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+---
+title: Genome Logic Modeling Project (GLMP)
+emoji: 🧬
+colorFrom: blue
+colorTo: green
+sdk: static
+sdk_version: latest
+app_file: README.md
+pinned: false
+---
+
+# 🧬 Programming Framework for Complex Systems
+
+**A systematic visualization methodology for analyzing complex systems across biology, chemistry, physics, and computer science using computational flowcharts and standardized color coding.**
+
+[![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
+[![Hugging Face Spaces](https://img.shields.io/badge/Hugging%20Face-Spaces-orange)](https://huggingface.co/spaces/garywelz/programming_framework)
+
+## 🎯 Overview
+
+The Programming Framework represents a revolutionary approach to understanding complex systems by translating them into standardized computational representations. Using Mermaid Markdown syntax and large language model (LLM) processing, we demonstrate the framework's application to representative biological and chemical systems.
+
+**Key Insight:** Complex systems across biology, chemistry, and physics exhibit remarkable similarities in their organizational principles despite operating at vastly different scales and domains. The Programming Framework reveals these common computational patterns.
+
+## 🔬 Methodology
+
+The Programming Framework methodology involves systematic analysis of complex systems through the following steps:
+
+1. **System Identification:** Identify the biological, chemical, or physical system to be analyzed
+2. **Component Categorization:** Classify system components into the five functional categories
+3. **Flowchart Construction:** Create Mermaid flowcharts with appropriate color coding
+4. **Logic Verification:** Verify computational logic and system dynamics
+5. **Cross-Disciplinary Comparison:** Identify patterns across different domains
+
+## 🎨 Universal Color Coding System
+
+Each process is represented as a computational flowchart with standardized color coding:
+
+| Color Category | Biology | Chemistry | Computer Science | Physics | Mathematics |
+|----------------|---------|-----------|------------------|---------|-------------|
+| 🔴 **Red** - Triggers & Inputs | Environmental signals, Nutrient availability | Reactant supply, Temperature | Input data, User commands | Energy input, Force application | Axioms, Given conditions |
+| 🟡 **Yellow** - Structures & Objects | Enzymes, Receptor proteins | Catalysts, Reaction vessels | Data structures, Algorithms | Fields, Particles | Theorems, Methods |
+| 🟢 **Green** - Processing & Operations | Metabolic reactions, Signal transduction | Chemical reactions, Equilibrium shifts | Algorithm execution, Data processing | Wave propagation, Quantum operations | Logical steps, Calculations |
+| 🔵 **Blue** - Intermediates & States | Metabolites, Signaling molecules | Reaction intermediates, Transition states | Variables, Memory states | Quantum states, Energy levels | Intermediate results, Sub-proofs |
+| 🟣 **Violet** - Products & Outputs | Biomolecules, Cellular responses | Final products, Reaction yields | Program outputs, Computed results | Measured quantities, Physical phenomena | Proven theorems, Mathematical results |
+
+**Note:** Yellow nodes use black text for optimal readability, while all other colors use white text.
+
+## 📊 Dataset and Evidence Base
+
+We analyzed a comprehensive dataset of biological processes spanning multiple organisms and systems:
+
+- **110 processes** from *Saccharomyces cerevisiae* (yeast) covering DNA replication, cell cycle control, signal transduction, energy metabolism, and stress responses
+- **Multiple processes** from *Escherichia coli* including DNA replication, gene regulation, central metabolism, motility, and specialized systems like the lac operon
+- **Advanced systems** including photosynthesis, bacterial sporulation, circadian clocks, and viral decision switches
+
+**Total:** 297+ processes across 36 individual collections
+
+The complete dataset is publicly available through the [Genome Logic Modeling Project (GLMP)](https://huggingface.co/spaces/garywelz/glmp) Hugging Face Space.
+
+## 🌟 Representative Applications
+
+### Case Study: β-Galactosidase Analysis (2025)
+The β-galactosidase system represents one of the most well-characterized examples of genetic regulation in molecular biology. Using modern tools and AI assistance, we can now create sophisticated and detailed visualizations that demonstrate the full computational complexity of the lac operon system.
+
+**Key Features:**
+- Environmental inputs (lactose, glucose, energy status)
+- Regulatory logic gates
+- Gene expression control
+- Metabolic pathway integration
+- Feedback control mechanisms
+
+### Case Study: Algorithm Execution Analysis
+To demonstrate the framework's applicability to computer science, we applied the methodology to algorithm execution, specifically sorting algorithms. This example shows how the same computational logic can be applied to fundamental computer science processes.
+
+**Key Features:**
+- Input data validation
+- Algorithm selection and execution
+- Performance analysis
+- Error handling mechanisms
+- Complexity analysis
+
+### Case Study: Mathematical Proof Tree Analysis
+To demonstrate the framework's applicability to pure mathematics, we applied the methodology to mathematical proof construction, a fundamental process in mathematical logic.
+
+**Key Features:**
+- Axiom processing
+- Logical deduction steps
+- Theorem application
+- Proof validation
+- Mathematical rigor verification
+
+## 🛠️ Technical Foundation
+
+The Programming Framework builds upon **Mermaid Markdown (MMD)**, a text-based diagram generation syntax developed by Knut Sveidqvist in 2014. MMD enables the creation of complex flowcharts and diagrams from simple text descriptions.
+
+**Key Capabilities:**
+- **Text-to-Diagram Conversion:** Process descriptions from scientific literature can be directly converted into visual representations
+- **Standardized Syntax:** Consistent formatting across different systems and domains
+- **Automated Generation:** LLMs can rapidly process text descriptions and generate MMD code
+- **Cross-Platform Compatibility:** MMD integrates with documentation platforms and can be rendered in multiple formats
+- **Automatic Color Coding:** Canvas automatically derives color categories from MMD syntax
+
+## 📈 Historical Evolution: From 1995 to 2025
+
+The Programming Framework represents the culmination of a 30-year evolution in computational biology visualization:
+
+### 1995: Manual Creation
+- Months of research and reading
+- Manual flowchart creation with Inspiration
+- Single process analysis
+- Community discussion on bionet.genome.chromosome
+- Foundation for computational biology
+
+### 2025: AI-Assisted Analysis
+- Hours of AI-assisted processing
+- Automated Mermaid Markdown generation
+- Systematic analysis of 297+ processes
+- Cross-disciplinary pattern recognition
+- Universal computational framework
+
+## 🚀 Getting Started
+
+### Quick Start Guide
+
+1. **Choose Your System:** Identify a biological, chemical, or physical system to analyze
+2. **Apply the Framework:** Use the five-category color coding system
+3. **Create Flowcharts:** Generate Mermaid Markdown representations
+4. **Verify Logic:** Ensure computational logic is sound
+5. **Compare Patterns:** Look for similarities across domains
+
+### Sample Analysis Prompt
+
+```
+"Analyze the [system name] using the Programming Framework methodology. Create a Mermaid Markdown file that will enable the creation in HTML of a computational flowchart showing how environmental inputs are processed through regulatory mechanisms to produce specific outputs. Use the universal color scheme: Red for triggers/inputs, Yellow for structures/catalysts, Green for processing operations, Blue for intermediates, and Violet for products. Include a discipline-specific color key beneath the flowchart."
+```
+
+## 📚 Applications
+
+### Biological Systems
+- Gene regulation networks
+- Metabolic pathways
+- Signal transduction cascades
+- Cell cycle control systems
+- Stress response mechanisms
+
+### Chemical Processes
+- Catalytic reactions
+- Equilibrium systems
+- Kinetic analysis
+- Industrial processes
+- Environmental chemistry
+
+### Physical Systems
+- Quantum processes
+- Thermodynamic cycles
+- Wave phenomena
+- Energy transfer systems
+- Field interactions
+
+### Computer Science
+- Algorithm analysis
+- Data structures
+- Computational complexity
+- Software architecture
+- System design
+
+### Mathematical Systems
+- Proof construction
+- Logical frameworks
+- Theorem development
+- Computational mathematics
+- Formal systems
+
+## 🎯 Key Applications
+
+- **Bio-inspired Computing:** Biological computational patterns can inspire revolutionary new computing paradigms
+- **Synthetic Biology:** Understanding cellular programming enables the design of programmable biological systems
+- **Medical Applications:** Diseases can be understood as software bugs that can be debugged and fixed
+- **Evolutionary Computation:** Evolution becomes visible as a programming process that optimizes biological software
+
+## 📖 Documentation
+
+- **[Methodology Guide](methodology/)** - Detailed step-by-step framework application
+- **[Examples Gallery](examples/)** - Comprehensive collection of analyzed systems
+- **[Tools & Resources](tools/)** - Templates, guidelines, and educational materials
+- **[Case Studies](case-studies/)** - Deep dives into specific applications
+
+## 🤝 Contributing
+
+We welcome contributions to expand the Programming Framework across new domains and applications. Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
+
+### How to Contribute
+1. **Submit Examples:** Share your own system analyses using the framework
+2. **Improve Documentation:** Help expand methodology guides and tutorials
+3. **Develop Tools:** Create software tools for framework application
+4. **Cross-Disciplinary Applications:** Apply the framework to new domains
+
+## 📄 License
+
+This project is licensed under the Creative Commons Attribution 4.0 International License - see the [LICENSE](LICENSE) file for details.
+
+## 👨‍🔬 Author
+
+**Gary Welz**
+- Retired Faculty Member, John Jay College, CUNY (Department of Mathematics and Computer Science)
+- Borough of Manhattan Community College, CUNY
+- CUNY Graduate Center (New Media Lab)
+- Email: gwelz@jjay.cuny.edu
+
+## 🔗 Related Projects
+
+- **[Genome Logic Modeling Project (GLMP)](https://huggingface.co/spaces/garywelz/glmp)** - Comprehensive biological systems analysis
+- **[Programming Framework Examples](https://huggingface.co/spaces/garywelz/programming_framework_examples)** - Extended case studies and applications
+
+## 📞 Contact
+
+For questions, suggestions, or collaborations:
+- **Email:** gwelz@jjay.cuny.edu
+- **Hugging Face:** [@garywelz](https://huggingface.co/garywelz)
+- **Issues:** Use the [GitHub Issues](https://github.com/garywelz/programming-framework/issues) page
+
+---
+
+**The genome is indeed like a computer program—not as a metaphor, but as a fundamental reality of how biological systems operate. This analysis provides the empirical evidence to support this revolutionary understanding of biological complexity.**
+
+*We stand at the threshold of a new era in biology - one where we understand life itself as an information processing phenomenon.* 

index.html

@@ -213,6 +213,18 @@ console.log(result); // Output: krowemarF gnimmargorP</code></pre>
                                 <li>Postman - API testing</li>
                             </ul>
                         </div>
+                        
+                        <div class="resource">
+                            <h3>📖 Documentation</h3>
+                            <ul>
+                                <li><a href="ProgFrame_README.md" target="_blank">Programming Framework README</a></li>
+                                <li><a href="programming_framework_article.html" target="_blank">Academic Article</a></li>
+                                <li><a href="computer_science_processes.html" target="_blank">Computer Science Examples</a></li>
+                                <li><a href="chemistry_examples.html" target="_blank">Chemistry Examples</a></li>
+                                <li><a href="physics_processes.html" target="_blank">Physics Examples</a></li>
+                                <li><a href="mathematics_processes.html" target="_blank">Mathematics Examples</a></li>
+                            </ul>
+                        </div>
                     </div>
                 </div>
             </div>

style.css

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+.resource a {
+    color: #667eea;
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+    transition: color 0.3s ease;
+}
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+.resource a:hover {
+    color: #764ba2;
+    text-decoration: underline;
+}
+
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 @media (max-width: 768px) {
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