaptation]
+    P --> X
+    W --> X
+    X --> Y[Metabolic Optimization]
+    Y --> Z[Energy Production]
+    Z --> AA[Growth Efficiency]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style Q fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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 R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    
+    style AA fill:#74c0fc,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>
 
-    --> L 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff
+            <!-- Process 6: Carbon Source Adaptation -->
+            <div class="process-item" id="carbon-source-adaptation">
+                <h3>6. Carbon Source Adaptation</h3>
+                <p>Detailed analysis of carbon source adaptation using the Programming Framework, revealing computational logic for carbon metabolism regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Glucose Repression
+    A[High Glucose] --> B[Mig1 Repressor]
+    B --> C[Mig1 Nuclear Localization]
+    C --> D[Mig1 DNA Binding]
+    D --> E[Alternative Carbon Source Gene Repression]
+    E --> F[Gluconeogenic Gene Repression]
+    F --> G[Glucose Utilization]
+    G --> H[Glycolysis Activation]
+    H --> I[Ethanol Production]
+    
+    %% Galactose Induction
+    J[Galactose Presence] --> K[Gal4 Transcription Factor]
+    K --> L[Gal4-Gal80 Interaction]
+    L --> M[Gal80 Inhibition Relief]
+    M --> N[Gal4 Activation]
+    N --> O[Galactose-Responsive Genes]
+    O --> P[Gal1 Galactokinase]
+    P --> Q[Gal7 Galactose-1-Phosphate Uridyltransferase]
+    Q --> R[Gal10 UDP-Galactose Epimerase]
+    R --> S[Galactose Metabolism]
+    
+    %% Lactose Utilization
+    T[Lactose Presence] --> U[Lac12 Lactose Permease]
+    U --> V[Lactose Transport]
+    V --> W[β-Galactosidase Expression]
+    W --> X[Lactose Hydrolysis]
+    X --> Y[Glucose + Galactose]
+    Y --> Z[Lactose Metabolism]
+    
+    %% Integration
+    I --> AA[Carbon Source Adaptation]
+    S --> AA
+    Z --> AA
+    AA --> BB[Metabolic Flexibility]
+    BB --> CC[Growth Optimization]
+    CC --> DD[Energy Production]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style T fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    
+    style DD fill:#74c0fc,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>
-    </div>
-    </div><div class="footer">
-        <p>
-        <strong>Generated using the Programming Framework methodology</strong>
+            <!-- Process 7: Nitrogen Sensing -->
+            <div class="process-item" id="nitrogen-sensing">
+                <h3>7. Nitrogen Sensing</h3>
+                <p>Detailed analysis of nitrogen sensing using the Programming Framework, revealing computational logic for nitrogen metabolism regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Nitrogen Catabolite Repression
+    A[Preferred Nitrogen Source] --> B[Gln3 Transcription Factor]
+    B --> C[Gln3 Phosphorylation]
+    C --> D[Gln3 Cytoplasmic Retention]
+    D --> E[Nitrogen-Responsive Gene Repression]
+    E --> F[Ure2 Inhibition]
+    F --> G[Preferred Source Utilization]
+    G --> H[Ammonia Assimilation]
+    H --> I[Glutamine Synthesis]
+    
+    %% Nitrogen Limitation Response
+    J[Nitrogen Limitation] --> K[Gln3 Dephosphorylation]
+    K --> L[Gln3 Nuclear Localization]
+    L --> M[Gln3 DNA Binding]
+    M --> N[Nitrogen-Responsive Gene Expression]
+    N --> O[Gap1 General Amino Acid Permease]
+    O --> P[Uga4 γ-Aminobutyric Acid Permease]
+    P --> Q[Put4 Proline Permease]
+    Q --> R[Alternative Nitrogen Source Utilization]
+    R --> S[Nitrogen Scavenging]
+    
+    %% TOR Pathway
+    T[Nitrogen Availability] --> U[TOR Complex 1]
+    U --> V[TORC1 Activation]
+    V --> W[Sch9 Kinase]
+    W --> X[Translation Regulation]
+    X --> Y[Growth Promotion]
+    Y --> Z[Nitrogen-Dependent Growth]
+    
+    %% Integration
+    I --> AA[Nitrogen Adaptation]
+    S --> AA
+    Z --> AA
+    AA --> BB[Nitrogen Homeostasis]
+    BB --> CC[Metabolic Optimization]
+    CC --> DD[Growth Regulation]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#ff6b6b,color:#fff
+    style T fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I 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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    style DD fill:#ffd43b,color:#000
+    
+    style DD fill:#74c0fc,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>
 
-    </p><p>
-        This batch demonstrates the computational nature of yeast environmental adaptation and homeostatic control systems
-    </p><p>
-        <em>Batch 13 of 15: Environmental Adaptation</em>
+            <!-- Process 8: Phosphate Sensing -->
+            <div class="process-item" id="phosphate-sensing">
+                <h3>8. Phosphate Sensing</h3>
+                <p>Detailed analysis of phosphate sensing using the Programming Framework, revealing computational logic for phosphate metabolism regulation.</p>
+                <div class="mermaid-container">
+                    <div class="mermaid">
+graph TD
+    %% Phosphate Limitation Response
+    A[Phosphate Limitation] --> B[Pho4 Transcription Factor]
+    B --> C[Pho4 Dephosphorylation]
+    C --> D[Pho4 Nuclear Localization]
+    D --> E[Pho4-Pho2 Complex Formation]
+    E --> F[Phosphate-Responsive Element Binding]
+    F --> G[Phosphate-Responsive Gene Expression]
+    G --> H[Pho84 High-Affinity Phosphate Transporter]
+    H --> I[Pho87 Low-Affinity Phosphate Transporter]
+    I --> J[Enhanced Phosphate Uptake]
+    J --> K[Phosphate Scavenging]
+    
+    %% Phosphatase Expression
+    L[Organic Phosphate Sources] --> M[Pho5 Acid Phosphatase]
+    M --> N[Pho11 Acid Phosphatase]
+    N --> O[Pho12 Acid Phosphatase]
+    O --> P[Organic Phosphate Hydrolysis]
+    P --> Q[Inorganic Phosphate Release]
+    Q --> R[Phosphate Supply]
+    
+    %% Phosphate Storage
+    S[Phosphate Excess] --> T[Polyphosphate Synthesis]
+    T --> U[Vtc Complex]
+    U --> V[Polyphosphate Accumulation]
+    V --> W[Phosphate Storage]
+    W --> X[Phosphate Homeostasis]
+    
+    %% Integration
+    K --> Y[Phosphate Adaptation]
+    R --> Y
+    X --> Y
+    Y --> Z[Phosphate Homeostasis]
+    Z --> AA[Metabolic Function]
+    AA --> BB[Growth Optimization]
+    
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style L fill:#ff6b6b,color:#fff
+    style S fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D 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:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K 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:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    
+    style BB fill:#74c0fc,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>
 
-    </p></div>
+            <div class="footer">
+                <p><strong>Generated using the Programming Framework methodology</strong></p>
+                <p>This batch demonstrates the computational nature of yeast environmental adaptation systems</p>
+                <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+                <p><em>Batch 13 of 15: Environmental Adaptation</em></p>
+            </div>
+        </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>
+</body>
 </html> 

yeast_batch13_epigenetic_regulation.html

@@ -137,6 +137,7 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Modification Signals] --> B[Histone Modifiers]
     B --> C[Acetylation]
     C --> D[Methylation]
@@ -144,7 +145,7 @@ graph TD
     E --> F[Ubiquitination]
     F --> G[Histone Code]
     G --> H[Chromatin State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -171,6 +172,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Remodeling Signals] --> B[Remodeling Complexes]
     B --> C[Nucleosome Sliding]
     C --> D[Histone Exchange]
@@ -178,7 +180,7 @@ graph TD
     E --> F[Accessibility Change]
     F --> G[Transcription Access]
     G --> H[Gene Expression]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -205,6 +207,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Methylation Signals] --> B[DNA Methyltransferases]
     B --> C[CpG Methylation]
     C --> D[Methylation Pattern]
@@ -212,7 +215,7 @@ graph TD
     E --> F[Transcription Repression]
     F --> G[Epigenetic Memory]
     G --> H[Heritable State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -239,6 +242,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Positioning Signals] --> B[Positioning Factors]
     B --> C[Nucleosome Assembly]
     C --> D[Position Determination]
@@ -246,7 +250,7 @@ graph TD
     E --> F[Accessibility Control]
     F --> G[Transcription Regulation]
     G --> H[Chromatin Structure]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -273,6 +277,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Silencing Signals] --> B[Silencing Complexes]
     B --> C[Chromatin Condensation]
     C --> D[Gene Repression]
@@ -280,7 +285,7 @@ graph TD
     E --> F[Epigenetic Mark]
     F --> G[Heritable Silencing]
     G --> H[Silenced State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -307,6 +312,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Activation Signals] --> B[Activation Complexes]
     B --> C[Chromatin Opening]
     C --> D[Gene Activation]
@@ -314,7 +320,7 @@ graph TD
     E --> F[Epigenetic Mark]
     F --> G[Heritable Activation]
     G --> H[Active State]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -341,6 +347,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Epigenetic Marks] --> B[Replication Machinery]
     B --> C[Mark Preservation]
     C --> D[Daughter Cell Inheritance]
@@ -348,7 +355,7 @@ graph TD
     E --> F[Heritable Information]
     F --> G[Generational Transmission]
     G --> H[Epigenetic Legacy]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff
@@ -375,6 +382,7 @@ graph TD
                 <div class="mermaid-container">
                     <div class="mermaid">
 graph TD
+    %% Initial Setup
     A[Reset Signals] --> B[Demethylases]
     B --> C[Histone Deacetylation]
     C --> D[Mark Removal]
@@ -382,7 +390,7 @@ graph TD
     E --> F[Epigenetic Erasure]
     F --> G[State Reset]
     G --> H[Epigenetic Clean Slate]
-    
+    %% Styling - Biological Color Scheme
     style A fill:#ff6b6b,color:#fff
     style B fill:#ffd43b,color:#000
     style C fill:#51cf66,color:#fff

yeast_batch14_developmental_processes.html

@@ -45,23 +45,18 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Mother Cell Division] --> B[HO Endonuclease Expression] B --> C[MAT Locus Cleavage] C --> D[Homologous Recombination] D 
-
-    --> E{Current Mating Type?} E 
-
-    -->|MATa| 
-F[HML α Cassette Copy] E 
-
-    -->|MATα| 
-G[HMR a Cassette Copy] F --> H[MATα Expression] G --> I[MATa Expression] H --> J[Mating Type Switch] I 
-
-    --> J J --> K[New Cell Identity] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Mother Cell Division] --> B[HO Endonuclease Expression] B --> C[MAT Locus Cleavage] C --> D[Homologous Recombination] D
+    --> E{Current Mating Type?} E
+    -->|MATa|
+    F[HML α Cassette Copy] E
+    -->|MATα|
+    G[HMR a Cassette Copy] F --> H[MATα Expression] G --> I[MATa Expression] H --> J[Mating Type Switch] I
+    --> J J --> K[New Cell Identity] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Process 2: Sporulation --> <div class="process-item" id="sporulation">
         <h3>
@@ -71,13 +66,12 @@ G[HMR a Cassette Copy] F --> H[MATα Expression] G --> I[MATa Expression] H -->
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nitrogen Starvation] --> B[Ume6/Ime1 Activation] B --> C[Meiotic Gene Expression] C --> D[Meiosis I Initiation] D --> E[Chromosome Pairing] E --> F[Crossing Over] F --> G[Chromosome Segregation] G --> H[Meiosis II] H --> I[Four Haploid Nuclei] I --> J[Spore Wall Formation] J --> K[Ascospore Development] K --> L[Mature Ascus] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Nitrogen Starvation] --> B[Ume6/Ime1 Activation] B --> C[Meiotic Gene Expression] C --> D[Meiosis I Initiation] D --> E[Chromosome Pairing] E --> F[Crossing Over] F --> G[Chromosome Segregation] G --> H[Meiosis II] H --> I[Four Haploid Nuclei] I --> J[Spore Wall Formation] J --> K[Ascospore Development] K --> L[Mature Ascus] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Process 3: Pseudohyphal Growth --> <div class="process-item" id="pseudohyphal-growth">
         <h3>
@@ -87,14 +81,13 @@ G[HMR a Cassette Copy] F --> H[MATα Expression] G --> I[MATa Expression] H -->
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Nutrient Limitation] --> B[cAMP/PKA Pathway] B --> C[Flo11 Expression] C --> D[Cell Adhesion] D --> E[Elongated Cell Morphology] E --> F[Unipolar Budding] F --> G[Filament Formation] G --> H[Invasive Growth] H --> I[Nutrient Foraging] J[MAPK Signaling] --> K[Ste12/Tec1 Activation] K --> L[Filamentous Growth Genes] L --> M[Pseudohyphal Development] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
-    style 
 fill:#b197fc,color:#fff 
+    A[Nutrient Limitation] --> B[cAMP/PKA Pathway] B --> C[Flo11 Expression] C --> D[Cell Adhesion] D --> E[Elongated Cell Morphology] E --> F[Unipolar Budding] F --> G[Filament Formation] G --> H[Invasive Growth] H --> I[Nutrient Foraging] J[MAPK Signaling] --> K[Ste12/Tec1 Activation] K --> L[Filamentous Growth Genes] L --> M[Pseudohyphal Development] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+    style 
 fill:#b197fc,color:#fff
+                    </div>
     </div>
     </div><div class="footer">
         <p>

yeast_batch14_metabolic_engineering.html

@@ -137,22 +137,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Target Product] --> B[Pathway Analysis]
-                            B --> C[Enzyme Selection]
-                            C --> D[Reaction Design]
-                            D --> E[Metabolic Route]
-                            E --> F[Pathway Assembly]
-                            F --> G[Synthetic Pathway]
-                            G --> H[Engineered Route]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Target Product] --> B[Pathway Analysis]
+    B --> C[Enzyme Selection]
+    C --> D[Reaction Design]
+    D --> E[Metabolic Route]
+    E --> F[Pathway Assembly]
+    F --> G[Synthetic Pathway]
+    G --> H[Engineered Route]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -171,22 +172,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Enzyme Target] --> B[Structure Analysis]
-                            B --> C[Mutation Design]
-                            C --> D[Active Site Modification]
-                            D --> E[Enzyme Optimization]
-                            E --> F[Activity Enhancement]
-                            F --> G[Engineered Enzyme]
-                            G --> H[Improved Catalyst]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Enzyme Target] --> B[Structure Analysis]
+    B --> C[Mutation Design]
+    C --> D[Active Site Modification]
+    D --> E[Enzyme Optimization]
+    E --> F[Activity Enhancement]
+    F --> G[Engineered Enzyme]
+    G --> H[Improved Catalyst]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -205,22 +207,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Flux Measurement] --> B[Metabolite Analysis]
-                            B --> C[Flux Calculation]
-                            C --> D[Network Modeling]
-                            D --> E[Flux Distribution]
-                            E --> F[Metabolic Map]
-                            F --> G[Flux Optimization]
-                            G --> H[Balanced Metabolism]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Flux Measurement] --> B[Metabolite Analysis]
+    B --> C[Flux Calculation]
+    C --> D[Network Modeling]
+    D --> E[Flux Distribution]
+    E --> F[Metabolic Map]
+    F --> G[Flux Optimization]
+    G --> H[Balanced Metabolism]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -239,22 +242,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Flux Analysis] --> B[Rate Limiting Steps]
-                            B --> C[Bottleneck Detection]
-                            C --> D[Enzyme Limitation]
-                            D --> E[Substrate Limitation]
-                            E --> F[Regulatory Block]
-                            F --> G[Bottleneck Map]
-                            G --> H[Optimization Targets]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Flux Analysis] --> B[Rate Limiting Steps]
+    B --> C[Bottleneck Detection]
+    C --> D[Enzyme Limitation]
+    D --> E[Substrate Limitation]
+    E --> F[Regulatory Block]
+    F --> G[Bottleneck Map]
+    G --> H[Optimization Targets]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -273,22 +277,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Optimization Targets] --> B[Enzyme Overexpression]
-                            B --> C[Regulatory Modification]
-                            C --> D[Competing Pathway Block]
-                            D --> E[Flux Redirection]
-                            E --> F[Pathway Balance]
-                            F --> G[Optimized Route]
-                            G --> H[Enhanced Production]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Optimization Targets] --> B[Enzyme Overexpression]
+    B --> C[Regulatory Modification]
+    C --> D[Competing Pathway Block]
+    D --> E[Flux Redirection]
+    E --> F[Pathway Balance]
+    F --> G[Optimized Route]
+    G --> H[Enhanced Production]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -307,22 +312,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Substrate Supply] --> B[Enzyme Catalysis]
-                            B --> C[Intermediate Formation]
-                            C --> D[Product Assembly]
-                            D --> E[Product Accumulation]
-                            E --> F[Product Secretion]
-                            F --> G[Product Recovery]
-                            G --> H[Target Product]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Substrate Supply] --> B[Enzyme Catalysis]
+    B --> C[Intermediate Formation]
+    C --> D[Product Assembly]
+    D --> E[Product Accumulation]
+    E --> F[Product Secretion]
+    F --> G[Product Recovery]
+    G --> H[Target Product]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -341,22 +347,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Yield Analysis] --> B[Byproduct Reduction]
-                            B --> C[Efficiency Enhancement]
-                            C --> D[Conversion Optimization]
-                            D --> E[Product Purity]
-                            E --> F[Yield Maximization]
-                            F --> G[Process Efficiency]
-                            G --> H[High Yield Production]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Yield Analysis] --> B[Byproduct Reduction]
+    B --> C[Efficiency Enhancement]
+    C --> D[Conversion Optimization]
+    D --> E[Product Purity]
+    E --> F[Yield Maximization]
+    F --> G[Process Efficiency]
+    G --> H[High Yield Production]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -375,22 +382,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Metabolic State] --> B[Redox Balance]
-                            B --> C[Energy Balance]
-                            C --> D[Carbon Balance]
-                            D --> E[Nitrogen Balance]
-                            E --> F[Metabolic Homeostasis]
-                            F --> G[Balanced Growth]
-                            G --> H[Stable Metabolism]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Metabolic State] --> B[Redox Balance]
+    B --> C[Energy Balance]
+    C --> D[Carbon Balance]
+    D --> E[Nitrogen Balance]
+    E --> F[Metabolic Homeostasis]
+    F --> G[Balanced Growth]
+    G --> H[Stable Metabolism]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>

yeast_batch15_quality_control_systems.html

@@ -45,13 +45,12 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
+    A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#b197fc,color:#fff
     style 
 fill:#ff6b6b,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Process 2: Nonsense-Mediated Decay --> <div class="process-item" id="nonsense-mediated-decay">
         <h3>
@@ -61,13 +60,12 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#74c0fc,color:#fff 
+    A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#74c0fc,color:#fff
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><!-- Process 3: Cell Wall Integrity --> <div class="process-item" id="cell-wall-integrity">
         <h3>
@@ -77,13 +75,12 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#b197fc,color:#fff 
+    A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
     style 
 fill:#b197fc,color:#fff
-
-    </div>
+    style 
 fill:#b197fc,color:#fff
+                    </div>
     </div>
     </div><!-- Process 4: Apoptosis --> <div class="process-item" id="apoptosis">
         <h3>
@@ -93,21 +90,17 @@
     </p><div class="mermaid-container">
         <div class="mermaid">
         graph TD
-    A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L 
-
-    --> M{Recovery Possible?} M 
-
-    -->|No| 
-N[Apoptotic Switch] N 
-
-    --> D 
-    style 
 fill:#ff6b6b,color:#fff 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ffd43b,color:#000 
-    style 
 fill:#ff6b6b,color:#fff 
+    A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
+    --> M{Recovery Possible?} M
+    -->|No|
+    N[Apoptotic Switch] N
+    --> D
+    style 
 fill:#ff6b6b,color:#fff
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ffd43b,color:#000
+    style 
 fill:#ff6b6b,color:#fff
     style 
 fill:#74c0fc,color:#fff
-
-    </div>
+                    </div>
     </div>
     </div><div class="footer">
         <p>

yeast_batch15_synthetic_biology.html

@@ -137,22 +137,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Function Specification] --> B[Component Selection]
-                            B --> C[Logic Design]
-                            C --> D[Circuit Architecture]
-                            D --> E[Connection Design]
-                            E --> F[Circuit Assembly]
-                            F --> G[Synthetic Circuit]
-                            G --> H[Functional System]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Function Specification] --> B[Component Selection]
+    B --> C[Logic Design]
+    C --> D[Circuit Architecture]
+    D --> E[Connection Design]
+    E --> F[Circuit Assembly]
+    F --> G[Synthetic Circuit]
+    G --> H[Functional System]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -171,22 +172,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Part Selection] --> B[Compatibility Check]
-                            B --> C[Assembly Design]
-                            C --> D[Part Integration]
-                            D --> E[Sequence Assembly]
-                            E --> F[Functional Testing]
-                            F --> G[Assembled Parts]
-                            G --> H[Modular System]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Part Selection] --> B[Compatibility Check]
+    B --> C[Assembly Design]
+    C --> D[Part Integration]
+    D --> E[Sequence Assembly]
+    E --> F[Functional Testing]
+    F --> G[Assembled Parts]
+    G --> H[Modular System]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -205,22 +207,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Promoter Design] --> B[Transcription Factor Binding]
-                            B --> C[Promoter Strength]
-                            C --> D[Regulatory Elements]
-                            D --> E[Expression Control]
-                            E --> F[Promoter Optimization]
-                            F --> G[Engineered Promoter]
-                            G --> H[Controlled Expression]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Promoter Design] --> B[Transcription Factor Binding]
+    B --> C[Promoter Strength]
+    C --> D[Regulatory Elements]
+    D --> E[Expression Control]
+    E --> F[Promoter Optimization]
+    F --> G[Engineered Promoter]
+    G --> H[Controlled Expression]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -239,22 +242,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[RBS Design] --> B[Shine-Dalgarno Sequence]
-                            B --> C[Ribosome Binding]
-                            C --> D[Translation Initiation]
-                            D --> E[Protein Synthesis]
-                            E --> F[Expression Level]
-                            F --> G[Optimized RBS]
-                            G --> H[Controlled Translation]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[RBS Design] --> B[Shine-Dalgarno Sequence]
+    B --> C[Ribosome Binding]
+    C --> D[Translation Initiation]
+    D --> E[Protein Synthesis]
+    E --> F[Expression Level]
+    F --> G[Optimized RBS]
+    G --> H[Controlled Translation]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -273,22 +277,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Terminator Design] --> B[Transcription Termination]
-                            B --> C[RNA Release]
-                            C --> D[Polymerase Dissociation]
-                            D --> E[Transcript Stability]
-                            E --> F[Expression Control]
-                            F --> G[Optimized Terminator]
-                            G --> H[Controlled Termination]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Terminator Design] --> B[Transcription Termination]
+    B --> C[RNA Release]
+    C --> D[Polymerase Dissociation]
+    D --> E[Transcript Stability]
+    E --> F[Expression Control]
+    F --> G[Optimized Terminator]
+    G --> H[Controlled Termination]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -307,22 +312,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Network Design] --> B[Transcription Factors]
-                            B --> C[Regulatory Logic]
-                            C --> D[Network Connections]
-                            D --> E[Signal Integration]
-                            E --> F[Response Generation]
-                            F --> G[Synthetic Network]
-                            G --> H[Regulated System]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Network Design] --> B[Transcription Factors]
+    B --> C[Regulatory Logic]
+    C --> D[Network Connections]
+    D --> E[Signal Integration]
+    E --> F[Response Generation]
+    F --> G[Synthetic Network]
+    G --> H[Regulated System]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -341,22 +347,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Loop Design] --> B[Signal Detection]
-                            B --> C[Response Generation]
-                            C --> D[Feedback Signal]
-                            D --> E[System Adjustment]
-                            E --> F[Stability Control]
-                            F --> G[Synthetic Loop]
-                            G --> H[Stable System]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Loop Design] --> B[Signal Detection]
+    B --> C[Response Generation]
+    C --> D[Feedback Signal]
+    D --> E[System Adjustment]
+    E --> F[Stability Control]
+    F --> G[Synthetic Loop]
+    G --> H[Stable System]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
@@ -375,22 +382,23 @@
                 <div class="mermaid-container">
                     <div class="mermaid">
                         graph TD
-                            A[Pathway Design] --> B[Enzyme Selection]
-                            B --> C[Reaction Assembly]
-                            C --> D[Metabolic Route]
-                            D --> E[Product Synthesis]
-                            E --> F[Pathway Optimization]
-                            F --> G[Synthetic Pathway]
-                            G --> H[Novel Function]
-                            
-                            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:#51cf66,color:#fff
-                            style F fill:#74c0fc,color:#fff
-                            style G fill:#51cf66,color:#fff
-                            style H fill:#b197fc,color:#fff
+    %% Initial Setup
+    A[Pathway Design] --> B[Enzyme Selection]
+    B --> C[Reaction Assembly]
+    C --> D[Metabolic Route]
+    D --> E[Product Synthesis]
+    E --> F[Pathway Optimization]
+    F --> G[Synthetic Pathway]
+    G --> H[Novel Function]
+    %% Styling - Biological Color Scheme
+    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:#51cf66,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#b197fc,color:#fff
                     </div>
                     <div class="color-legend">
                         <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>