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README.md

@@ -12,6 +12,12 @@ license: mit
 
 A Universal Method for Process Analysis
 
+## Summary
+
+The **Programming Framework** is a universal meta-tool for analyzing complex processes across any discipline by combining Large Language Models (LLMs) with visual flowchart representation. The Framework transforms textual process descriptions into structured, interactive Mermaid flowcharts stored as JSON, enabling systematic analysis, visualization, and integration with knowledge systems.
+
+Successfully demonstrated through GLMP (Genome Logic Modeling Project) with 50+ biological processes, and applied across Chemistry, Mathematics, Physics, and Computer Science. The Framework serves as the foundational methodology for the CopernicusAI Knowledge Engine, enabling domain-specific process visualization and analysis.
+
 ## 📚 Prior Work & Research Contributions
 
 ### Overview
@@ -85,8 +91,8 @@ The Programming Framework has been applied across multiple scientific discipline
 - [Chemistry Index](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/chemistry_index.html) - Main index for chemistry processes with links to all chemistry batches
 
 ### 🔢 Mathematics
-- [Mathematics Processes Database Table](https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/math-processes-database/mathematics-database-table.html) - Interactive database table with all mathematics processes (5 processes, 227 nodes, 212 entities)
-- [Mathematics Processes Collection](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_processes.html) - Overview of mathematics process diagrams
+- [Mathematics Index](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_index.html) - Main index for mathematics processes with links to all mathematics batches
+- **Note:** A comprehensive mathematics processes database with ~50 processes is planned for implementation. Mathematics processes are accessible through the [Knowledge Engine Dashboard](https://copernicus-frontend-phzp4ie2sq-uc.a.run.app/knowledge-engine) (12,000+ indexed mathematics papers).
 
 ### ⚛️ Physics
 - [Physics Processes Collection](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_processes.html) - Overview of physics process diagrams

biology_processes.html

@@ -114,15 +114,15 @@
     <div class="container">
         <h1>Biology Processes - Programming Framework Analysis</h1>
         
-        <div class="glmp-link">
+        <div class="glmp-link" style="background: #e8f5e9; padding: 1.5rem; margin: 1.5rem 0; border-left: 4px solid #4caf50; border-radius: 5px;">
             <h3>🔗 GLMP (Genome Logic Modeling Project) Connection</h3>
-            <p>This analysis is based on the comprehensive biological dataset from the <strong>Genome Logic Modeling Project (GLMP)</strong>, which contains 100+ analyzed biological processes across multiple organisms and systems.</p>
+            <p>This analysis is based on the comprehensive biological dataset from the <strong>Genome Logic Modeling Project (GLMP)</strong>, which contains 50+ analyzed biological processes across multiple organisms and systems.</p>
             <p><strong>GLMP Resources:</strong></p>
             <ul>
-                <li><a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank">GLMP Hugging Face Space</a> - Live demonstration and evidence base</li>
-                <li><a href="https://github.com/garywelz/glmp" target="_blank">GLMP GitHub Repository</a> - Complete dataset and methodology</li>
+                <li><a href="https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/glmp-database-table.html" target="_blank" style="font-weight: bold; color: #1976d2;">🗄️ GLMP Database Table</a> - Interactive database with all biological processes (opens in new tab)</li>
+                <li><a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank">GLMP Hugging Face Space</a> - Live demonstration and evidence base (opens in new tab)</li>
             </ul>
-            <p>The GLMP represents the most comprehensive biological computing system analysis ever created, demonstrating how biological systems function as sophisticated computational programs with complex regulatory logic, decision trees, and feedback mechanisms.</p>
+            <p>The GLMP represents the first successful application of the Programming Framework to biological processes, demonstrating how biological systems function as sophisticated computational programs with complex regulatory logic, decision trees, and feedback mechanisms.</p>
         </div>
         
         <p>This document presents representative biological processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>

index.html

@@ -35,6 +35,19 @@
         </div>
     </header>
 
+    <!-- Abstract/Summary -->
+    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-12">
+        <div class="bg-white rounded-xl shadow-lg p-8 mb-8 border-l-4 border-orange-600">
+            <h2 class="text-2xl font-bold text-gray-900 mb-4">📋 Summary</h2>
+            <p class="text-lg text-gray-700 leading-relaxed mb-3">
+                The <strong>Programming Framework</strong> is a universal meta-tool for analyzing complex processes across any discipline by combining Large Language Models (LLMs) with visual flowchart representation. The Framework transforms textual process descriptions into structured, interactive Mermaid flowcharts stored as JSON, enabling systematic analysis, visualization, and integration with knowledge systems.
+            </p>
+            <p class="text-gray-600">
+                Successfully demonstrated through GLMP (Genome Logic Modeling Project) with 50+ biological processes, and applied across Chemistry, Mathematics, Physics, and Computer Science. The Framework serves as the foundational methodology for the CopernicusAI Knowledge Engine, enabling domain-specific process visualization and analysis.
+            </p>
+        </div>
+    </section>
+
     <!-- Prior Work & Research Contributions -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-12">
         <div class="bg-gradient-to-r from-orange-50 to-yellow-50 rounded-xl shadow-lg p-8 mb-8">
@@ -274,13 +287,20 @@
                         <span class="text-2xl mr-2">🧬</span> Biology
                     </h3>
                     <p class="text-gray-600 text-sm mb-3">
-                        Biological process visualizations linking to the Genome Logic Modeling Project (GLMP).
+                        Biological process visualizations from the Genome Logic Modeling Project (GLMP) - the first application of the Programming Framework.
                     </p>
-                    <a href="biology_processes.html" 
-                       class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
-                       target="_blank" rel="noopener noreferrer">
-                        Biology Processes →
-                    </a>
+                    <div class="space-y-2">
+                        <a href="https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/glmp-database-table.html" 
+                           class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block mr-4"
+                           target="_blank" rel="noopener noreferrer">
+                            🗄️ GLMP Database Table →
+                        </a>
+                        <a href="biology_processes.html" 
+                           class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
+                           target="_blank" rel="noopener noreferrer">
+                            📚 Biology Processes Collection →
+                        </a>
+                    </div>
                 </div>
 
                 <!-- Chemistry -->
@@ -296,6 +316,9 @@
                        target="_blank" rel="noopener noreferrer">
                         Chemistry Index →
                     </a>
+                    <p class="text-xs text-gray-500 mt-2 italic">
+                        Note: New comprehensive database coming soon
+                    </p>
                 </div>
 
                 <!-- Mathematics -->
@@ -306,11 +329,14 @@
                     <p class="text-gray-600 text-sm mb-3">
                         Mathematical algorithms, proof methods, and computational processes.
                     </p>
-                    <a href="https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/math-processes-database/mathematics-database-table.html" 
+                    <a href="mathematics_index.html" 
                        class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
                        target="_blank" rel="noopener noreferrer">
-                        Mathematics Processes Database →
+                        Mathematics Index →
                     </a>
+                    <p class="text-xs text-gray-500 mt-2 italic">
+                        Note: New comprehensive database coming soon
+                    </p>
                 </div>
 
                 <!-- Physics -->
@@ -326,6 +352,9 @@
                        target="_blank" rel="noopener noreferrer">
                         Physics Processes →
                     </a>
+                    <p class="text-xs text-gray-500 mt-2 italic">
+                        Note: New comprehensive database coming soon
+                    </p>
                 </div>
 
                 <!-- Computer Science -->
@@ -341,6 +370,9 @@
                        target="_blank" rel="noopener noreferrer">
                         Computer Science Index →
                     </a>
+                    <p class="text-xs text-gray-500 mt-2 italic">
+                        Note: New comprehensive database coming soon
+                    </p>
                 </div>
             </div>
         </div>
@@ -409,7 +441,7 @@
                 <a href="https://huggingface.co/spaces/garywelz/glmp" 
                    class="text-orange-600 hover:text-orange-700 font-semibold"
                    target="_blank" rel="noopener noreferrer">
-                    Explore GLMP →
+                    Explore GLMP → (opens in new tab)
                 </a>
             </div>
 
@@ -422,7 +454,7 @@
                 <a href="https://www.copernicusai.fyi" 
                    class="text-orange-600 hover:text-orange-700 font-semibold"
                    target="_blank" rel="noopener noreferrer">
-                    Visit Copernicus AI →
+                    Visit Copernicus AI → (opens in new tab)
                 </a>
             </div>
         </div>
@@ -434,15 +466,25 @@
             <h2 class="text-3xl font-bold text-gray-900 mb-6">How to Cite This Work</h2>
             <div class="bg-gray-50 rounded-lg p-6 mb-4 space-y-4">
                 <div>
-                    <p class="text-gray-800 font-mono text-lg leading-relaxed">
+                    <p class="text-gray-800 font-mono text-lg leading-relaxed mb-3">
                         Welz, G. (2024–2025). <em>The Programming Framework: A Universal Method for Process Analysis</em>.<br>
-                        Hugging Face Spaces. <a href="https://huggingface.co/spaces/garywelz/programming_framework" class="text-orange-600 hover:text-orange-700 underline" target="_blank" rel="noopener noreferrer">https://huggingface.co/spaces/garywelz/programming_framework</a>
+                        Hugging Face Spaces. <a href="https://huggingface.co/spaces/garywelz/programming_framework" class="text-orange-600 hover:text-orange-700 underline" target="_blank" rel="noopener noreferrer">https://huggingface.co/spaces/garywelz/programming_framework</a> (opens in new tab)
                     </p>
+                    <div class="bg-white rounded p-3 mt-3">
+                        <p class="text-sm font-semibold text-gray-700 mb-2">BibTeX Format:</p>
+                        <pre class="bg-gray-900 text-orange-400 p-3 rounded text-xs overflow-x-auto"><code>@misc{welz2025programmingframework,
+  title={The Programming Framework: A Universal Method for Process Analysis},
+  author={Welz, Gary},
+  year={2024--2025},
+  url={https://huggingface.co/spaces/garywelz/programming_framework},
+  note={Hugging Face Spaces}
+}</code></pre>
+                    </div>
                 </div>
                 <div class="border-t border-gray-300 pt-4">
                     <p class="text-gray-800 font-mono text-lg leading-relaxed">
                         Welz, G. (2024). <em>From Inspiration to AI: Biology as Visual Programming</em>.<br>
-                        Medium. <a href="https://medium.com/@garywelz_47126/from-inspiration-to-ai-biology-as-visual-programming-520ee523029a" class="text-orange-600 hover:text-orange-700 underline" target="_blank" rel="noopener noreferrer">https://medium.com/@garywelz_47126/from-inspiration-to-ai-biology-as-visual-programming-520ee523029a</a>
+                        Medium. <a href="https://medium.com/@garywelz_47126/from-inspiration-to-ai-biology-as-visual-programming-520ee523029a" class="text-orange-600 hover:text-orange-700 underline" target="_blank" rel="noopener noreferrer">https://medium.com/@garywelz_47126/from-inspiration-to-ai-biology-as-visual-programming-520ee523029a</a> (opens in new tab)
                     </p>
                 </div>
             </div>