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README.md

@@ -13,6 +13,10 @@ short_description: Cross-disciplinary methodology for complex systems
 
 A systematic visualization methodology for analyzing complex systems across disciplines using Mermaid Markdown and a universal five-color code.
 
+### Purpose and Goals
+
+The Programming Framework project aims to advance the use of Mermaid Markdown syntax and Large Language Models (LLMs) to create standardized, color-coded flowcharts representing complex processes across all academic disciplines. By providing a universal methodology for translating system dynamics into computational representations, this framework enables systematic comparison and pattern recognition across traditionally separate fields including biology, chemistry, physics, computer science, and mathematics. The project builds upon three decades of computational biology research and demonstrates how modern AI tools can democratize complex system analysis, making sophisticated visualization accessible to researchers, educators, and students worldwide.
+
 ### Universal Color Coding Table
 
 | Color | Hex | Biology | Chemistry | Computer Science | Physics | Mathematics |

chemistry_examples.html

@@ -86,95 +86,74 @@
         <div class="figure">
             <div class="mermaid">
 graph TD
-    %% Initial Setup
-    %% Input Conditions
-    A1[Alkene Substrate] --> B1[Substrate Analysis]
-    C1[Hydrogen Gas H₂] --> D1[Gas Supply]
-    E1[Catalyst (Pt/Pd/Ni)] --> F1[Catalyst Preparation]
+    A[Alkene Substrate] --> B[Substrate Analysis]
+    C[Hydrogen Gas H₂] --> D[Gas Supply]
+    E[Catalyst Pt/Pd/Ni] --> F[Catalyst Preparation]
     
-    %% Reactant Preparation
-    B1 --> G1[Substrate Purity Check]
-    D1 --> H1[Gas Pressure Control]
-    F1 --> I1[Catalyst Activation]
+    B --> G[Substrate Purity Check]
+    D --> H[Gas Pressure Control]
+    F --> I[Catalyst Activation]
     
-    %% Reaction Setup
-    G1 --> J1[Reaction Vessel Loading]
-    H1 --> K1[Pressure Regulation]
-    I1 --> L1[Catalyst Dispersion]
+    G --> J[Reaction Vessel Loading]
+    H --> K[Pressure Regulation]
+    I --> L[Catalyst Dispersion]
     
-    %% Catalytic Process
-    J1 --> M1[Substrate Adsorption]
-    K1 --> N1[Hydrogen Dissociation]
-    L1 --> O1[Active Site Formation]
+    J --> M[Substrate Adsorption]
+    K --> N[Hydrogen Dissociation]
+    L --> O[Active Site Formation]
     
-    %% Surface Reactions
-    M1 --> P1[π-Bond Activation]
-    N1 --> Q1[H• Radical Formation]
-    O1 --> R1[Catalytic Surface]
+    M --> P[π-Bond Activation]
+    N --> Q[H• Radical Formation]
+    O --> R[Catalytic Surface]
     
-    %% Hydrogenation Steps
-    P1 --> S1[First H Addition]
-    Q1 --> T1[Hydrogen Transfer]
-    R1 --> U1[Surface Complex]
+    P --> S[First H Addition]
+    Q --> T[Hydrogen Transfer]
+    R --> U[Surface Complex]
     
-    %% Product Formation
-    S1 --> V1[Alkyl Intermediate]
-    T1 --> W1[Second H Addition]
-    U1 --> X1[Product Desorption]
+    S --> V[Alkyl Intermediate]
+    T --> W[Second H Addition]
+    U --> X[Product Desorption]
     
-    %% Final Products
-    V1 --> Y1[Alkane Product]
-    W1 --> Z1[Complete Hydrogenation]
-    X1 --> AA1[Catalyst Recovery]
+    V --> Y[Alkane Product]
+    W --> Z[Complete Hydrogenation]
+    X --> AA[Catalyst Recovery]
     
-    %% Process Control
-    Y1 --> BB1[Product Analysis]
-    Z1 --> CC1[Conversion Check]
-    AA1 --> DD1[Catalyst Regeneration]
+    %% Red: Reactants & Inputs
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
     
-    %% Output
-    BB1 --> EE1[Hydrogenation Complete]
-    CC1 --> FF1[Yield Optimization]
-    DD1 --> GG1[Process Efficiency]
+    %% Yellow: Catalysts & Equipment
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
     
-    %% Styling - Chemistry Color Scheme
-    style A1 fill:#ff6b6b,color:#fff
-    style C1 fill:#ff6b6b,color:#fff
-    style E1 fill:#ff6b6b,color:#fff
-    
-    style G1 fill:#ffd43b,color:#000
-    style H1 fill:#ffd43b,color:#000
-    style I1 fill:#ffd43b,color:#000
-    style J1 fill:#ffd43b,color:#000
-    style K1 fill:#ffd43b,color:#000
-    style L1 fill:#ffd43b,color:#000
-    
-    style M1 fill:#51cf66,color:#fff
-    style N1 fill:#51cf66,color:#fff
-    style O1 fill:#51cf66,color:#fff
-    style P1 fill:#51cf66,color:#fff
-    style Q1 fill:#51cf66,color:#fff
-    style R1 fill:#51cf66,color:#fff
-    style S1 fill:#51cf66,color:#fff
-    style T1 fill:#51cf66,color:#fff
-    style U1 fill:#51cf66,color:#fff
-    style V1 fill:#51cf66,color:#fff
-    style W1 fill:#51cf66,color:#fff
-    style X1 fill:#51cf66,color:#fff
+    %% Green: Chemical Reactions
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#51cf66,color:#fff
+    style W fill:#51cf66,color:#fff
+    style X fill:#51cf66,color:#fff
     
-    style B1 fill:#74c0fc,color:#fff
-    style D1 fill:#74c0fc,color:#fff
-    style F1 fill:#74c0fc,color:#fff
-    style Y1 fill:#74c0fc,color:#fff
-    style Z1 fill:#74c0fc,color:#fff
-    style AA1 fill:#74c0fc,color:#fff
-    style BB1 fill:#74c0fc,color:#fff
-    style CC1 fill:#74c0fc,color:#fff
-    style DD1 fill:#74c0fc,color:#fff
+    %% Blue: Intermediates & States
+    style V fill:#74c0fc,color:#fff
     
-    style EE1 fill:#b197fc,color:#fff
-    style FF1 fill:#b197fc,color:#fff
-    style GG1 fill:#b197fc,color:#fff
+    %% Violet: Final Products
+    style Y fill:#b197fc,color:#fff
+    style Z fill:#b197fc,color:#fff
+    style AA fill:#b197fc,color:#fff
                     </div>
             
             <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
@@ -625,6 +604,16 @@ graph TD
         <p>This collection demonstrates the computational nature of chemical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+        
+        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
+            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
+            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
+            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
+            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
+            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
+            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
+            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
+        </div>
     </div>
 </body>
 </html>

computer_science_processes.html

@@ -142,87 +142,38 @@ graph TD
         <div class="figure">
             <div class="mermaid">
 graph TD
-    %% Input Data
-    A[Search Key 7] --> B[Key Validation]
-    C[BST Root Node] --> D[Tree Structure Analysis]
-    E[Search Operation] --> F[Algorithm Selection]
-    
-    %% Tree Traversal Setup
-    B --> G[Key Comparison Logic]
-    D --> H[Node Structure]
-    F --> I[Binary Search Strategy]
-    
-    %% Root Node Processing
-    G --> J[Compare Key with Root]
-    H --> K[Left Child Pointer]
-    I --> L[Right Child Pointer]
-    
-    %% Decision Logic
-    J --> M{Key < Root Value?}
-    K --> N[Left Subtree]
-    L --> O[Right Subtree]
-    
-    %% Left Subtree Search
-    M -->|Yes| P[Traverse Left]
-    N --> Q[Left Child Node]
-    P --> R[Recursive Search]
-    
-    %% Right Subtree Search
-    M -->|No| S[Traverse Right]
-    O --> T[Right Child Node]
-    S --> U[Recursive Search]
-    
-    %% Search Completion
-    R --> V{Key Found?}
-    U --> W{Key Found?}
-    V -->|Yes| X[Return Node]
-    V -->|No| Y[Return Null]
-    W -->|Yes| Z[Return Node]
-    W -->|No| AA[Return Null]
+    A[Search Key] --> B[Compare with Root]
+    B --> C{Key < Root?}
+    C -->|Yes| D[Search Left Subtree]
+    C -->|No| E[Search Right Subtree]
+    D --> F[Recursive Search]
+    E --> G[Recursive Search]
+    F --> H{Key Found?}
+    G --> I{Key Found?}
+    H -->|Yes| J[Return Node]
+    H -->|No| K[Return Null]
+    I -->|Yes| L[Return Node]
+    I -->|No| M[Return Null]
+    J --> N[Search Successful]
+    L --> N
+    K --> O[Search Unsuccessful]
+    M --> O
     
-    %% Final Result
-    X --> BB[Search Successful]
-    Z --> BB
-    Y --> CC[Search Unsuccessful]
-    AA --> CC
-    
-    %% Styling - Computer Science Color Scheme
-    %% Red: Inputs & Triggers
     style A fill:#ff6b6b,color:#fff
-    style C fill:#ff6b6b,color:#fff
-    style E fill:#ff6b6b,color:#fff
-    
-    %% Yellow: Structures & Objects
     style B fill:#ffd43b,color:#000
-    style D fill:#ffd43b,color:#000
-    style F fill:#ffd43b,color:#000
-    style G fill:#ffd43b,color:#000
-    style H fill:#ffd43b,color:#000
-    style I fill:#ffd43b,color:#000
-    style J fill:#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 X fill:#ffd43b,color:#000
-    style Y fill:#ffd43b,color:#000
-    style Z fill:#ffd43b,color:#000
-    style AA fill:#ffd43b,color:#000
-    
-    %% Green: Processing & Operations
-    style M fill:#51cf66,color:#fff
-    style V fill:#51cf66,color:#fff
-    style W fill:#51cf66,color:#fff
-    
-    %% Blue: Intermediates & States
-    style BB fill:#74c0fc,color:#fff
-    style CC fill:#74c0fc,color:#fff
+    style C fill:#51cf66,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style E fill:#74c0fc,color:#fff
+    style F fill:#51cf66,color:#fff
+    style G fill:#51cf66,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style J fill:#74c0fc,color:#fff
+    style K fill:#74c0fc,color:#fff
+    style L fill:#74c0fc,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#b197fc,color:#fff
             </div>
             <div class="color-legend">
                 <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>

mathematics_processes.html

@@ -133,19 +133,25 @@ graph TD
     HH1 --> II1[Mathematical Truth Established]
     II1 --> JJ1[Proof Tree Complete]
     %% Styling - Mathematical Color Scheme
-    %% Styling - Biological Color Scheme
+    %% Red: Axioms & Inputs
     style A1 fill:#ff6b6b,color:#fff
     style C1 fill:#ff6b6b,color:#fff
     style E1 fill:#ff6b6b,color:#fff
+    
+    %% Yellow: Logical Structures & Methods
     style J1 fill:#ffd43b,color:#000
     style P1 fill:#ffd43b,color:#000
     style Q1 fill:#ffd43b,color:#000
+    
+    %% Green: Deductions & Operations
     style S1 fill:#51cf66,color:#fff
     style T1 fill:#51cf66,color:#fff
     style U1 fill:#51cf66,color:#fff
     style V1 fill:#51cf66,color:#fff
     style W1 fill:#51cf66,color:#fff
     style X1 fill:#51cf66,color:#fff
+    
+    %% Blue: Intermediates & States
     style B1 fill:#74c0fc,color:#fff
     style D1 fill:#74c0fc,color:#fff
     style F1 fill:#74c0fc,color:#fff
@@ -167,6 +173,8 @@ graph TD
     style EE1 fill:#74c0fc,color:#fff
     style FF1 fill:#74c0fc,color:#fff
     style GG1 fill:#74c0fc,color:#fff
+    
+    %% Violet: Final Results
     style HH1 fill:#b197fc,color:#fff
     style II1 fill:#b197fc,color:#fff
     style JJ1 fill:#b197fc,color:#fff
@@ -660,6 +668,16 @@ graph TD
         <p>This collection demonstrates the computational nature of mathematical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+        
+        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
+            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
+            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
+            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
+            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
+            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
+            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
+            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
+        </div>
     </div>
 </body>
 </html> 

physics_processes.html

@@ -648,6 +648,16 @@ graph TD
         <p>This collection demonstrates the computational nature of physical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+        
+        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
+            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
+            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
+            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
+            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
+            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
+            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
+            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
+        </div>
     </div>
 </body>
 </html>